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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Genome, Bacterial

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Disease relevance of Genome, Bacterial

  • The tetranucleotide CTAG is observed to be rare in virtually all bacterial genomes and some phage genomes [1].
  • tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter [2].
  • The availability of the complete sequences of a number of bacterial genomes prompted us to assess the evolutionarily conservation of bacterial RNase E. We show here that the sequence of the N-terminal endoribonucleolytic domain of RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria [3].
  • Screening the Pseudomonas aeruginosa genome has led to the identification of the highest number of putative genes encoding two-component regulatory systems of all bacterial genomes sequenced to date (64 and 63 encoding response regulators and histidine kinases, respectively) [4].
  • Inspection of bacterial genome sequences has revealed the presence of similar ABC transporters, as well as genes encoding peptides with double-glycine-type leader sequences in Gram-negative bacteria, and it is suggested that the postulated transported peptides could perform a signaling function [5].

High impact information on Genome, Bacterial

  • Of the 174 bacterial genomes (136 bacterial species) analyzed, 30 diverse species have no PTS homologues, and 29 species have cytoplasmic PTS phosphoryl transfer protein homologues but lack recognizable PTS permeases [6].
  • We browsed bacterial genomes to search proteins functionally equivalent to Cox17, and we identified a class of proteins of unknown function displaying a conserved gene neighborhood to bacterial Sco1 genes, all sharing a potential metal binding motif H(M)X10MX21HXM [7].
  • In prokaryotes, a major poly P synthetic enzyme is poly P kinase 1 (PPK1), which is found in 100 bacterial genomes, including numerous pathogens [8].
  • In contrast to other host-adapted bacteria, W. succinogenes does harbor the highest density of bacterial sensor kinases found in any bacterial genome to date, together with an elaborate signaling circuitry of the GGDEF family of proteins [9].
  • These observations are relevant to our view of the evolution of the bacterial genome and may be significant in the virulence of S. typhi [10].

Chemical compound and disease context of Genome, Bacterial


Biological context of Genome, Bacterial

  • Using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the BirA regulon in most available bacterial genomes [16].
  • Using comparative analysis of genes, operons, and regulatory elements, we describe the thiamin biosynthetic pathway in available bacterial genomes [17].
  • As revealed by phylogenetic analyses, orthologs of the T. tenax and P. furiosus enzyme appear to be present in almost all sequenced archaeal genomes, as well as in some bacterial genomes, strongly suggesting that this new enzyme family represents the typical archaeal FBP aldolase [18].
  • We show that the tetranucleotide CTAG is extremely rare in most bacterial genomes with G+C contents above 45% [19].
  • Group II self-splicing introns were shown to be present in bacteria in 1993, since when the various bacterial genome sequencing projects have led to a significant increase in the number of group II intron sequences present in databases [20].

Anatomical context of Genome, Bacterial


Associations of Genome, Bacterial with chemical compounds

  • The mutation rate of the bacterial genome of such strains after exposure to either UV light or ethyl methanesulfonate was measured by its rifampicin resistance or amino acid requirements [22].
  • This was accomplished by searching bacterial genomes for genes in close proximity to the methylmalonyl-CoA mutase gene that might encode a protein with the properties of an adenosyltransferase [23].
  • Finally, we propose a protein signature for proline racemases and suggest that the enzyme is present in several other pathogenic and non-pathogenic bacterial genomes of medical and agricultural interest, yet absent in mammalian host, suggesting that inhibition of proline racemases may have therapeutic potential [24].
  • First, we analyzed the composition asymmetry of 28 complete bacterial genomes and used it to test the possibility that asymmetric deamination of cytosine might be at the origin of the bias [25].
  • In addition, bacterial genome data were analyzed for the frequency of unmethylated cytosine-guanosine ([CG]) dinucleotides [26].

Gene context of Genome, Bacterial

  • A set of hns-lacZ protein and operon fusions was constructed in vitro and integrated in single copy into the attB site of the bacterial genome [27].
  • The presence of circular excision intermediates and the results of an analysis of sequenced bacterial genomes suggest that the region downstream of the guaA gene is a hotspot for site-specific integration of foreign DNA mediated by a CP4-like integrase [28].
  • The deletion covered a small fragment of the bacterial genome not extending in the ptsI and lig genes [29].
  • In this study, a typing strategy, based on the amplification of a conserved repeat-motif in the bacterial genome, was applied in a hospital setting to analyse an MRSA collection [30].
  • Computer analysis of bacterial genome databases identified the presence of orthologues of the acnA gene (encodes aconitase A) in a number of putative prp operons [31].


