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Title: Comparative genomics of the lactic acid bacteria

item Makarova, K
item Slesarev, A
item Wolf, Y
item Sorokin, A
item Mirkin, B
item Koonin, E
item Pavlov, A
item Pavlova, N
item Karamychev, V
item Polouchine, N
item Shakhova, V
item Grigoriev, I
item Lou, Y
item Rohksar, D
item Lucas, S
item Huang, K
item Goodstein, D
item Hawkins, T
item Plengvidhya, V
item Welker, D
item Hughes, J
item Goh, Y
item Benson, A
item Baldwin, K
item Lee, J
item Perez Diaz, Ilenys
item Dosti, B
item Smeianov, V
item Wechter, William - Pat
item Barabote, R
item Lorca, G
item Altermann, E
item Barrangou, R
item Ganesan, B
item Xie, Y
item Rawsthorne, H
item Tamir, D
item Parker, C
item Breidt, Frederick
item Broadbent, J
item Hutkins, R
item O'sullivan, D
item Steele, J
item Unlu, G
item Saier, M
item Klaenhammer, T
item Richardson, P
item Kozyavkin, S
item Weimer, B
item Mills, D

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2006
Publication Date: 10/17/2006
Citation: Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., Shakhova, V., Grigoriev, I., Lou, Y., Rohksar, D., Lucas, S., Huang, K., Goodstein, D.M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J.H., Perez Diaz, I.M., Dosti, B., Smeianov, V., Wechter, W.P., Barabote, R., Lorca, G., Altermann, E., Barrangou, R., Ganesan, B., Xie, Y., Rawsthorne, H., Tamir, D., Parker, C., Breidt, F., Broadbent, J., Hutkins, R., O'Sullivan, D., Steele, J., Unlu, G., Saier, M., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., Mills, D. 2006. Comparative genomics of the lactic acid bacteria. Proceedings of the National Academy of Sciences. 103(42):15611-15616.

Interpretive Summary: This manuscript contains a report of the complete sequencing of the chromosomal DNA from nine lactic bacteria. These bacteria are all important in industrial food fermentations. Currently only six complete lactic acid bacterial genome sequences are known, so this manuscript represents a significant leap forward in the understanding of genetics (genomics) of this important group of bacteria. A comparative analysis of the sequence results for the nine bacteria is presented. The results give important clues to how this group of bacteria evolved, as well as the potential for biochemical reactions encoded the DNA. The DNA sequences will be submitted to public databases with the publication of this manuscript, allowing researchers around the world to have access to this valuable resource. The results of studies based on these data will very likely lead to significant advances in our understanding food fermentations.

Technical Abstract: Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic pathways. Phylogenetic analyses, comparison of gene content across the group and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during co-evolution of lactic acid bacteria with their habitats.