Evolutionary genomics of lactic acid bacteria - PubMed (original) (raw)

Review

. 2007 Feb;189(4):1199-208.

doi: 10.1128/JB.01351-06. Epub 2006 Nov 3.

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Review

Evolutionary genomics of lactic acid bacteria

Kira S Makarova et al. J Bacteriol. 2007 Feb.

No abstract available

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Figures

FIG. 1.

FIG. 1.

Projection of LaCOGs onto COGs, showing the finer granularity of ortholog identification among Lactobacillales.

FIG. 2.

FIG. 2.

Phylogenetic analysis of the MurE family of UDP-_N_-acetylmuramyl tripeptide synthases. The maximum-likelihood unrooted tree was built using the MOLPHY program (1). Each terminal node is labeled with the numeric GenBank identifier number (where available) and the respective species name. The Lactobacillales species are shown in blue (temporary numeric identifiers were assigned for new genomes). The circles at some of the nodes in the relevant subtree indicate bootstrap support >70% (not shown for the rest of the tree).

FIG. 3.

FIG. 3.

Coverage of Lactobacillales by LaCOGs and COGs. (A) Species that were used for LaCOG construction. (B) Species that were not included in the original LaCOGs.

FIG. 4.

FIG. 4.

Two putative genomic markers of Lactobacillales. (A) Domain composition of proteins from LaCOG01826. (B) Genome context of genes from LaCOG01826. aa, amino acids.

FIG. 5.

FIG. 5.

A phylogenetic tree of Lactobacillales constructed on the basis of concatenated alignments of four subunits (α, β, β′, and δ) of the DNA-dependent RNA polymerase. The maximum-likelihood unrooted tree was built using the MOLPHY program (1). All branches are supported with >75% bootstrap values. The species are colored according to the current taxonomy: Lactobacillaceae, blue; Leuconostocaceae, magenta; Streptococcaceae, red.

FIG. 6.

FIG. 6.

Reconstruction of gene content evolution in Lactobacillales. The tree is a subset of that shown in Fig. 5, rooted by using Bacillus subtilis as the outgroup. For each species and each internal node of the tree, the inferred number of LaCOGs present and the numbers of LaCOGs lost (blue) and gained (red) along the branch leading to the given node (species) are indicated. Modified from reference 28 with permission of the publisher.

FIG. 7.

FIG. 7.

Gene clusters in Lactobacillales encoding known and predicted bacteriocins and bacteriocin export systems. Modified from reference 28 with permission of the publisher.

References

    1. Adachi, J., and M. Hasegawa. 1992. MOLPHY: programs for molecular phylogenetics. Computer Science Monographs 27. Institute of Statistical Mathematics, Tokyo, Japan.
    1. Altermann, E., W. M. Russell, M. A. Azcarate-Peril, R. Barrangou, B. L. Buck, O. McAuliffe, N. Souther, A. Dobson, T. Duong, M. Callanan, S. Lick, A. Hamrick, R. Cano, and T. R. Klaenhammer. 2005. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc. Natl. Acad. Sci. USA 102:3906-3912. - PMC - PubMed
    1. Barynin, V. V., M. M. Whittaker, S. V. Antonyuk, V. S. Lamzin, P. M. Harrison, P. J. Artymiuk, and J. W. Whittaker. 2001. Crystal structure of manganese catalase from Lactobacillus plantarum. Structure 9:725-738. - PubMed
    1. Blewett, A. M., A. J. Lloyd, A. Echalier, V. Fulop, C. G. Dowson, T. D. Bugg, and D. I. Roper. 2004. Expression, purification, crystallization and preliminary characterization of uridine 5′-diphospho-N-acetylmuramoyl l-alanyl-d-glutamate:lysine ligase (MurE) from Streptococcus pneumoniae 110K/70. Acta Crystallogr. D 60:359-361. - PubMed
    1. Bolotin, A., B. Quinquis, P. Renault, A. Sorokin, S. D. Ehrlich, S. Kulakauskas, A. Lapidus, E. Goltsman, M. Mazur, G. D. Pusch, M. Fonstein, R. Overbeek, N. Kyprides, B. Purnelle, D. Prozzi, K. Ngui, D. Masuy, F. Hancy, S. Burteau, M. Boutry, J. Delcour, A. Goffeau, and P. Hols. 2004. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat. Biotechnol. 22:1554-1558. - PMC - PubMed

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