Essential genes in Bacillus subtilis: a re-evaluation after ten years

Commichau, Fabian M.; Pietack, Nico; Stülke, Jörg

doi:10.1039/c3mb25595f

Cited by 98 publications

(88 citation statements)

References 63 publications

(81 reference statements)

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“…In the genome-reduced strains, only five of the essential genes have been deleted. These genes are part of prophages and encode protective functions (Commichau et al 2013). In contrast, about 300 of the genes of unknown function have been deleted.…”

Section: General Results Of the Multi-omics Analysismentioning

confidence: 99%

“…Thus, the identification and evaluation of the essential gene set is important for the construction of a viable minimal cell. However, the genome of a minimal organism is much more than an essential gene set because many cellular processes can be achieved in different ways (Commichau et al 2013). For instance, paralogous proteins may carry out the same function and only loss of all of them is lethal.…”

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confidence: 99%

“…Moreover, essential building blocks can either be acquired by uptake or by de novo synthesis. Genes can also be essential because of their role in the protection of the cell against harmful molecules (Commichau et al 2013). Large-scale studies identified 253 and 295 genes as being individually essential for growth of B. subtilis and E. coli, respectively, on rich medium at 37°C (Gerdes et al 2003;Kobayashi et al 2003;Reuß et al 2016a).…”

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confidence: 99%

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Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

et al. 2016

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Understanding cellular life requires a comprehensive knowledge of the essential cellular functions, the components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains of the model bacterium, Bacillus subtilis, whose genomes have been reduced by ∼36%. These strains are fully viable, and their growth rates in complex medium are comparable to those of wild type strains. An in-depth multi-omics analysis of the genome reduced strains revealed how the deletions affect the transcription regulatory network of the cell, translation resource allocation, and metabolism. A comparison of gene counts and resource allocation demonstrates drastic differences in the two parameters, with 50% of the genes using as little as 10% of translation capacity, whereas the 6% essential genes require 57% of the translation resources. Taken together, the results are a valuable resource on gene dispensability in B. subtilis, and they suggest the roads to further genome reduction to approach the final aim of a minimal cell in which all functions are understood.

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Section: General Results Of the Multi-omics Analysismentioning

confidence: 99%

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Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

et al. 2016

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“…Limitation of the Method-For B. subtilis 259 genes are described as being essential (27,28) of which 192 could be quantified absolutely (60% of the cytosolic essential proteins). The average concentration of these proteins (2902 m/c in condition S) is higher compared with the average amount of all proteins (1557 m/c).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Absolute Quantification of the Cytosolic Proteome of Bacillus subtilis by Data Independent, Parallel Fragmentation in Liquid Chromatography/Mass Spectrometry (LC/MSE)

Muntel¹,

Fromion²,

Goelzer³

et al. 2014

Molecular & Cellular Proteomics

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In the growing field of systems biology, the knowledge of protein concentrations is highly required to truly understand metabolic and adaptational networks within the cells. Therefore we established a workflow relying on long chromatographic separation and mass spectrometric analysis by data independent, parallel fragmentation of all precursor ions at the same time (LC/MS E ). By prevention of discrimination of co-eluting low and high abundant peptides a high average sequence coverage of 40% could be achieved, resulting in identification of almost half of the predicted cytosolic proteome of the Gram-positive model organism Bacillus subtilis (>1,050 proteins). Absolute quantification was achieved by correlation of average MS signal intensities of the three most intense peptides of a protein to the signal intensity of a spiked standard protein digest. Comparative analysis with heavily labeled peptides (AQUA approach) showed the use of only one standard digest is sufficient for global quantification.The quantification results covered almost four orders of magnitude, ranging roughly from 10 to 150,000 copies per cell. To prove this method for its biological relevance selected physiological aspects of B. subtilis cells grown under conditions requiring either amino acid synthesis or alternatively amino acid degradation were analyzed. This allowed both in particular the validation of the adjustment of protein levels by known regulatory events and in general a perspective of new insights into bacterial physiology. Within new findings the analysis of "protein costs" of cellular processes is extremely important. Such a comprehensive and detailed characterization of cellular protein concentrations based on data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS E ) data has been performed for the first time and should pave the way for future comprehensive quantitative characterization of microorganisms as physiological entities. Molecular & Cellular

