Abstract
The presence of bona fide outer membranes in members of the class Negativicutes is anomalous as phylogenetic analyses place this class within the phylum Firmicutes. To explore the relationships of a representative member of Negativicutes, we have performed a whole proteome BLAST analysis of Acidaminococcus intestini, which indicates that a substantial proportion (7 %) of the A. intestini proteome is closely related to sequences from members of the phylum Proteobacteria. In addition, we have identified key proteins involved in outer membrane biogenesis in A. intestini. This work highlights the need for further studies to define the relationships and evolutionary history of the Negativicutes.
References
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
D’Auria G, Galan J-C, Rodriguez-Alcayna M, Moya A, Baquero F, Latorre A (2011) Complete genome sequence of Acidaminococcus intestini RYC-MR95, a Gram-negative bacterium from the phylum Firmicutes. J Bacteriol 193:7008–7009
Gupta RS (2011) Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Anton Van Leeuwenhoek 100:171–182
Koski LB, Golding GB (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52:540–542
Marchandin H, Teyssier C, Campos J, Jean-Pierre H, Roger F, Gay B, Carlier J-P, Jumas-Bilak E (2010) Negativicoccus succinicivorans gen. nov., sp nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov and Acidaminococcaceae fam. nov in the bacterial phylum Firmicutes. Int J Syst Evol Microbiol 60:1271–1279
Mavromatis K, Ivanova N, Anderson I, Lykidis A, Hooper SD, Sun H, Kunin V, Lapidus A, Hugenholtz P, Patel B, Kyrpides NC (2009) Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS ONE 4:e4192
Metzget LE IV, Raetz CRH (2010) An alternative route for UDP-diacylglucosamine hydrolysis in bacterial lipid A synthesis. Biochemistry 49:6715–6726
Ogawa Y, Ooka T, Shi F, Ogura Y, Nakayama K, Hayashi T, Shimoji Y (2011) The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of Firmicutes and the organism’s intracellular adaptations. J Bacteriol 193:2959–2971
Opiyo SO, Pardy RL, Moriyama H, Moriyama EN (2010) Evolution of the Kdo2-lipid A biosynthesis in bacteria. BMC Evol Biol 10:362
Segata N, Boernigen D, Morgan XC, Huttenhower C (2013) PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304. doi:10.1038/ncomms3304
Sutcliffe IC (2010) A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18:464–470
Sutcliffe IC, Harrington DJ, Hutchings MI (2012) A phylum level analysis reveals lipoprotein biosynthesis to be a fundamental property of bacteria. Protein Cell 3:163–170
Tocheva E, Matson EG, Morris DM, Moussavi F, Leadbetter JR, Jensen GJ (2011) Peptidoglycan remodeling and conversion of an inner membrane into an outer membrane during sporulation. Cell 146:799–812
Webb CT, Heinz E, Lithgow T (2013) Evolution of the β-barrel assembly machinery. Trends Microbiol 20:612–620
Yutin N, Galperin MY (2013) A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia. Environ Microbiol 15:2631–2641
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The work from McMaster University was supported by a research grant from the Natural Sciences and Engineering Research Council of Canada.
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Communicated by Erko Stackebrandt.
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Campbell, C., Sutcliffe, I.C. & Gupta, R.S. Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria . Arch Microbiol 196, 307–310 (2014). https://doi.org/10.1007/s00203-014-0964-4
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DOI: https://doi.org/10.1007/s00203-014-0964-4