@article{pmid32576650,

title = {GapMind: Automated Annotation of Amino Acid Biosynthesis},

author = {M N Price and A M Deutschbauer and A P Arkin},

year  = {2020},

date = {2020-06-01},

journal = {mSystems},

volume = {5},

number = {3},

abstract = {GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.},

keywords = {arkin lab},

pubstate = {published},

tppubtype = {article}

}

@article{sean,

title = {Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins},

author = {Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik, Adam P. Arkin},

year  = {2020},

date = {2020-05-27},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{adler2020systematic,

title = {Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens},

author = {Benjamin A. Adler, Crystal Zhong, Hualan Liu, Elizabeth Kutter, Adam M.

Deutschbauer, Vivek K. Mutalik, Adam P. Arkin},

year  = {2020},

date = {2020-04-28},

journal = {bioRxiv},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{morgan,

title = {Short Methionine Synthases},

author = {Morgan N. Price and Adam P. Arkin},

year  = {2020},

date = {2020-04-23},

keywords = {arkin lab},

pubstate = {published},

tppubtype = {article}

}

@article{lui2020method,

title = {A method for achieving complete microbial genomes and better quality bins from metagenomics data},

author = {Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin},

year  = {2020},

date = {2020-03-06},

journal = {BioRxiv},

keywords = {arkin lab, enigma},

pubstate = {published},

tppubtype = {article}

}

@article{Mutalik2020,

title = {High-throughput mapping of the phage resistance landscape in E. coli},

author = {Vivek K. Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong,Britt Koskella, Richard Calendar, Pavel Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin},

year  = {2020},

date = {2020-02-16},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32372050,

title = {Selective carbon sources influence the end products of microbial nitrate respiration},

author = {H K Carlson and L M Lui and M N Price and A E Kazakov and A V Carr and J V Kuehl and T K Owens and T Nielsen and A P Arkin and A M Deutschbauer},

year  = {2020},

date = {2020-00-01},

journal = {ISME J},

volume = {14},

number = {8},

pages = {2034--2045},

abstract = {Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.},

keywords = {arkin lab, enigma},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30788501,

title = {A versatile platform strain for high-fidelity multiplex genome editing},

author = {R G Egbert and H S Rishi and B A Adler and D M McCormick and E Toro and R T Gill and A P Arkin},

year  = {2019},

date = {2019-01-01},

journal = {Nucleic Acids Res.},

volume = {47},

number = {6},

pages = {3244--3256},

abstract = {Precision genome editing accelerates the discovery of the genetic determinants of phenotype and the engineering of novel behaviors in organisms. Advances in DNA synthesis and recombineering have enabled high-throughput engineering of genetic circuits and biosynthetic pathways via directed mutagenesis of bacterial chromosomes. However, the highest recombination efficiencies have to date been reported in persistent mutator strains, which suffer from reduced genomic fidelity. The absence of inducible transcriptional regulators in these strains also prevents concurrent control of genome engineering tools and engineered functions. Here, we introduce a new recombineering platform strain, BioDesignER, which incorporates (i) a refactored λ-Red recombination system that reduces toxicity and accelerates multi-cycle recombination, (ii) genetic modifications that boost recombination efficiency, and (iii) four independent inducible regulators to control engineered functions. These modifications resulted in single-cycle recombineering efficiencies of up to 25% with a 7-fold increase in recombineering fidelity compared to the widely used recombineering strain EcNR2. To facilitate genome engineering in BioDesignER, we have curated eight context--neutral genomic loci, termed Safe Sites, for stable gene expression and consistent recombination efficiency. BioDesignER is a platform to develop and optimize engineered cellular functions and can serve as a model to implement comparable recombination and regulatory systems in other bacteria.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30943208,

title = {Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics},

author = {M N Price and G M Zane and J V Kuehl and R A Melnyk and J D Wall and A M Deutschbauer and A P Arkin},

year  = {2019},

date = {2019-01-01},

journal = {PLoS Genet.},

volume = {15},

number = {4},

pages = {e1008106},

abstract = {[This corrects the article DOI: 10.1371/journal.pgen.1007147.].},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30944879,

