ENIGMA
A program for predictive and causal microbial ecology
The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Scientific Focus Area that we help lead is dedicated to developing a generalizable approach to predictive causal microbial ecology. We seek to molecularly dissect the dispersal, drift, and selective forces that shape the assembly and activity of microbial communities in complex spatially and temporally variable niches. Our driving biological problem focused on the Y12 site at the Oak Ridge National Lab, a watershed that is highly contaminated by high nitrate and heavy metal contamination that resulted from nuclear programs over the last century. We seek to quantify the anthropogenic impact on the structure and function of the microbial communities that are present in this complex environment and to develop a predictive, increasingly mechanistic, understanding of the multiscale, interlinked environmental and biological processes that mediate denitrification and metal reduction activities of the microbial communities of sufficient resolution to allow effective optimization of these processes.
In this large collaborative project, for which we have a lead role in visioning, our central work is to help identify from sophisticated field measurements the critical active and interacting microbial subcommunities emblematic of the most active interactive subcommunities in different field conditions and to capture and characterize this diversity at gene-level resolution in the laboratory. We are most interested in understanding the novel phyla and pathways that carry out and mediate these critical activities and the role of predation and carbon constraints on overall community efficiency and selection.
For more information visit https://enigma.lbl.gov
Selected Publications
Somenahally, Anil C; Mosher, Jennifer J; Yuan, Tong; Podar, Mircea; Phelps, Tommy J; Brown, Steven D; Yang, Zamin K; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Nostrand, Joy D Van; Zhou, Jizhong; Elias, Dwayne A
Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. Journal Article
In: Plos One, vol. 8, no. 12, pp. e83909, 2013.
@article{somenahally_2013,
title = {Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities.},
author = {Anil C Somenahally and Jennifer J Mosher and Tong Yuan and Mircea Podar and Tommy J Phelps and Steven D Brown and Zamin K Yang and Terry C Hazen and Adam P Arkin and Anthony V Palumbo and Joy D Van Nostrand and Jizhong Zhou and Dwayne A Elias},
url = {http://dx.doi.org/10.1371/journal.pone.0083909},
doi = {10.1371/journal.pone.0083909},
year = {2013},
date = {2013-12-23},
urldate = {2021-05-25},
journal = {Plos One},
volume = {8},
number = {12},
pages = {e83909},
abstract = {Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.
Louie, Katherine B; Bowen, Benjamin P; Cheng, Xiaoliang; Berleman, James E; Chakraborty, Romy; Deutschbauer, Adam; Arkin, Adam; Northen, Trent R
"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Journal Article
In: Analytical Chemistry, vol. 85, no. 22, pp. 10856-10862, 2013.
@article{louie_2013,
title = {"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria.},
author = {Katherine B Louie and Benjamin P Bowen and Xiaoliang Cheng and James E Berleman and Romy Chakraborty and Adam Deutschbauer and Adam Arkin and Trent R Northen},
url = {http://dx.doi.org/10.1021/ac402240q},
doi = {10.1021/ac402240q},
year = {2013},
date = {2013-11-19},
urldate = {2021-05-25},
journal = {Analytical Chemistry},
volume = {85},
number = {22},
pages = {10856-10862},
abstract = {Traditionally, microbes are studied under controlled laboratory conditions as isolates in planktonic culture. However, this is a vast extrapolation from their natural state; development of new techniques is required to decipher the largely unknown world of microbial chemical interactions in more realistic environments. The field of mass spectrometry imaging has made significant progress in localizing metabolites in and around bacterial colonies, primarily by using MALDI and ESI-based techniques that interrogate the top surface of the sample. Unfortunately, surface-based laser-desorption techniques, such as nanostructure-initiator mass spectrometry (NIMS), which has advantages in detection of small metabolite compounds and low background, has not been suitable for direct microbe imaging because desorption/ionization occurs on the bottom of the sample. Here, we describe a "replica-extraction-transfer" (REX) technique that overcomes this barrier by transferring biomolecules from agar cultures of spatially arrayed bacterial colonies onto NIMS surfaces; further, we demonstrate that acoustic printing of bacteria can be used to create complex colony geometries to probe microbial interactions with NIMS imaging. REX uses a solvent-laden semisolid (e.g., gel) to first extract metabolites from a microbial sample, such as a biofilm or agar culture; the metabolites are then replica "stamped" onto the NIMS surface. Using analytical standards we show that REX-NIMS effectively transfers and detects a range of small molecule compounds including amino acids and polyamines. This approach is then used to analyze the metabolite composition of streaked Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2 colonies and further resolve complex patterns produced by acoustic printing of liquid microbial cultures. Applying multivariate statistical analysis of the NIMS imaging data identified ions that were localized to different regions between and within colonies, as well as to the agar gel. Subsequent high-resolution tandem mass spectrometry was used to characterize two species-specific lipids that correlated with the spatial location of each microbial species and were found to be highly abundant in cell extracts. Overall, the use of acoustic printing of bacteria with REX-NIMS imaging will extend the range of analytical capabilities available for characterization of microbial interactions with mass spectrometry.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Traditionally, microbes are studied under controlled laboratory conditions as isolates in planktonic culture. However, this is a vast extrapolation from their natural state; development of new techniques is required to decipher the largely unknown world of microbial chemical interactions in more realistic environments. The field of mass spectrometry imaging has made significant progress in localizing metabolites in and around bacterial colonies, primarily by using MALDI and ESI-based techniques that interrogate the top surface of the sample. Unfortunately, surface-based laser-desorption techniques, such as nanostructure-initiator mass spectrometry (NIMS), which has advantages in detection of small metabolite compounds and low background, has not been suitable for direct microbe imaging because desorption/ionization occurs on the bottom of the sample. Here, we describe a "replica-extraction-transfer" (REX) technique that overcomes this barrier by transferring biomolecules from agar cultures of spatially arrayed bacterial colonies onto NIMS surfaces; further, we demonstrate that acoustic printing of bacteria can be used to create complex colony geometries to probe microbial interactions with NIMS imaging. REX uses a solvent-laden semisolid (e.g., gel) to first extract metabolites from a microbial sample, such as a biofilm or agar culture; the metabolites are then replica "stamped" onto the NIMS surface. Using analytical standards we show that REX-NIMS effectively transfers and detects a range of small molecule compounds including amino acids and polyamines. This approach is then used to analyze the metabolite composition of streaked Shewanella oneidensis MR1 and Pseudomonas stutzeri RCH2 colonies and further resolve complex patterns produced by acoustic printing of liquid microbial cultures. Applying multivariate statistical analysis of the NIMS imaging data identified ions that were localized to different regions between and within colonies, as well as to the agar gel. Subsequent high-resolution tandem mass spectrometry was used to characterize two species-specific lipids that correlated with the spatial location of each microbial species and were found to be highly abundant in cell extracts. Overall, the use of acoustic printing of bacteria with REX-NIMS imaging will extend the range of analytical capabilities available for characterization of microbial interactions with mass spectrometry.
Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. Journal Article
In: BMC Genomics, vol. 14, pp. 745, 2013.
