Abstract
BackgroundLactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing Firmicutes. They have been extensively used in food fermentations, including the production of various dairy products. The proteolytic system of LAB converts proteins to peptides and then to amino acids, which is essential for bacterial growth and also contributes significantly to flavor compounds as end-products. Recent developments in high-throughput genome sequencing and comparative genomics hybridization arrays provide us with opportunities to explore the diversity of the proteolytic system in various LAB strains.ResultsWe performed a genome-wide comparative genomics analysis of proteolytic system components, including cell-wall bound proteinase, peptide transporters and peptidases, in 22 sequenced LAB strains. The peptidase families PepP/PepQ/PepM, PepD and PepI/PepR/PepL are described as examples of our in silico approach to refine the distinction of subfamilies with different enzymatic activities. Comparison of protein 3D structures of proline peptidases PepI/PepR/PepL and esterase A allowed identification of a conserved core structure, which was then used to improve phylogenetic analysis and functional annotation within this protein superfamily.The diversity of proteolytic system components in 39 Lactococcus lactis strains was explored using pangenome comparative genome hybridization analysis. Variations were observed in the proteinase PrtP and its maturation protein PrtM, in one of the Opp transport systems and in several peptidases between strains from different Lactococcus subspecies or from different origin.ConclusionsThe improved functional annotation of the proteolytic system components provides an excellent framework for future experimental validations of predicted enzymatic activities. The genome sequence data can be coupled to other "omics" data e.g. transcriptomics and metabolomics for prediction of proteolytic and flavor-forming potential of LAB strains. Such an integrated approach can be used to tune the strain selection process in food fermentations.
Highlights
Lactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing Firmicutes
Over ten additional LAB genomes have become publicly available. These include 8 LAB strains from the Joint Genome Institute and the LAB Genome Consortium [10], the model laboratory strain Lactococcus lactis subsp. cremoris MG1363 [11], a Lactobacillus helveticus strain [12] which is known for its proteolytic capacity as an adjunct culture in cheese, and the probiotic strain Lactobacillus rhamnosus GG [13]
The LAB genomes in the L. acidophilus group [4], including L. acidophilus, L. johnsonii, L. gasseri, L. bulgaricus, and L. helveticus strains, encode a relatively higher number and variety of proteolytic system components
Summary
Lactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing Firmicutes. They have been extensively used in food fermentations, including the production of various dairy products. Recent developments in high-throughput genome sequencing and comparative genomics hybridization arrays provide us with opportunities to explore the diversity of the proteolytic system in various LAB strains. The breakdown of milk proteins (proteolysis) by LAB plays an important role in generating peptides and amino acids for bacterial growth and in the formation of metabolites that contribute to flavor formation of fermented products. We described a comparative analysis of cell-wall-bound proteinase and various peptidases from 13 fully or incompletely sequenced LAB which were publicly available in May 2006 [9]. A recent comparative genome hybridization (CGH) analysis of 39 L. lactis strains [14] provides opportunities to explore the diversity of the proteolytic system within the same species
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