title = {Curated BLASŦ for Genomes},

author = {M N Price and A P Arkin},

year  = {2019},

date = {2019-01-01},

journal = {mSystems},

volume = {4},

number = {2},

abstract = {Curated BLAST for Genomes finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme's name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated. IMPORTANCE Given a microbe's genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually from other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.},

keywords = {arkin lab},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30540439,

title = {Đesigning Spatially Đistributed Gene Regulatory Networks Ŧo Elicit Contrasting Patterns},

author = {M Tei and M L Perkins and J Hsia and M Arcak and A P Arkin},

year  = {2019},

date = {2019-01-01},

volume = {8},

number = {1},

pages = {119--126},

abstract = {Pattern formation and differential interactions are important for microbial consortia to divide labor and perform complex functions. To obtain further insight into such interactions, we present a computational method for simulating physically separated microbial colonies, each implementing different gene regulatory networks. We validate our theory by experimentally demonstrating control over gene expression patterns in a diffusion-mediated lateral inhibition circuit. We highlight the importance of spatial arrangement as a control knob for modulating system behavior. Our systematic approach provides a foundation for future applications that require understanding and engineering of multistrain microbial communities for sophisticated, synergistic functions.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30659179,

title = {Đual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria},

author = {V K Mutalik and P S Novichkov and M N Price and T K Owens and M Callaghan and S Carim and A M Deutschbauer and A P Arkin},

year  = {2019},

date = {2019-01-01},

journal = {Nat Commun},

volume = {10},

number = {1},

pages = {308},

abstract = {A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31064836,

title = {Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism},

author = {M G Thompson and J M Blake-Hedges and P Cruz-Morales and J F Barajas and S C Curran and C B Eiben and N C Harris and V T Benites and J W Gin and W A Sharpless and F F Twigg and W Skyrud and R N Krishna and J H Pereira and E E K Baidoo and C J Petzold and P D Adams and A P Arkin and A M Deutschbauer and J D Keasling},

year  = {2019},

date = {2019-01-01},

journal = {mBio},

volume = {10},

number = {3},

abstract = {Despite intensive study for 50 years, the biochemical and genetic links between lysine metabolism and central metabolism in Pseudomonas putida remain unresolved. To establish these biochemical links, we leveraged random barcode transposon sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both l- and d-lysine metabolism. We first describe three pathway enzymes that catabolize l-2-aminoadipate (l-2AA) to 2-ketoglutarate (2KG), connecting d-lysine to the TCA cycle. One of these enzymes, P. putida 5260 (PP_5260), contains a DUF1338 domain, representing a family with no previously described biological function. Our work also identified the recently described coenzyme A (CoA)-independent route of l-lysine degradation that results in metabolization to succinate. We expanded on previous findings by demonstrating that glutarate hydroxylase CsiD is promiscuous in its 2-oxoacid selectivity. Proteomics of selected pathway enzymes revealed that expression of catabolic genes is highly sensitive to the presence of particular pathway metabolites, implying intensive local and global regulation. This work demonstrated the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria, as well as its utility a powerful tool for validating previous research.IMPORTANCEP. putida lysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, the connection of lysine catabolism to central metabolism in P. putida remained undefined. Here, we used random barcode transposon sequencing to fill the gaps of lysine metabolism in P. putida We describe a route of 2-oxoadipate (2OA) catabolism, which utilizes DUF1338-containing protein P. putida 5260 (PP_5260) in bacteria. Despite its prevalence in many domains of life, DUF1338-containing proteins have had no known biochemical function. We demonstrate that PP_5260 is a metalloenzyme which catalyzes an unusual route of decarboxylation of 2OA to d-2-hydroxyglutarate (d-2HG). Our screen also identified a recently described novel glutarate metabolic pathway. We validate previous results and expand the understanding of glutarate hydroxylase CsiD by showing that can it use either 2OA or 2KG as a cosubstrate. Our work demonstrated that biological novelty can be rapidly identified using unbiased experimental genetics and that RB-TnSeq can be used to rapidly validate previous results.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31253673,

title = {Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Ħeavily Contaminated Oak Ridge Reservation},

author = {M P Thorgersen and X Ge and F L Poole and M N Price and A P Arkin and M W W Adams},