@article{novichkov_2013,
title = {RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.},
author = {Pavel S Novichkov and Alexey E Kazakov and Dmitry A Ravcheev and Semen A Leyn and Galina Y Kovaleva and Roman A Sutormin and Marat D Kazanov and William Riehl and Adam P Arkin and Inna Dubchak and Dmitry A Rodionov},
url = {http://dx.doi.org/10.1186/1471-2164-14-745},
doi = {10.1186/1471-2164-14-745},
year = {2013},
date = {2013-11-01},
urldate = {2021-05-25},
journal = {BMC Genomics},
volume = {14},
pages = {745},
abstract = {BACKGROUND: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). DESCRIPTION: RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. CONCLUSIONS: RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). DESCRIPTION: RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. CONCLUSIONS: RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.
Meyer, Birte; Kuehl, Jennifer V; Deutschbauer, Adam M; Arkin, Adam P; Stahl, David A
Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal Article
In: Journal of Bacteriology, vol. 195, no. 21, pp. 4900-4914, 2013.
@article{meyer_2013a,
title = {Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes.},
author = {Birte Meyer and Jennifer V Kuehl and Adam M Deutschbauer and Adam P Arkin and David A Stahl},
url = {http://dx.doi.org/10.1128/JB.00504-13},
doi = {10.1128/JB.00504-13},
year = {2013},
date = {2013-11-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {195},
number = {21},
pages = {4900-4914},
abstract = {The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments.
Kazakov, Alexey E; Rajeev, Lara; Luning, Eric G; Zane, Grant M; Siddartha, Kavya; Rodionov, Dmitry A; Dubchak, Inna; Arkin, Adam P; Wall, Judy D; Mukhopadhyay, Aindrila; Novichkov, Pavel S
New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. Journal Article
In: Journal of Bacteriology, vol. 195, no. 19, pp. 4466-4475, 2013.
@article{kazakov_2013,
title = {New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.},
author = {Alexey E Kazakov and Lara Rajeev and Eric G Luning and Grant M Zane and Kavya Siddartha and Dmitry A Rodionov and Inna Dubchak and Adam P Arkin and Judy D Wall and Aindrila Mukhopadhyay and Pavel S Novichkov},
url = {http://dx.doi.org/10.1128/JB.00679-13},
doi = {10.1128/JB.00679-13},
year = {2013},
date = {2013-10-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {195},
number = {19},
pages = {4466-4475},
abstract = {The trace elements molybdenum and tungsten are essential components of cofactors of many metalloenzymes. However, in sulfate-reducing bacteria, high concentrations of molybdate and tungstate oxyanions inhibit growth, thus requiring the tight regulation of their homeostasis. By a combination of bioinformatic and experimental techniques, we identified a novel regulator family, tungstate-responsive regulator (TunR), controlling the homeostasis of tungstate and molybdate in sulfate-reducing deltaproteobacteria. The effector-sensing domains of these regulators are similar to those of the known molybdate-responsive regulator ModE, while their DNA-binding domains are homologous to XerC/XerD site-specific recombinases. Using a comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family members. Positional analysis of TunR sites and putative promoters allowed us to classify most TunR proteins into two groups: (i) activators of modABC genes encoding a high-affinity molybdenum and tungsten transporting system and (ii) repressors of genes for toluene sulfonate uptake (TSUP) family transporters. The activation of modA and modBC genes by TunR in Desulfovibrio vulgaris Hildenborough was confirmed in vivo, and we discovered that the activation was diminished in the presence of tungstate. A predicted 30-bp TunR-binding motif was confirmed by in vitro binding assays. A novel TunR family of bacterial transcriptional factors controls tungstate and molybdate homeostasis in sulfate-reducing deltaproteobacteria. We proposed that TunR proteins participate in protection of the cells from the inhibition by these oxyanions. To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The trace elements molybdenum and tungsten are essential components of cofactors of many metalloenzymes. However, in sulfate-reducing bacteria, high concentrations of molybdate and tungstate oxyanions inhibit growth, thus requiring the tight regulation of their homeostasis. By a combination of bioinformatic and experimental techniques, we identified a novel regulator family, tungstate-responsive regulator (TunR), controlling the homeostasis of tungstate and molybdate in sulfate-reducing deltaproteobacteria. The effector-sensing domains of these regulators are similar to those of the known molybdate-responsive regulator ModE, while their DNA-binding domains are homologous to XerC/XerD site-specific recombinases. Using a comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family members. Positional analysis of TunR sites and putative promoters allowed us to classify most TunR proteins into two groups: (i) activators of modABC genes encoding a high-affinity molybdenum and tungsten transporting system and (ii) repressors of genes for toluene sulfonate uptake (TSUP) family transporters. The activation of modA and modBC genes by TunR in Desulfovibrio vulgaris Hildenborough was confirmed in vivo, and we discovered that the activation was diminished in the presence of tungstate. A predicted 30-bp TunR-binding motif was confirmed by in vitro binding assays. A novel TunR family of bacterial transcriptional factors controls tungstate and molybdate homeostasis in sulfate-reducing deltaproteobacteria. We proposed that TunR proteins participate in protection of the cells from the inhibition by these oxyanions. To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases.
Zhou, Aifen; He, Zhili; Qin, Yujia; Lu, Zhenmei; Deng, Ye; Tu, Qichao; Hemme, Christopher L; Nostrand, Joy D Van; Wu, Liyou; Hazen, Terry C; Arkin, Adam P; Zhou, Jizhong
StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Journal Article
In: Environmental Science & Technology, vol. 47, no. 17, pp. 9841-9849, 2013.
@article{zhou_2013a,
title = {StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses.},
author = {Aifen Zhou and Zhili He and Yujia Qin and Zhenmei Lu and Ye Deng and Qichao Tu and Christopher L Hemme and Joy D Van Nostrand and Liyou Wu and Terry C Hazen and Adam P Arkin and Jizhong Zhou},
url = {http://dx.doi.org/10.1021/es4018656},
doi = {10.1021/es4018656},
year = {2013},
date = {2013-09-03},
urldate = {2021-05-25},
journal = {Environmental Science & Technology},
volume = {47},
number = {17},
pages = {9841-9849},
abstract = {Microbial community responses to environmental stresses are critical for microbial growth, survival, and adaptation. To fill major gaps in our ability to discern the influence of environmental changes on microbial communities from engineered and natural environments, a functional gene-based microarray, termed StressChip, has been developed. First, 46 functional genes involved in microbial responses to environmental stresses such as changes to temperature, osmolarity, oxidative status, nutrient limitation, or general stress response were selected and curated. A total of 22,855 probes were designed, covering 79,628 coding sequences from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains. Probe specificity was computationally verified. Second, the usefulness of functional genes as indicators of stress response was examined by surveying their distribution in metagenome data sets. The abundance of individual stress response genes is consistent with expected distributions based on respective habitats. Third, the StressChip was used to analyze marine microbial communities from the Deepwater Horizon oil spill. That functional stress response genes were detected in higher abundance (p textless 0.05) in oil plume compared to nonplume samples indicated shifts in community composition and structure, consistent with previous results. In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Microbial community responses to environmental stresses are critical for microbial growth, survival, and adaptation. To fill major gaps in our ability to discern the influence of environmental changes on microbial communities from engineered and natural environments, a functional gene-based microarray, termed StressChip, has been developed. First, 46 functional genes involved in microbial responses to environmental stresses such as changes to temperature, osmolarity, oxidative status, nutrient limitation, or general stress response were selected and curated. A total of 22,855 probes were designed, covering 79,628 coding sequences from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains. Probe specificity was computationally verified. Second, the usefulness of functional genes as indicators of stress response was examined by surveying their distribution in metagenome data sets. The abundance of individual stress response genes is consistent with expected distributions based on respective habitats. Third, the StressChip was used to analyze marine microbial communities from the Deepwater Horizon oil spill. That functional stress response genes were detected in higher abundance (p textless 0.05) in oil plume compared to nonplume samples indicated shifts in community composition and structure, consistent with previous results. In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes.
