A vast collection of microbial genes that are toxic to bacteria

Kimelman, Aya; Levy, Asaf; Sberro, Hila; Kidron, Shahar; Leavitt, Azita; Amitai, Gil; Yoder-Himes, Deborah R.; Wurtzel, Omri; Zhu, Yiwen; Rubin, Edward M.; Sorek, Rotem

doi:10.1101/gr.133850.111

Cited by 71 publications

(73 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These results support that YgfX is not a toxin. Finally, in a recent shotgun cloning study to identify novel TA systems from a range of microbial genomes, YgfX was not identified as being toxic (Kimelman et al, 2012;Sberro et al, 2013). These independent lines of experimental investigation provide further evidence that YgfX-SdhE is not a TA system.…”

Section: Discussionmentioning

confidence: 73%

YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY)

et al. 2013

View full text Add to dashboard Cite

Serratia sp. strain ATCC 39006 produces the red-pigmented antibiotic prodigiosin. Prodigiosin biosynthesis is regulated by a complex hierarchy that includes the uncharacterized protein YgfX (DUF1434). The ygfX gene is co-transcribed with sdhE, an FAD assembly factor essential for the flavinylation and activation of the SdhA subunit of succinate dehydrogenase (SDH), a central enzyme in the tricarboxylic acid cycle and electron transport chain. The sdhEygfX operon is highly conserved within the Enterobacteriaceae, suggesting that SdhE and YgfX function together. We performed an extensive mutagenesis to gain molecular insights into the uncharacterized protein YgfX, and have investigated the relationship between YgfX and SdhE. YgfX localized to the membrane, interacted with itself, forming dimers or larger multimers, and interacted with SdhE. The transmembrane helices of YgfX were critical for protein function and the formation of YgfX multimers. Site-directed mutagenesis of residues conserved in DUF1434 proteins revealed a periplasmic tryptophan and a cytoplasmic aspartate that were crucial for YgfX activity. Both of these amino acids were required for the formation of YgfX multimers and interactions with SdhE but not membrane localization. Multiple cell division proteins were identified as putative interaction partners of YgfX and overexpression of YgfX had effects on cell morphology. These findings represent an important step in understanding the function of DUF1434 proteins. In contrast to a recent report, we found no evidence that YgfX and SdhE form a toxin-antitoxin system. In summary, YgfX functions as a multimeric membrane-bound protein that interacts with SdhE, an important FAD assembly factor that controls SDH activity.

show abstract

Section: Discussionmentioning

confidence: 73%

YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY)

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Each point represents one bacterial species. For each of its metabolic genes, EDGE predicted whether its transfer to E. coli would be successful, and the results were compared with previously published experimental data (20,21). The predictor's quality was quantified by the area under the ROC curve (AUC) (y axis).…”

Section: Genes Whose Expression Impedes Growth (According To Edge) Arementioning

confidence: 99%

“…It was previously observed that gaps in Sanger-based genome sequencing are often caused by toxic genes that cannot be expressed in an E. coli host (20). To study EDGE's ability to predict failed gene transfer between organisms due to toxic effects, we used the recently published PanDaTox dataset (21) of genes found to be unclonable into E. coli. We simulated in silico the process of gene transfer from 50 different Gammaproteobacteria into E. coli, and then used EDGE to predict which of the heterologous genes should be toxic to the E. coli host (SI Appendix).…”

Section: Edge Predicts Reduced Fitness Due To Overexpression Of Foreignmentioning