year  = {2019},

date = {2019-01-01},

volume = {85},

number = {17},

abstract = {Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.},

keywords = {arkin lab, enigma},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30746495,

title = {Oxidative Pathways of Đeoxyribose and Đeoxyribonate Catabolism},

author = {M N Price and J Ray and A T Iavarone and H K Carlson and E M Ryan and R R Malmstrom and A P Arkin and A M Deutschbauer},

year  = {2019},

date = {2019-01-01},

journal = {mSystems},

volume = {4},

number = {1},

abstract = {Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either nonspecific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism. IMPORTANCE Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants' abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29930200,

title = {Đeciphering microbial interactions in synthetic human gut microbiome communities},

author = {O S Venturelli and A C Carr and G Fisher and R H Hsu and R Lau and B P Bowen and S Hromada and T Northen and A P Arkin},

year  = {2018},

date = {2018-01-01},

journal = {Mol. Syst. Biol.},

volume = {14},

number = {6},

pages = {e8157},

abstract = {The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30247489,

title = {Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli},

author = {G Cambray and J C Guimaraes and A P Arkin},

year  = {2018},

date = {2018-01-01},

journal = {Nat. Biotechnol.},

volume = {36},

number = {10},

pages = {1005--1015},

abstract = {Comparative analyses of natural and mutated sequences have been used to probe mechanisms of gene expression, but small sample sizes may produce biased outcomes. We applied an unbiased design-of-experiments approach to disentangle factors suspected to affect translation efficiency in E. coli. We precisely designed 244,000 DNA sequences implementing 56 replicates of a full factorial design to evaluate nucleotide, secondary structure, codon and amino acid properties in combination. For each sequence, we measured reporter transcript abundance and decay, polysome profiles, protein production and growth rates. Associations between designed sequences properties and these consequent phenotypes were dominated by secondary structures and their interactions within transcripts. We confirmed that transcript structure generally limits translation initiation and demonstrated its physiological cost using an epigenetic assay. Codon composition has a sizable impact on translatability, but only in comparatively rare elongation-limited transcripts. We propose a set of design principles to improve translation efficiency that would benefit from more accurate prediction of secondary structures in vivo.},

keywords = {arkin lab},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29324779,

title = {Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics},

author = {M N Price and G M Zane and J V Kuehl and R A Melnyk and J D Wall and A M Deutschbauer and A P Arkin},

year  = {2018},

date = {2018-01-01},

journal = {PLoS Genet.},

volume = {14},

number = {1},

pages = {e1007147},

abstract = {For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29521624,

title = {Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides},

author = {S T Coradetti and D Pinel and G M Geiselman and M Ito and S J Mondo and M C Reilly and Y F Cheng and S Bauer and I V Grigoriev and J M Gladden and B A Simmons and R B Brem and A P Arkin and J M Skerker},

year  = {2018},

date = {2018-01-01},

journal = {Elife},

volume = {7},

abstract = {The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.},

keywords = {arkin lab, biodesign},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30297967,

title = {Genetic dissection of interspecific differences in yeast thermotolerance},

author = {C V Weiss and J I Roop and R K Hackley and J N Chuong and I V Grigoriev and A P Arkin and J M Skerker and R B Brem},

year  = {2018},

date = {2018-01-01},

journal = {Nat. Genet.},

volume = {50},

number = {11},

pages = {1501--1504},

abstract = {Some of the most unique and compelling survival strategies in the natural world are fixed in isolated species1. To date, molecular insight into these ancient adaptations has been limited, as classic experimental genetics has focused on interfertile individuals in populations2. Here we use a new mapping approach, which screens mutants in a sterile interspecific hybrid, to identify eight housekeeping genes that underlie the growth advantage of Saccharomyces cerevisiae over its distant relative Saccharomyces paradoxus at high temperature. Pro-thermotolerance alleles at these mapped loci were required for the adaptive trait in S. cerevisiae and sufficient for its partial reconstruction in S. paradoxus. The emerging picture is one in which S. cerevisiae improved the heat resistance of multiple components of the fundamental growth machinery in response to selective pressure. Our study lays the groundwork for the mapping of genotype to phenotype in clades of sister species across Eukarya.},

keywords = {arkin lab},

pubstate = {published},

tppubtype = {article}

}