Zhou, Aifen; Baidoo, Edward; He, Zhili; Mukhopadhyay, Aindrila; Baumohl, Jason K; Benke, Peter; Joachimiak, Marcin P; Xie, Ming; Song, Rong; Arkin, Adam P; Hazen, Terry C; Keasling, Jay D; Wall, Judy D; Stahl, David A; Zhou, Jizhong
Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. Journal Article
In: The ISME Journal, vol. 7, no. 9, pp. 1790-1802, 2013.
@article{zhou_2013,
title = {Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.},
author = {Aifen Zhou and Edward Baidoo and Zhili He and Aindrila Mukhopadhyay and Jason K Baumohl and Peter Benke and Marcin P Joachimiak and Ming Xie and Rong Song and Adam P Arkin and Terry C Hazen and Jay D Keasling and Judy D Wall and David A Stahl and Jizhong Zhou},
url = {http://dx.doi.org/10.1038/ismej.2013.60},
doi = {10.1038/ismej.2013.60},
year = {2013},
date = {2013-09-01},
urldate = {2021-05-25},
journal = {The ISME Journal},
volume = {7},
number = {9},
pages = {1790-1802},
abstract = {Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100- or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 ømega9c, a17:1 ømega9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na(+) contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100- or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 ømega9c, a17:1 ømega9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na(+) contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris.
Price, Morgan N; Deutschbauer, Adam M; Skerker, Jeffrey M; Wetmore, Kelly M; Ruths, Troy; Mar, Jordan S; Kuehl, Jennifer V; Shao, Wenjun; Arkin, Adam P
Indirect and suboptimal control of gene expression is widespread in bacteria. Journal Article
In: Molecular Systems Biology, vol. 9, pp. 660, 2013.
@article{price_2013,
title = {Indirect and suboptimal control of gene expression is widespread in bacteria.},
author = {Morgan N Price and Adam M Deutschbauer and Jeffrey M Skerker and Kelly M Wetmore and Troy Ruths and Jordan S Mar and Jennifer V Kuehl and Wenjun Shao and Adam P Arkin},
url = {http://dx.doi.org/10.1038/msb.2013.16},
doi = {10.1038/msb.2013.16},
year = {2013},
date = {2013-04-16},
urldate = {2021-05-25},
journal = {Molecular Systems Biology},
volume = {9},
pages = {660},
abstract = {Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes' function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR-1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes' function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR-1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory.
Brown, Steven D; Utturkar, Sagar M; Arkin, Adam P; Deutschbauer, Adam M; Elias, Dwayne A; Hazen, Terry C; Chakraborty, Romy
Draft Genome Sequence for Desulfovibrio africanus Strain PCS. Journal Article
In: Genome announcements, vol. 1, no. 2, pp. e0014413, 2013.
@article{brown_2013,
title = {Draft Genome Sequence for Desulfovibrio africanus Strain PCS.},
author = {Steven D Brown and Sagar M Utturkar and Adam P Arkin and Adam M Deutschbauer and Dwayne A Elias and Terry C Hazen and Romy Chakraborty},
url = {http://dx.doi.org/10.1128/genomeA.00144-13},
doi = {10.1128/genomeA.00144-13},
year = {2013},
date = {2013-04-11},
urldate = {2021-05-25},
journal = {Genome announcements},
volume = {1},
number = {2},
pages = {e0014413},
abstract = {Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence.
Cipriano, Michael J; Novichkov, Pavel N; Kazakov, Alexey E; Rodionov, Dmitry A; Arkin, Adam P; Gelfand, Mikhail S; Dubchak, Inna
In: BMC Genomics, vol. 14, pp. 213, 2013.
@article{cipriano_2013,
title = {RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.},
author = {Michael J Cipriano and Pavel N Novichkov and Alexey E Kazakov and Dmitry A Rodionov and Adam P Arkin and Mikhail S Gelfand and Inna Dubchak},
url = {http://dx.doi.org/10.1186/1471-2164-14-213},
doi = {10.1186/1471-2164-14-213},
year = {2013},
date = {2013-04-02},
urldate = {2021-05-25},
journal = {BMC Genomics},
volume = {14},
pages = {213},
abstract = {BACKGROUND: Due to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly remains a field of semi-manual examination since absence of a knowledgebase and informatics platform for automated and systematic investigation restricts opportunities for computational prediction. Additionally, confirming computationally inferred regulons by experimental data is critically important. DESCRIPTION: RegTransBase is an open-access platform with a user-friendly web interface publicly available at http://regtransbase.lbl.gov. It consists of two databases - a manually collected hierarchical regulatory interactions database based on more than 7000 scientific papers which can serve as a knowledgebase for verification of predictions, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools. RegTransBase captures the knowledge from published scientific literature using controlled vocabularies and contains various types of experimental data, such as: the activation or repression of transcription by an identified direct regulator; determination of the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA; mapping of binding sites for a regulatory protein; characterization of regulatory mutations. Analysis of the data collected from literature resulted in the creation of Putative Regulons from Experimental Data that are also available in RegTransBase. CONCLUSIONS: RegTransBase is a powerful user-friendly platform for the investigation of regulation in prokaryotes. It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation of transcriptional regulation data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Due to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly remains a field of semi-manual examination since absence of a knowledgebase and informatics platform for automated and systematic investigation restricts opportunities for computational prediction. Additionally, confirming computationally inferred regulons by experimental data is critically important. DESCRIPTION: RegTransBase is an open-access platform with a user-friendly web interface publicly available at http://regtransbase.lbl.gov. It consists of two databases - a manually collected hierarchical regulatory interactions database based on more than 7000 scientific papers which can serve as a knowledgebase for verification of predictions, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools. RegTransBase captures the knowledge from published scientific literature using controlled vocabularies and contains various types of experimental data, such as: the activation or repression of transcription by an identified direct regulator; determination of the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA; mapping of binding sites for a regulatory protein; characterization of regulatory mutations. Analysis of the data collected from literature resulted in the creation of Putative Regulons from Experimental Data that are also available in RegTransBase. CONCLUSIONS: RegTransBase is a powerful user-friendly platform for the investigation of regulation in prokaryotes. It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation of transcriptional regulation data.
Meyer, Birte; Kuehl, Jennifer; Deutschbauer, Adam M; Price, Morgan N; Arkin, Adam P; Stahl, David A
Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. Journal Article
In: Journal of Bacteriology, vol. 195, no. 5, pp. 990-1004, 2013.