confidence: 99%

See 1 more Smart Citation

Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious

Wagner¹,

Zarecki²,

Reshef

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Gene suppression and overexpression are both fundamental tools in linking genotype to phenotype in model organisms. Computational methods have proven invaluable in studying and predicting the deleterious effects of gene deletions, and yet parallel computational methods for overexpression are still lacking. Here, we present Expression-Dependent Gene Effects (EDGE), an in silico method that can predict the deleterious effects resulting from overexpression of either native or foreign metabolic genes. We first test and validate EDGE's predictive power in bacteria through a combination of small-scale growth experiments that we performed and analysis of extant large-scale datasets. Second, a broad cross-species analysis, ranging from microorganisms to multiple plant and human tissues, shows that genes that EDGE predicts to be deleterious when overexpressed are indeed typically downregulated. This reflects a universal selection force keeping the expression of potentially deleterious genes in check. Third, EDGEbased analysis shows that cancer genetic reprogramming specifically suppresses genes whose overexpression impedes proliferation. The magnitude of this suppression is large enough to enable an almost perfect distinction between normal and cancerous tissues based solely on EDGE results. We expect EDGE to advance our understanding of human pathologies associated with up-regulation of particular transcripts and to facilitate the utilization of gene overexpression in metabolic engineering.systems metabolic engineering | metabolic modeling | constraint-based modeling | flux balance analysis | horizontal gene transfer

show abstract

“…By experimenting with cumulatively more than 100 gap-residing genes from numerous different organisms, we have verified that our gap-based prediction of gene toxicity exceeds 80% of accuracy. 13,14 The accuracy in our predictions of gene clonability into E. coli stems from several factors. First, the high sequencing coverage, needed for proper genome assembly, dictates that on average more than 25 independent clones would contain each gene.…”

Section: Acknowledgmentsmentioning

confidence: 99%

PanDaTox: A tool for accelerated metabolic engineering

Amitai

Sorek

2012

biobugs

Self Cite

View full text Add to dashboard Cite

Metabolic engineering is often facilitated by cloning of genes encoding enzymes from various heterologous organisms into E. coli. Such engineering efforts are frequently hampered by foreign genes that are toxic to the E. coli host. We have developed PanDaTox (www.weizmann.ac.il/pandatox), a web-based resource that provides experimental toxicity information for more than 1.5 million genes from hundreds of different microbial genomes. The toxicity predictions, which were extensively experimentally verified, are based on serial cloning of genes into E. coli as part of the Sanger whole genome shotgun sequencing process. PanDaTox can accelerate metabolic engineering projects by allowing researchers to exclude toxic genes from the engineering plan and verify the clonability of selected genes before the actual metabolic engineering experiments are conducted. Metabolic Engineering and the Problem of Toxic GenesMetabolic engineering is a rapidly growing field where enzymatic pathways for the biosynthesis of desired molecules are genetically engineered into model microorganisms in order to harness bacterial productivity into industrial use. 1Metabolic engineering is often practiced in close connection with synthetic biology and systems biology, as significant theoretical modeling is conducted in order to model pathways to be engineered into a given organism. 2-5The bacterial species Escherichia coli is one of the most widely used PanDaToxA tool for accelerated metabolic engineering Gil Amitai and Rotem Sorek* Department of Molecular Genetics; Weizmann Institute of Science; Rehovot, Israel microorganisms in metabolic engineering and had been utilized for numerous bio-production applications. For example, massive production of precursors for the antimalarial drug artimisinin was facilitated by inserting genes from several microorganisms into E. coli; 6,7 polyketides, which are the precursors for many antibiotics, have been produced within E. coli by introducing a combination of genes from three different bacteria into this organism;8 various nutritional molecules such as acetate, pyruvate, succinate and an array of amino acids are also among the products produced within E. coli through metabolic engineering.9 Recently, metabolic engineering has taken center stage in the global efforts for the design and generation of biofuel-producing organisms, in attempts to generate biological alternatives to fossil fuels. 1,10Thousands of microbial genomes have been sequenced to date 5,11 and these genomes cumulatively harbor millions of enzymes that can be used as "building blocks" in the toolbox of the metabolic engineer. Following detailed planning of the pathway of new enzymes to engineer into E. coli, the metabolic engineer will usually search for these enzymes in the set of available genomes and will select genes encoding the desired enzymes from organisms in which these genes exist. The selected genes will then be cloned into E. coli with or without optimization for expression through codon and promoter alterations. 3,12One of th...

show abstract

A vast collection of microbial genes that are toxic to bacteria

Cited by 71 publications

References 44 publications

YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY)

YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY)

Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious

PanDaTox: A tool for accelerated metabolic engineering

Contact Info

Product

Resources

About