The essential genome of a bacterium

Christen, Beat; Abeliuk, Eduardo; Collier, John M.; Kalogeraki, Virginia S.; Passarelli, Ben; Coller, John A.; Fero, M.J.; McAdams, Harley H.; Shapiro, Lucy

doi:10.1038/msb.2011.58

Cited by 302 publications

(400 citation statements)

References 28 publications

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“…In those three categories, B. subvibrioides has 35 essential genes and A. tumefaciens has 39 essential genes (15). C. crescentus TnSeq found 49 essential genes of unknown function (14), and P. aeruginosa has 72 essential genes listed as hypothetical alone (16). While this unknown essential gene content may represent biology yet to be discovered, the number of genes in these categories is likely also dependent on the age or effectiveness of genome annotation.…”

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

“…Other COG categories with large numbers of essential genes include H (coenzyme transport and metabolism) (36 genes), I (lipid transport and metabolism) (20 genes), and M (cell wall/membrane/envelope biogenesis) (35 genes). It is unsurprising that there are many essential genes in the last category, as it contains genes for peptidoglycan synthesis as well as assembly, which tend to be essential in other organisms (14,15,21). Essential genes in category I not only include genes for fatty acid and phospholipid biosynthesis but several genes involved in isoprenoid biosynthesis as well.…”

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

“…There were very few essential genes from any of the glycolytic pathways. This result is not unusual; few glycolytic genes are essential in other organisms (13)(14)(15)(16)(17). TnSeq is usually performed on rich media containing combinations of tryptone, peptone, and yeast extract; therefore, the principal carbon and energy sources in these media are amino acids and small peptides.…”

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

“…Organisms with more genomic content tend to have lower essential gene content by percentage. For example, Salmonella typhi has 356 essential ORFs of its total 4,537 (7.8%) (13), Agrobacterium tumefaciens has 372 of 5,460 (6.8%) (15), and Pseudomonas aeruginosa has 352 of 5,678 (6.2%) (16); conversely, Caulobacter crescentus has 480 of 3,876 (12.4%) (14), Brevundimonas subvibrioides has 447 of 3,393 (13.2%) (15), and Streptococcus pyogenes has 241 of 1,785 (13.5%) (20). Another contributing factor to lower essential gene content is the general lack of metabolic genes.…”

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

“…Mutants are pooled, and high-throughput sequencing is used to map hundreds of thousands of unique insertions; these data are then used to find genes that are essential under mutagenesis conditions by identifying genes that cannot tolerate disruptive insertions. This technique has been used on a number of model bacterial systems (13)(14)(15)(16)(17). Here, TnSeq was applied to R. gelatinosus, not only to investigate its metabolism but also to reveal other unusual features of the organism.…”

Section: R Ubrivivax Gelatinosus (Formerly Rhodocyclus Gelatinosus) Is Amentioning

confidence: 99%

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Essential Genes Predicted in the Genome of Rubrivivax gelatinosus

Curtis

2016

J Bacteriol

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Rubrivivax gelatinosus is a betaproteobacterium with impressive metabolic diversity. It is capable of phototrophy, chemotrophy, two different mechanisms of sugar metabolism, fermentation, and H 2 gas production. To identify core essential genes, R. gelatinosus was subjected to saturating transposon mutagenesis and high-throughput sequencing (TnSeq) analysis using nutrient-rich, aerobic conditions. Results revealed that virtually no primary metabolic genes are essential to the organism and that genomic redundancy only explains a portion of the nonessentiality, but some biosynthetic pathways are still essential under nutrient-rich conditions. Different essentialities of different portions of the Pho regulatory pathway suggest that overexpression of the regulon is toxic and hint at a larger connection between phosphate regulation and cellular health. Lastly, various essentialities of different tRNAs hint at a more complex situation than would be expected for such a core process. These results expand upon research regarding cross-organism gene essentiality and further enrich the study of purple nonsulfur bacteria. IMPORTANCEMicrobial genomic data are increasing at a tremendous rate, but physiological characterization of those data lags far behind. One mechanism of high-throughput physiological characterization is TnSeq, which uses high-volume transposon mutagenesis and highthroughput sequencing to identify all of the essential genes in a given organism's genome. Here TnSeq was used to identify essential genes in the metabolically versatile betaproteobacterium Rubrivivax gelatinosus. The results presented here add to the growing TnSeq field and also reveal important aspects of R. gelatinosus physiology, which are applicable to researchers working on metabolically flexible organisms. R ubrivivax gelatinosus (formerly Rhodocyclus gelatinosus) is apurple nonsulfur bacterium in the Betaproteobacteria clade. Its physiology has principally been studied for its photosynthetic capability (1-8), but the organism is very metabolically versatile; it is capable of growing phototrophically (including photoheterotrophically) in anaerobic light conditions and chemoheterotrophically under aerobic conditions in light or dark (9, 10). It has the necessary components for the Embden-Meyerhof-Parnas pathway and the Entner-Doudoroff pathway as well as for the pentose phosphate pathway (11). It is capable of carbon and nitrogen fixation, fermentation, and H 2 gas production, making it of interest in biofuel production. Interestingly, while 16S rRNA gene sequencing places the organism in the Betaproteobacteria, the phylogenetic history of the photosynthesis genes strongly suggests that they were horizontally transferred from purple photosynthetic Alphaproteobacteria (12).To identify a minimal set of essential genes in R. gelatinosus IL-144, saturating transposon mutagenesis and high-throughput sequencing (TnSeq) was performed on the organism using aerobic, dark, nutrient-rich conditions. TnSeq is a method of identifying essential ge...

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Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

Section: Analysis Of Insertion Bias and Identification Of Essential Gmentioning

confidence: 99%

Section: R Ubrivivax Gelatinosus (Formerly Rhodocyclus Gelatinosus) Is Amentioning

confidence: 99%

See 3 more Smart Citations

Essential Genes Predicted in the Genome of Rubrivivax gelatinosus

Curtis

2016

J Bacteriol

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The Minimal Gene-Set Machinery

Gil

2014

Encyclopedia of Molecular Cell Biology and Molecular Medicine

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Construction of Signature‐Tagged Mutant Libraries and Its Application to Plant‐Symbiotic Bacteria

Becker

Pobigaylo

2013

Molecular Microbial Ecology of the Rhizosphere

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The essential genome of a bacterium

Abstract: This study reports the essential Caulobacter genome at 8 bp resolution determined by saturated transposon mutagenesis and high-throughput sequencing. This strategy is applicable to full genome essentiality studies in a broad class of bacterial species.

Cited by 302 publications

References 28 publications

Essential Genes Predicted in the Genome of Rubrivivax gelatinosus

Essential Genes Predicted in the Genome of Rubrivivax gelatinosus

The Minimal Gene-Set Machinery

Construction of Signature‐Tagged Mutant Libraries and Its Application to Plant‐Symbiotic Bacteria

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