@article{meyer_2013,
title = {Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth.},
author = {Birte Meyer and Jennifer Kuehl and Adam M Deutschbauer and Morgan N Price and Adam P Arkin and David A Stahl},
url = {http://dx.doi.org/10.1128/JB.01959-12},
doi = {10.1128/JB.01959-12},
year = {2013},
date = {2013-03-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {195},
number = {5},
pages = {990-1004},
abstract = {Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H(+)/CO(2) reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H(+) reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (textgreater70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H(+)/CO(2) reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H(+) reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (textgreater70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle.
Wang, Liming; Wang, Xiaodong; Arkin, Adam P; Samoilov, Michael S
Inference of gene regulatory networks from genome-wide knockout fitness data. Journal Article
In: Bioinformatics, vol. 29, no. 3, pp. 338-346, 2013.
@article{wang_2013,
title = {Inference of gene regulatory networks from genome-wide knockout fitness data.},
author = {Liming Wang and Xiaodong Wang and Adam P Arkin and Michael S Samoilov},
url = {http://dx.doi.org/10.1093/bioinformatics/bts634},
doi = {10.1093/bioinformatics/bts634},
year = {2013},
date = {2013-02-01},
urldate = {2021-05-25},
journal = {Bioinformatics},
volume = {29},
number = {3},
pages = {338-346},
abstract = {MOTIVATION: Genome-wide fitness is an emerging type of high-throughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene regulatory interactions, when compared with results of more conventional gene expression analysis. Yet, to date, few algorithms have been proposed for systematically using genome-wide mutant fitness data for gene regulatory network inference. RESULTS: In this article, we describe a model and propose an inference algorithm for using fitness data from knockout libraries to identify underlying gene regulatory networks. Unlike most prior methods, the presented approach captures not only structural, but also dynamical and non-linear nature of biomolecular systems involved. A state-space model with non-linear basis is used for dynamically describing gene regulatory networks. Network structure is then elucidated by estimating unknown model parameters. Unscented Kalman filter is used to cope with the non-linearities introduced in the model, which also enables the algorithm to run in on-line mode for practical use. Here, we demonstrate that the algorithm provides satisfying results for both synthetic data as well as empirical measurements of GAL network in yeast Saccharomyces cerevisiae and TyrR-LiuR network in bacteria Shewanella oneidensis. AVAILABILITY: MATLAB code and datasets are available to download at http://www.duke.edu/∼lw174/Fitness.zip and http://genomics.lbl.gov/supplemental/fitness-bioinf/},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
MOTIVATION: Genome-wide fitness is an emerging type of high-throughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene regulatory interactions, when compared with results of more conventional gene expression analysis. Yet, to date, few algorithms have been proposed for systematically using genome-wide mutant fitness data for gene regulatory network inference. RESULTS: In this article, we describe a model and propose an inference algorithm for using fitness data from knockout libraries to identify underlying gene regulatory networks. Unlike most prior methods, the presented approach captures not only structural, but also dynamical and non-linear nature of biomolecular systems involved. A state-space model with non-linear basis is used for dynamically describing gene regulatory networks. Network structure is then elucidated by estimating unknown model parameters. Unscented Kalman filter is used to cope with the non-linearities introduced in the model, which also enables the algorithm to run in on-line mode for practical use. Here, we demonstrate that the algorithm provides satisfying results for both synthetic data as well as empirical measurements of GAL network in yeast Saccharomyces cerevisiae and TyrR-LiuR network in bacteria Shewanella oneidensis. AVAILABILITY: MATLAB code and datasets are available to download at http://www.duke.edu/∼lw174/Fitness.zip and http://genomics.lbl.gov/supplemental/fitness-bioinf/
Baran, Richard; Bowen, Benjamin P; Price, Morgan N; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R
Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. Journal Article
In: ACS Chemical Biology, vol. 8, no. 1, pp. 189-199, 2013.
@article{baran_2013,
title = {Metabolic footprinting of mutant libraries to map metabolite utilization to genotype.},
author = {Richard Baran and Benjamin P Bowen and Morgan N Price and Adam P Arkin and Adam M Deutschbauer and Trent R Northen},
url = {http://dx.doi.org/10.1021/cb300477w},
doi = {10.1021/cb300477w},
year = {2013},
date = {2013-01-18},
urldate = {2021-05-25},
journal = {ACS Chemical Biology},
volume = {8},
number = {1},
pages = {189-199},
abstract = {The discrepancy between the pace of sequencing and functional characterization of genomes is a major challenge in understanding complex microbial metabolic processes and metabolic interactions in the environment. Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains. Untargeted mass spectrometry based metabolomics was used to identify metabolites utilized by Escherichia coli and Shewanella oneidensis MR-1. Targeted high-throughput metabolite profiling of spent media of 8042 individual mutant strains was performed to link utilization to specific genes. Using this approach we identified genes of known function as well as novel transport proteins and enzymes required for the utilization of tested metabolites. Specific examples include two subunits of a predicted ABC transporter encoded by the genes SO1043 and SO1044 required for the utilization of citrulline and a predicted histidase encoded by the gene SO3057 required for the utilization of ergothioneine by S. oneidensis. In vitro assays with purified proteins showed substrate specificity of SO3057 toward ergothioneine and histidine betaine in contrast to substrate specificity of a paralogous histidase SO0098 toward histidine. This generally applicable, high-throughput workflow has the potential both to discover novel metabolic capabilities of microorganisms and to identify the corresponding genes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The discrepancy between the pace of sequencing and functional characterization of genomes is a major challenge in understanding complex microbial metabolic processes and metabolic interactions in the environment. Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains. Untargeted mass spectrometry based metabolomics was used to identify metabolites utilized by Escherichia coli and Shewanella oneidensis MR-1. Targeted high-throughput metabolite profiling of spent media of 8042 individual mutant strains was performed to link utilization to specific genes. Using this approach we identified genes of known function as well as novel transport proteins and enzymes required for the utilization of tested metabolites. Specific examples include two subunits of a predicted ABC transporter encoded by the genes SO1043 and SO1044 required for the utilization of citrulline and a predicted histidase encoded by the gene SO3057 required for the utilization of ergothioneine by S. oneidensis. In vitro assays with purified proteins showed substrate specificity of SO3057 toward ergothioneine and histidine betaine in contrast to substrate specificity of a paralogous histidase SO0098 toward histidine. This generally applicable, high-throughput workflow has the potential both to discover novel metabolic capabilities of microorganisms and to identify the corresponding genes.
Pang, Lee W; Kaur, Amardeep; Ratushny, Alexander V; Cvetkovic, Aleksandar; Kumar, Sunil; Pan, Min; Arkin, Adam P; Aitchison, John D; Adams, Michael W W; Baliga, Nitin S
Metallochaperones regulate intracellular copper levels. Journal Article
In: PLoS Computational Biology, vol. 9, no. 1, pp. e1002880, 2013.