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“…1B). However, the proportion of genes encoding translation-related functions [with the COG letter (J)] is lower in the library, likely because of the high number of essential genes related to protein synthesis (22). Because most bacterial genes are organized in operons [1.5 genes per transcription unit predicted for L. casei, according to genome analysis using the Biocyc website (23)], transposon integration can cause a polar effect; thus the location of each gene of interest in a given operon is specified.…”

Section: Significancementioning

confidence: 99%

Functional genomics of Lactobacillus casei establishment in the gut

Licandro

Scornec

Pédron

et al. 2014

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

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Although the composition of the gut microbiota and its symbiotic contribution to key host physiological functions are well established, little is known as yet about the bacterial factors that account for this symbiosis. We selected Lactobacillus casei as a model microorganism to proceed to genomewide identification of the functions required for a symbiont to establish colonization in the gut. As a result of our recent development of a transposonmutagenesis tool that overcomes the barrier that had prevented L. casei random mutagenesis, we developed a signature-tagged mutagenesis approach combining whole-genome reverse genetics using a set of tagged transposons and in vivo screening using the rabbit ligated ileal loop model. After sequencing transposon insertion sites in 9,250 random mutants, we assembled a library of 1,110 independent mutants, all disrupted in a different gene, that provides a representative view of the L. casei genome. By determining the relative quantity of each of the 1,110 mutants before and after the in vivo challenge, we identified a core of 47 L. casei genes necessary for its establishment in the gut. They are involved in housekeeping functions, metabolism (sugar, amino acids), cell wall biogenesis, and adaptation to environment. Hence we provide what is, to our knowledge, the first global functional genomics analysis of L. casei symbiosis.commensalism | Lactic acid bacteria T he pioneering studies that led to the characterization of the gut microbiota were reviewed in 2001 (1). These studies and recent investigations have revealed mutualistic functions (2), including a barrier effect against allogenic microbes (3), fermentation of complex sugars (4, 5), and maturation and homeostasis of the immune system (6). Recent metagenomic studies have revealed an extraordinary diversity of genes constituting the gut microbiome (7), opening the way to correlative studies linking microbiome diversity, homeostasis, and diseases (5,8,9).In parallel, some representative species, i.e., "model symbionts," now are being studied functionally (10). As it was done for pathogens, it is essential to develop the cellular microbiology of symbionts and particularly to identify the genes required for their establishment and persistence in the gut. Transcriptomic profiling identified up-regulated genes linked to metabolic functions, stress responses, and pili synthesis during early colonization (11-13). Comparative genomics among Lactobacilli identified strain-specific candidate genes for extended colonization: In Lactobacillus rhamnosus, persistence was attributed to an spaCBA locus encoding LPXTG-like pilins (14), and in Lactobacillus johnsonii it was attributed to specific glycosyltransferases, a phosphotransfer system, and a protease (15). Otherwise, a functional in vivo screening based on the expression of a genomic library of Bacteroides fragilis identified a locus encoding polysaccharide utilization as essential for stable colonization of murine colonic crypts (16). Alternatively, colonization of germ-free mic...

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Essential genes in Bacillus subtilis: a re-evaluation after ten years

Cited by 98 publications

References 63 publications

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

Comprehensive Absolute Quantification of the Cytosolic Proteome of Bacillus subtilis by Data Independent, Parallel Fragmentation in Liquid Chromatography/Mass Spectrometry (LC/MSE)

Functional genomics of Lactobacillus casei establishment in the gut

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