  1. Over- and under-representation of short oligonucleotides in DNA sequences. Burge, C., Campbell, A.M., Karlin, S. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  2. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Keiler, K.C., Shapiro, L., Williams, K.P. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  3. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Kaberdin, V.R., Miczak, A., Jakobsen, J.S., Lin-Chao, S., McDowall, K.J., von Gabain, A. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  4. Two-component systems in Pseudomonas aeruginosa: why so many? Rodrigue, A., Quentin, Y., Lazdunski, A., Méjean, V., Foglino, M. Trends Microbiol. (2000) [Pubmed]
  5. Processing and export of peptide pheromones and bacteriocins in Gram-negative bacteria. Michiels, J., Dirix, G., Vanderleyden, J., Xi, C. Trends Microbiol. (2001) [Pubmed]
  6. Comparative genomic analyses of the bacterial phosphotransferase system. Barabote, R.D., Saier, M.H. Microbiol. Mol. Biol. Rev. (2005) [Pubmed]
  7. A copper(I) protein possibly involved in the assembly of CuA center of bacterial cytochrome c oxidase. Banci, L., Bertini, I., Ciofi-Baffoni, S., Katsari, E., Katsaros, N., Kubicek, K., Mangani, S. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  8. Inorganic polyphosphate in the origin and survival of species. Brown, M.R., Kornberg, A. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  9. Complete genome sequence and analysis of Wolinella succinogenes. Baar, C., Eppinger, M., Raddatz, G., Simon, J., Lanz, C., Klimmek, O., Nandakumar, R., Gross, R., Rosinus, A., Keller, H., Jagtap, P., Linke, B., Meyer, F., Lederer, H., Schuster, S.C. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  10. Rearrangements in the genome of the bacterium Salmonella typhi. Liu, S.L., Sanderson, K.E. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  11. Transaldolase exhibits a protective role against menadione toxicity in Xanthomonas campestris pv. phaseoli. Vatanaviboon, P., Varaluksit, T., Seeanukun, C., Mongkolsuk, S. Biochem. Biophys. Res. Commun. (2002) [Pubmed]
  12. Novel PTS proteins revealed by bacterial genome sequencing: a unique fructose-specific phosphoryl transfer protein with two HPr-like domains in Haemophilus influenzae. Reizer, J., Reizer, A., Saier, M.H. Res. Microbiol. (1996) [Pubmed]
  13. The elusive roles of bacterial glutathione S-transferases: new lessons from genomes. Vuilleumier, S., Pagni, M. Appl. Microbiol. Biotechnol. (2002) [Pubmed]
  14. Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Albert, T.J., Dailidiene, D., Dailide, G., Norton, J.E., Kalia, A., Richmond, T.A., Molla, M., Singh, J., Green, R.D., Berg, D.E. Nat. Methods (2005) [Pubmed]
  15. Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily. Liger, D., Quevillon-Cheruel, S., Sorel, I., Bremang, M., Blondeau, K., Aboulfath, I., Janin, J., van Tilbeurgh, H., Leulliot, N. Proteins (2005) [Pubmed]
  16. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Rodionov, D.A., Mironov, A.A., Gelfand, M.S. Genome Res. (2002) [Pubmed]
  17. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., Gelfand, M.S. J. Biol. Chem. (2002) [Pubmed]
  18. Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. Siebers, B., Brinkmann, H., Dörr, C., Tjaden, B., Lilie, H., van der Oost, J., Verhees, C.H. J. Biol. Chem. (2001) [Pubmed]
  19. Restriction endonucleases for pulsed field mapping of bacterial genomes. McClelland, M., Jones, R., Patel, Y., Nelson, M. Nucleic Acids Res. (1987) [Pubmed]
  20. Group II introns in the bacterial world. Martínez-Abarca, F., Toro, N. Mol. Microbiol. (2000) [Pubmed]
  21. Response to bleomycin of Escherichia coli mutants deficient in DNA repair. Yamamoto, K., Hutchinson, F. J. Antibiot. (1979) [Pubmed]
  22. DNA polymerase III of Escherichia coli is required for UV and ethyl methanesulfonate mutagenesis. Hagensee, M.E., Timme, T.L., Bryan, S.K., Moses, R.E. Proc. Natl. Acad. Sci. U.S.A. (1987) [Pubmed]
  23. Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria. Dobson, C.M., Wai, T., Leclerc, D., Kadir, H., Narang, M., Lerner-Ellis, J.P., Hudson, T.J., Rosenblatt, D.S., Gravel, R.A. Hum. Mol. Genet. (2002) [Pubmed]
  24. Biochemical characterization of proline racemases from the human protozoan parasite Trypanosoma cruzi and definition of putative protein signatures. Chamond, N., Grégoire, C., Coatnoan, N., Rougeot, C., Freitas-Junior, L.H., da Silveira, J.F., Degrave, W.M., Minoprio, P. J. Biol. Chem. (2003) [Pubmed]
  25. Ongoing evolution of strand composition in bacterial genomes. Rocha, E.P., Danchin, A. Mol. Biol. Evol. (2001) [Pubmed]
  26. Activation of toll-like receptor 9 by DNA from different bacterial species. Dalpke, A., Frank, J., Peter, M., Heeg, K. Infect. Immun. (2006) [Pubmed]
  27. Synthesis of the Escherichia coli K-12 nucleoid-associated DNA-binding protein H-NS is subjected to growth-phase control and autoregulation. Dersch, P., Schmidt, K., Bremer, E. Mol. Microbiol. (1993) [Pubmed]
  28. The IncP island in the genome of Brucella suis 1330 was acquired by site-specific integration. Lavigne, J.P., Vergunst, A.C., Bourg, G., O'Callaghan, D. Infect. Immun. (2005) [Pubmed]
  29. Repression of inducible enzyme synthesis in a mutant of Escherichia coli K 12 deleted for the ptsH gene. Gershanovitch, V.N., Ilyina, T.S., Rusina, O.Y., Yourovitskaya, N.V., Bolshakova, T.N. Mol. Gen. Genet. (1977) [Pubmed]
  30. Motif-dependent DNA analysis of a methicillin-resistant Staphylococcus aureus collection. Cotter, L., Daly, M., Greer, P., Cryan, B., Fanning, S. Br. J. Biomed. Sci. (1998) [Pubmed]
  31. In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase Enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Horswill, A.R., Escalante-Semerena, J.C. Biochemistry (2001) [Pubmed]
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