@article{pang_2013,
title = {Metallochaperones regulate intracellular copper levels.},
author = {Lee W Pang and Amardeep Kaur and Alexander V Ratushny and Aleksandar Cvetkovic and Sunil Kumar and Min Pan and Adam P Arkin and John D Aitchison and Michael W W Adams and Nitin S Baliga},
url = {http://dx.doi.org/10.1371/journal.pcbi.1002880},
doi = {10.1371/journal.pcbi.1002880},
year = {2013},
date = {2013-01-17},
urldate = {2021-05-25},
journal = {PLoS Computational Biology},
volume = {9},
number = {1},
pages = {e1002880},
abstract = {Copper (Cu) is an important enzyme co-factor that is also extremely toxic at high intracellular concentrations, making active efflux mechanisms essential for preventing Cu accumulation. Here, we have investigated the mechanistic role of metallochaperones in regulating Cu efflux. We have constructed a computational model of Cu trafficking and efflux based on systems analysis of the Cu stress response of Halobacterium salinarum. We have validated several model predictions via assays of transcriptional dynamics and intracellular Cu levels, discovering a completely novel function for metallochaperones. We demonstrate that in addition to trafficking Cu ions, metallochaperones also function as buffers to modulate the transcriptional responsiveness and efficacy of Cu efflux. This buffering function of metallochaperones ultimately sets the upper limit for intracellular Cu levels and provides a mechanistic explanation for previously observed Cu metallochaperone mutation phenotypes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Copper (Cu) is an important enzyme co-factor that is also extremely toxic at high intracellular concentrations, making active efflux mechanisms essential for preventing Cu accumulation. Here, we have investigated the mechanistic role of metallochaperones in regulating Cu efflux. We have constructed a computational model of Cu trafficking and efflux based on systems analysis of the Cu stress response of Halobacterium salinarum. We have validated several model predictions via assays of transcriptional dynamics and intracellular Cu levels, discovering a completely novel function for metallochaperones. We demonstrate that in addition to trafficking Cu ions, metallochaperones also function as buffers to modulate the transcriptional responsiveness and efficacy of Cu efflux. This buffering function of metallochaperones ultimately sets the upper limit for intracellular Cu levels and provides a mechanistic explanation for previously observed Cu metallochaperone mutation phenotypes.
Chivian, Dylan; Dehal, Paramvir S; Keller, Keith; Arkin, Adam P
MetaMicrobesOnline: phylogenomic analysis of microbial communities. Journal Article
In: Nucleic Acids Research, vol. 41, no. Database issue, pp. D648-54, 2013.
@article{chivian_2013,
title = {MetaMicrobesOnline: phylogenomic analysis of microbial communities.},
author = {Dylan Chivian and Paramvir S Dehal and Keith Keller and Adam P Arkin},
url = {http://dx.doi.org/10.1093/nar/gks1202},
doi = {10.1093/nar/gks1202},
year = {2013},
date = {2013-01-01},
urldate = {2021-05-25},
journal = {Nucleic Acids Research},
volume = {41},
number = {Database issue},
pages = {D648-54},
abstract = {The metaMicrobesOnline database (freely available at http://meta.MicrobesOnline.org) offers phylogenetic analysis of genes from microbial genomes and metagenomes. Gene trees are constructed for canonical gene families such as COG and Pfam. Such gene trees allow for rapid homologue analysis and subfamily comparison of genes from multiple metagenomes and comparisons with genes from microbial isolates. Additionally, the genome browser permits genome context comparisons, which may be used to determine the closest sequenced genome or suggest functionally associated genes. Lastly, the domain browser permits rapid comparison of protein domain organization within genes of interest from metagenomes and complete microbial genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The metaMicrobesOnline database (freely available at http://meta.MicrobesOnline.org) offers phylogenetic analysis of genes from microbial genomes and metagenomes. Gene trees are constructed for canonical gene families such as COG and Pfam. Such gene trees allow for rapid homologue analysis and subfamily comparison of genes from multiple metagenomes and comparisons with genes from microbial isolates. Additionally, the genome browser permits genome context comparisons, which may be used to determine the closest sequenced genome or suggest functionally associated genes. Lastly, the domain browser permits rapid comparison of protein domain organization within genes of interest from metagenomes and complete microbial genomes.
Kazakov, Alexey E; Rodionov, Dmitry A; Price, Morgan N; Arkin, Adam P; Dubchak, Inna; Novichkov, Pavel S
In: Journal of Bacteriology, vol. 195, no. 1, pp. 29-38, 2013.
@article{kazakov_2013a,
title = {Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.},
author = {Alexey E Kazakov and Dmitry A Rodionov and Morgan N Price and Adam P Arkin and Inna Dubchak and Pavel S Novichkov},
url = {http://dx.doi.org/10.1128/JB.01977-12},
doi = {10.1128/JB.01977-12},
year = {2013},
date = {2013-01-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {195},
number = {1},
pages = {29-38},
abstract = {Accurate detection of transcriptional regulatory elements is essential for high-quality genome annotation, metabolic reconstruction, and modeling of regulatory networks. We developed a computational approach for reconstruction of regulons operated by transcription factors (TFs) from large protein families and applied this novel approach to three TF families in 10 Desulfovibrionales genomes. Phylogenetic analyses of 125 regulators from the ArsR, Crp/Fnr, and GntR families revealed that 65% of these regulators (termed reference TFs) are well conserved in Desulfovibrionales, while the remaining 35% of regulators (termed singleton TFs) are species specific and show a mosaic distribution. For regulon reconstruction in the group of singleton TFs, the standard orthology-based approach was inefficient, and thus, we developed a novel approach based on the simultaneous study of all homologous TFs from the same family in a group of genomes. As a result, we identified binding for 21 singleton TFs and for all reference TFs in all three analyzed families. Within each TF family we observed structural similarities between DNA-binding motifs of different reference and singleton TFs. The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Accurate detection of transcriptional regulatory elements is essential for high-quality genome annotation, metabolic reconstruction, and modeling of regulatory networks. We developed a computational approach for reconstruction of regulons operated by transcription factors (TFs) from large protein families and applied this novel approach to three TF families in 10 Desulfovibrionales genomes. Phylogenetic analyses of 125 regulators from the ArsR, Crp/Fnr, and GntR families revealed that 65% of these regulators (termed reference TFs) are well conserved in Desulfovibrionales, while the remaining 35% of regulators (termed singleton TFs) are species specific and show a mosaic distribution. For regulon reconstruction in the group of singleton TFs, the standard orthology-based approach was inefficient, and thus, we developed a novel approach based on the simultaneous study of all homologous TFs from the same family in a group of genomes. As a result, we identified binding for 21 singleton TFs and for all reference TFs in all three analyzed families. Within each TF family we observed structural similarities between DNA-binding motifs of different reference and singleton TFs. The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp).
Walker, Christopher B; Redding-Johanson, Alyssa M; Baidoo, Edward E; Rajeev, Lara; He, Zhili; Hendrickson, Erik L; Joachimiak, Marcin P; Stolyar, Sergey; Arkin, Adam P; Leigh, John A; Zhou, Jizhong; Keasling, Jay D; Mukhopadhyay, Aindrila; Stahl, David A
Functional responses of methanogenic archaea to syntrophic growth. Journal Article
In: The ISME Journal, vol. 6, no. 11, pp. 2045-2055, 2012.
