Essential Bacillus subtilis genes

By Kazutomo Kobayashi, S. Ehrlich, A. Albertini, G. Amati, Kasper Krogh Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, P. Bessières and 89 more. Proceedings of the National Academy of Sciences of the United States of America, 2003

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To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among ≈4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden–Meyerhof–Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/404c6829c088af96c02b1bb6628c6d6477993c7f

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Citations in the corpus

Proteomics of Protein Secretion by Bacillus subtilis: Separating the “Secrets” of the Secretome (2004, background): “In addition, the availability of the complete genome sequence (58) and about 3,000 “y”-mutants constructed within the Bacillus subtilis Functional Analysis program (54, 115) make B.”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “In parallel to this, collections of knockout mutants are being built for a growing number of bacteria (Akerley et al ., 2002; Jacobs et al ., 2003; Kobayashi et al ., 2003; Baba et al ., 2006; Liberati et al ., 2006; Suzuki et al ., 2006; de Berardinis et al ., 2008).”
DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements (2013, methodology): “Bacteria Acinetobacter baylyi 499 Single-gene knockout Yes (50) Bacillus subtilis 261 2 Single-gene knockout Yes (6,51) Bacteroides thetaiotaomicron 325 INSeq Yes (14) Burkholderia thailandensis 406 Tn-seq Yes (52) Campylobacter jejuni 233 Transposon mutagenesis Yes (53) Caulobacter crescentus 480 5”
EG: a database of essential genes (2004, background): “Some essential genes, however, are somewhat unexpected, such as Embden± Meyerhof±Parnas pathway genes and a purine biosynthesis gene (1).”
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes (2008, result): “…results contain identical records or are only partially published. single-gene deletion studies in Acinetobacter baylyi (23) and Bacillus subtilis (24), those determined by global transposon mutagenesis in Francisella novicida (25), Helicobacter pylori (26), Mycobacterium tuberculosis (27),…”
Cytoplasmic steps of peptidoglycan biosynthesis. (2008, methodology): “With the perdeuterated, 13C/15N-labelled MurB studied by NMR spectroscopy (Farmer et al., 1996; Constantine et al., 1997), it was deduced that NADP1 binds in the same pocket as UDP-GlcNAc-enolpyruvate, inducing structural changes,”