@article{walker_2012,
title = {Functional responses of methanogenic archaea to syntrophic growth.},
author = {Christopher B Walker and Alyssa M Redding-Johanson and Edward E Baidoo and Lara Rajeev and Zhili He and Erik L Hendrickson and Marcin P Joachimiak and Sergey Stolyar and Adam P Arkin and John A Leigh and Jizhong Zhou and Jay D Keasling and Aindrila Mukhopadhyay and David A Stahl},
url = {http://dx.doi.org/10.1038/ismej.2012.60},
doi = {10.1038/ismej.2012.60},
year = {2012},
date = {2012-11-01},
urldate = {2021-05-25},
journal = {The ISME Journal},
volume = {6},
number = {11},
pages = {2045-2055},
abstract = {Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)). The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)). The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism.
Rajeev, Lara; Hillesland, Kristina L; Zane, Grant M; Zhou, Aifen; Joachimiak, Marcin P; He, Zhili; Zhou, Jizhong; Arkin, Adam P; Wall, Judy D; Stahl, David A
Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal Article
In: Journal of Bacteriology, vol. 194, no. 21, pp. 5783-5793, 2012.
@article{rajeev_2012,
title = {Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription.},
author = {Lara Rajeev and Kristina L Hillesland and Grant M Zane and Aifen Zhou and Marcin P Joachimiak and Zhili He and Jizhong Zhou and Adam P Arkin and Judy D Wall and David A Stahl},
url = {http://dx.doi.org/10.1128/JB.00749-12},
doi = {10.1128/JB.00749-12},
year = {2012},
date = {2012-11-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {194},
number = {21},
pages = {5783-5793},
abstract = {The carbon monoxide-sensing transcriptional factor CooA has been studied only in hydrogenogenic organisms that can grow using CO as the sole source of energy. Homologs for the canonical CO oxidation system, including CooA, CO dehydrogenase (CODH), and a CO-dependent Coo hydrogenase, are present in the sulfate-reducing bacterium Desulfovibrio vulgaris, although it grows only poorly on CO. We show that D. vulgaris Hildenborough has an active CO dehydrogenase capable of consuming exogenous CO and that the expression of the CO dehydrogenase, but not that of a gene annotated as encoding a Coo hydrogenase, is dependent on both CO and CooA. Carbon monoxide did not act as a general metabolic inhibitor, since growth of a strain deleted for cooA was inhibited by CO on lactate-sulfate but not pyruvate-sulfate. While the deletion strain did not accumulate CO in excess, as would have been expected if CooA were important in the cycling of CO as a metabolic intermediate, global transcriptional analyses suggested that CooA and CODH are used during normal metabolism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The carbon monoxide-sensing transcriptional factor CooA has been studied only in hydrogenogenic organisms that can grow using CO as the sole source of energy. Homologs for the canonical CO oxidation system, including CooA, CO dehydrogenase (CODH), and a CO-dependent Coo hydrogenase, are present in the sulfate-reducing bacterium Desulfovibrio vulgaris, although it grows only poorly on CO. We show that D. vulgaris Hildenborough has an active CO dehydrogenase capable of consuming exogenous CO and that the expression of the CO dehydrogenase, but not that of a gene annotated as encoding a Coo hydrogenase, is dependent on both CO and CooA. Carbon monoxide did not act as a general metabolic inhibitor, since growth of a strain deleted for cooA was inhibited by CO on lactate-sulfate but not pyruvate-sulfate. While the deletion strain did not accumulate CO in excess, as would have been expected if CooA were important in the cycling of CO as a metabolic intermediate, global transcriptional analyses suggested that CooA and CODH are used during normal metabolism.
León, Kara Bowen De; Young, Mary Lynn; Camilleri, Laura B; Brown, Steven D; Skerker, Jeffrey M; Deutschbauer, Adam M; Arkin, Adam P; Fields, Matthew W
Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction. Journal Article
In: Journal of Bacteriology, vol. 194, no. 19, pp. 5456-5457, 2012.
@article{bowendelen_2012,
title = {Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction.},
author = {Kara Bowen De León and Mary Lynn Young and Laura B Camilleri and Steven D Brown and Jeffrey M Skerker and Adam M Deutschbauer and Adam P Arkin and Matthew W Fields},
url = {http://dx.doi.org/10.1128/JB.01224-12},
doi = {10.1128/JB.01224-12},
year = {2012},
date = {2012-10-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {194},
number = {19},
pages = {5456-5457},
abstract = {Pelosinus fermentans JBW45 is an anaerobic, lactate-fermenting bacterium isolated from Cr(VI)-contaminated groundwater at the Hanford Nuclear Reservation 100-H site (Washington) that was collected after stimulation with a polylactate compound. The genome sequence of this organism will provide insight into the metabolic potential of a predominant population during stimulation for metal-reducing conditions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pelosinus fermentans JBW45 is an anaerobic, lactate-fermenting bacterium isolated from Cr(VI)-contaminated groundwater at the Hanford Nuclear Reservation 100-H site (Washington) that was collected after stimulation with a polylactate compound. The genome sequence of this organism will provide insight into the metabolic potential of a predominant population during stimulation for metal-reducing conditions.
Brown, Steven D; Podar, Mircea; Klingeman, Dawn M; Johnson, Courtney M; Yang, Zamin K; Utturkar, Sagar M; Land, Miriam L; Mosher, Jennifer J; Hurt, Richard A; Phelps, Tommy J; Palumbo, Anthony V; Arkin, Adam P; Hazen, Terry C; Elias, Dwayne A
Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. Journal Article
In: Journal of Bacteriology, vol. 194, no. 18, pp. 5147-5148, 2012.
@article{brown_2012,
title = {Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7.},
author = {Steven D Brown and Mircea Podar and Dawn M Klingeman and Courtney M Johnson and Zamin K Yang and Sagar M Utturkar and Miriam L Land and Jennifer J Mosher and Richard A Hurt and Tommy J Phelps and Anthony V Palumbo and Adam P Arkin and Terry C Hazen and Dwayne A Elias},
url = {http://dx.doi.org/10.1128/JB.01174-12},
doi = {10.1128/JB.01174-12},
year = {2012},
date = {2012-09-01},
urldate = {2021-05-25},
journal = {Journal of Bacteriology},
volume = {194},
number = {18},
pages = {5147-5148},
abstract = {Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.
Novichkov, Pavel S; Brettin, Thomas S; Novichkova, Elena S; Dehal, Paramvir S; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A
In: Nucleic Acids Research, vol. 40, no. Web Server issue, pp. W604-8, 2012.
@article{novichkov_2012,
title = {RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.},
author = {Pavel S Novichkov and Thomas S Brettin and Elena S Novichkova and Paramvir S Dehal and Adam P Arkin and Inna Dubchak and Dmitry A Rodionov},
url = {http://dx.doi.org/10.1093/nar/gks562},
doi = {10.1093/nar/gks562},
year = {2012},
date = {2012-07-01},
urldate = {2021-05-25},
journal = {Nucleic Acids Research},
volume = {40},
number = {Web Server issue},
pages = {W604-8},
abstract = {Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes textgreater1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in textgreater250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes textgreater1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in textgreater250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements.
Clark, Melinda E; He, Zhili; Redding, Alyssa M; Joachimiak, Marcin P; Keasling, Jay D; Zhou, Jizhong Z; Arkin, Adam P; Mukhopadhyay, Aindrila; Fields, Matthew W
In: BMC Genomics, vol. 13, pp. 138, 2012.
@article{clark_2012,
title = {Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.},
author = {Melinda E Clark and Zhili He and Alyssa M Redding and Marcin P Joachimiak and Jay D Keasling and Jizhong Z Zhou and Adam P Arkin and Aindrila Mukhopadhyay and Matthew W Fields},
url = {http://dx.doi.org/10.1186/1471-2164-13-138},
doi = {10.1186/1471-2164-13-138},
year = {2012},
date = {2012-04-16},
urldate = {2021-05-25},
journal = {BMC Genomics},
volume = {13},
pages = {138},
abstract = {BACKGROUND: Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. RESULTS: The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. CONCLUSIONS: Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. RESULTS: The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. CONCLUSIONS: Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
Mosher, Jennifer J; Phelps, Tommy J; Podar, Mircea; Hurt, Richard A; Campbell, James H; Drake, Meghan M; Moberly, James G; Schadt, Christopher W; Brown, Steven D; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Faybishenko, Boris A; Elias, Dwayne A
Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Journal Article
In: Applied and Environmental Microbiology, vol. 78, no. 7, pp. 2082-2091, 2012.
@article{mosher_2012,
title = {Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp.},
author = {Jennifer J Mosher and Tommy J Phelps and Mircea Podar and Richard A Hurt and James H Campbell and Meghan M Drake and James G Moberly and Christopher W Schadt and Steven D Brown and Terry C Hazen and Adam P Arkin and Anthony V Palumbo and Boris A Faybishenko and Dwayne A Elias},
url = {http://dx.doi.org/10.1128/AEM.07165-11},
doi = {10.1128/AEM.07165-11},
year = {2012},
date = {2012-04-01},
urldate = {2021-05-25},
journal = {Applied and Environmental Microbiology},
volume = {78},
number = {7},
pages = {2082-2091},
abstract = {The determination of the success of in situ bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N(2) gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp., with low levels of other organisms, including methanogens. Four new strains of Pelosinus were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including Desulfovibrio spp., were outcompeted. These results suggest that during times of electron acceptor limitation in situ, organisms such as Pelosinus spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The determination of the success of in situ bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N(2) gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp., with low levels of other organisms, including methanogens. Four new strains of Pelosinus were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including Desulfovibrio spp., were outcompeted. These results suggest that during times of electron acceptor limitation in situ, organisms such as Pelosinus spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed.
Zhou, Aifen; Chen, Yunyu I; Zane, Grant M; He, Zhili; Hemme, Christopher L; Joachimiak, Marcin P; Baumohl, Jason K; He, Qiang; Fields, Matthew W; Arkin, Adam P; Wall, Judy D; Hazen, Terry C; Zhou, Jizhong
Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Journal Article
In: Applied and Environmental Microbiology, vol. 78, no. 4, pp. 1168-1177, 2012.
@article{zhou_2012,
title = {Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.},
author = {Aifen Zhou and Yunyu I Chen and Grant M Zane and Zhili He and Christopher L Hemme and Marcin P Joachimiak and Jason K Baumohl and Qiang He and Matthew W Fields and Adam P Arkin and Judy D Wall and Terry C Hazen and Jizhong Zhou},
url = {http://dx.doi.org/10.1128/AEM.05666-11},
doi = {10.1128/AEM.05666-11},
year = {2012},
date = {2012-02-01},
urldate = {2021-05-25},
journal = {Applied and Environmental Microbiology},
volume = {78},
number = {4},
pages = {1168-1177},
abstract = {Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a DeltaDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a DeltaDVU2547 mutant (JW9011) under nitrite stress conditions and a DeltaDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a DeltaDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a DeltaDVU2547 mutant (JW9011) under nitrite stress conditions and a DeltaDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.
Deutschbauer, Adam; Price, Morgan N; Wetmore, Kelly M; Shao, Wenjun; Baumohl, Jason K; Xu, Zhuchen; Nguyen, Michelle; Tamse, Raquel; Davis, Ronald W; Arkin, Adam P
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. Journal Article
In: PLoS Genetics, vol. 7, no. 11, pp. e1002385, 2011.
@article{deutschbauer_2011,
title = {Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.},
author = {Adam Deutschbauer and Morgan N Price and Kelly M Wetmore and Wenjun Shao and Jason K Baumohl and Zhuchen Xu and Michelle Nguyen and Raquel Tamse and Ronald W Davis and Adam P Arkin},
url = {http://dx.doi.org/10.1371/journal.pgen.1002385},
doi = {10.1371/journal.pgen.1002385},
year = {2011},
date = {2011-11-17},
urldate = {2021-06-04},
journal = {PLoS Genetics},
volume = {7},
number = {11},
pages = {e1002385},
abstract = {Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes.
Jajamovich, Guido H; Wang, Xiaodong; Arkin, Adam P; Samoilov, Michael S
Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites. Journal Article
In: Nucleic Acids Research, vol. 39, no. 21, pp. e146, 2011.
@article{jajamovich_2011,
title = {Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites.},
author = {Guido H Jajamovich and Xiaodong Wang and Adam P Arkin and Michael S Samoilov},
url = {http://dx.doi.org/10.1093/nar/gkr745},
doi = {10.1093/nar/gkr745},
year = {2011},
date = {2011-11-01},
urldate = {2021-06-04},
journal = {Nucleic Acids Research},
volume = {39},
number = {21},
pages = {e146},
abstract = {Finding conserved motifs in genomic sequences represents one of essential bioinformatic problems. However, achieving high discovery performance without imposing substantial auxiliary constraints on possible motif features remains a key algorithmic challenge. This work describes BAMBI-a sequential Monte Carlo motif-identification algorithm, which is based on a position weight matrix model that does not require additional constraints and is able to estimate such motif properties as length, logo, number of instances and their locations solely on the basis of primary nucleotide sequence data. Furthermore, should biologically meaningful information about motif attributes be available, BAMBI takes advantage of this knowledge to further refine the discovery results. In practical applications, we show that the proposed approach can be used to find sites of such diverse DNA-binding molecules as the cAMP receptor protein (CRP) and Din-family site-specific serine recombinases. Results obtained by BAMBI in these and other settings demonstrate better statistical performance than any of the four widely-used profile-based motif discovery methods: MEME, BioProspector with BioOptimizer, SeSiMCMC and Motif Sampler as measured by the nucleotide-level correlation coefficient. Additionally, in the case of Din-family recombinase target site discovery, the BAMBI-inferred motif is found to be the only one functionally accurate from the underlying biochemical mechanism standpoint. C++ and Matlab code is available at http://www.ee.columbia.edu/~guido/BAMBI or http://genomics.lbl.gov/BAMBI/.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Finding conserved motifs in genomic sequences represents one of essential bioinformatic problems. However, achieving high discovery performance without imposing substantial auxiliary constraints on possible motif features remains a key algorithmic challenge. This work describes BAMBI-a sequential Monte Carlo motif-identification algorithm, which is based on a position weight matrix model that does not require additional constraints and is able to estimate such motif properties as length, logo, number of instances and their locations solely on the basis of primary nucleotide sequence data. Furthermore, should biologically meaningful information about motif attributes be available, BAMBI takes advantage of this knowledge to further refine the discovery results. In practical applications, we show that the proposed approach can be used to find sites of such diverse DNA-binding molecules as the cAMP receptor protein (CRP) and Din-family site-specific serine recombinases. Results obtained by BAMBI in these and other settings demonstrate better statistical performance than any of the four widely-used profile-based motif discovery methods: MEME, BioProspector with BioOptimizer, SeSiMCMC and Motif Sampler as measured by the nucleotide-level correlation coefficient. Additionally, in the case of Din-family recombinase target site discovery, the BAMBI-inferred motif is found to be the only one functionally accurate from the underlying biochemical mechanism standpoint. C++ and Matlab code is available at http://www.ee.columbia.edu/~guido/BAMBI or http://genomics.lbl.gov/BAMBI/.
Price, Morgan N; Deutschbauer, Adam M; Kuehl, Jennifer V; Liu, Haichuan; Witkowska, Ewa H; Arkin, Adam P
Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Journal Article
In: Journal of Bacteriology, vol. 193, no. 20, pp. 5716-5727, 2011.
@article{price_2011,
title = {Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.},
author = {Morgan N Price and Adam M Deutschbauer and Jennifer V Kuehl and Haichuan Liu and Ewa H Witkowska and Adam P Arkin},
url = {http://dx.doi.org/10.1128/JB.05563-11},
doi = {10.1128/JB.05563-11},
year = {2011},
date = {2011-10-01},
urldate = {2021-06-04},
journal = {Journal of Bacteriology},
volume = {193},
number = {20},
pages = {5716-5727},
abstract = {We used high-resolution tiling microarrays and 5' RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. vulgaris prefers -10 and -35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5' ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We used high-resolution tiling microarrays and 5' RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. vulgaris prefers -10 and -35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5' ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/.
Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup K
Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH). Journal Article
In: Lab on A Chip, vol. 11, no. 16, pp. 2673-2679, 2011.
@article{liu_2011,
title = {Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH).},
author = {Peng Liu and Robert J Meagher and Yooli K Light and Suzan Yilmaz and Romy Chakraborty and Adam P Arkin and Terry C Hazen and Anup K Singh},
url = {http://dx.doi.org/10.1039/c1lc20151d},
doi = {10.1039/c1lc20151d},
year = {2011},
date = {2011-08-21},
urldate = {2021-06-04},
journal = {Lab on A Chip},
volume = {11},
number = {16},
pages = {2673-2679},
abstract = {We describe an integrated microfluidic device (μFlowFISH) capable of performing 16S rRNA fluorescence in situ hybridization (FISH) followed by flow cytometric detection for identifying bacteria in natural microbial communities. The device was used for detection of species involved in bioremediation of Cr(vi) and other metals in groundwater samples from a highly-contaminated environmental site (Hanford, WA, USA). The μFlowFISH seamlessly integrates two components: a hybridization chamber formed between two photopolymerized membranes, where cells and probes are electrophoretically loaded, incubated and washed, and a downstream cross structure for electrokinetically focusing cells into a single-file flow for flow cytometry analysis. The device is capable of analyzing a wide variety of bacteria including aerobic, facultative and anaerobic bacteria and was initially tested and validated using cultured microbes, including Escherichia coli, as well as two strains isolated from Hanford site: Desulfovibrio vulgaris strain RCH1, and Pseudomonas sp.strain RCH2 that are involved in Cr(vi) reduction and immobilization. Combined labeling and detection efficiencies of 74-97% were observed in experiments with simple mixtures of cultured cells, confirming specific labeling. Results obtained were in excellent agreement with those obtained by conventional flow cytometry confirming the accuracy of μFlowFISH. Finally, the device was used for analyzing water samples collected on different dates from the Hanford site. We were able to monitor the numbers of Pseudomonas sp. with only 100-200 cells loaded into the microchip. The μFlowFISH approach provides an automated platform for quantitative detection of microbial cells from complex samples, and is ideally suited for analysis of precious samples with low cell numbers such as those found at extreme environmental niches, bioremediation sites, and the human microbiome. This journal is copyright The Royal Society of Chemistry 2011},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe an integrated microfluidic device (μFlowFISH) capable of performing 16S rRNA fluorescence in situ hybridization (FISH) followed by flow cytometric detection for identifying bacteria in natural microbial communities. The device was used for detection of species involved in bioremediation of Cr(vi) and other metals in groundwater samples from a highly-contaminated environmental site (Hanford, WA, USA). The μFlowFISH seamlessly integrates two components: a hybridization chamber formed between two photopolymerized membranes, where cells and probes are electrophoretically loaded, incubated and washed, and a downstream cross structure for electrokinetically focusing cells into a single-file flow for flow cytometry analysis. The device is capable of analyzing a wide variety of bacteria including aerobic, facultative and anaerobic bacteria and was initially tested and validated using cultured microbes, including Escherichia coli, as well as two strains isolated from Hanford site: Desulfovibrio vulgaris strain RCH1, and Pseudomonas sp.strain RCH2 that are involved in Cr(vi) reduction and immobilization. Combined labeling and detection efficiencies of 74-97% were observed in experiments with simple mixtures of cultured cells, confirming specific labeling. Results obtained were in excellent agreement with those obtained by conventional flow cytometry confirming the accuracy of μFlowFISH. Finally, the device was used for analyzing water samples collected on different dates from the Hanford site. We were able to monitor the numbers of Pseudomonas sp. with only 100-200 cells loaded into the microchip. The μFlowFISH approach provides an automated platform for quantitative detection of microbial cells from complex samples, and is ideally suited for analysis of precious samples with low cell numbers such as those found at extreme environmental niches, bioremediation sites, and the human microbiome. This journal is copyright The Royal Society of Chemistry 2011
Price, Morgan N; Dehal, Paramvir S; Arkin, Adam P
FastTree 2 — approximately maximum-likelihood trees for large alignments. Journal Article
In: Plos One, vol. 5, no. 3, pp. e9490, 2010.
@article{price_2010,
title = {FastTree 2 — approximately maximum-likelihood trees for large alignments.},
author = {Morgan N Price and Paramvir S Dehal and Adam P Arkin},
url = {http://dx.doi.org/10.1371/journal.pone.0009490},
doi = {10.1371/journal.pone.0009490},
year = {2010},
date = {2010-03-10},
urldate = {2017-12-18},
journal = {Plos One},
volume = {5},
number = {3},
pages = {e9490},
abstract = {BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. METHODOLOGY/PRINCIPAL FINDINGS: Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the "CAT" approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100-1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. CONCLUSIONS/SIGNIFICANCE: FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. METHODOLOGY/PRINCIPAL FINDINGS: Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the "CAT" approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100-1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. CONCLUSIONS/SIGNIFICANCE: FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
Mengting Yuan Daliang Ning, Linwei Wu; Zhou, Jizhong
A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming Journal Article
In: 0000.
@article{ning2020quantitative,
title = {A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming},
author = {Daliang Ning
, Mengting Yuan
, Linwei Wu
, Ya Zhang
, Xue Guo,
, Xishu Zhou , Yunfeng
Yang
, Adam P. Arkin
, Mary K. Firestone
, and Jizhong Zhou},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
