Comparative Genomics of Enzymes in Flavor-Forming Pathways from Amino Acids in Lactic Acid Bacteria

Abstract

Lactic acid bacteria (LAB) have been widely used as starter or nonstarter cultures in the dairy industry for over a thousand years. They play an essential role in flavor formation during the fermentation of dairy products. Several metabolic routes can lead to the formation of flavor compounds when LAB are growing in milk. One of the main precursors for flavor com- pounds in milk is casein, although they can also be derived from fatty acids and sugars. The proteolytic system of LAB degrades casein into its constituent amino acids, which can be converted to flavor compounds. Although amino acid catabo- lism by LAB has been well researched (5, 31, 65, 78), many flavor-forming routes are yet to be discovered. Over 20 LAB genomes have been fully sequenced (1, 11, 12, 16, 19, 41, 44, 45, 53, 68, 71). The available genomic informa- tion provides us with new opportunities to study the flavor- forming potential of LAB. However, one of the main problems that one encounters while reconstructing flavor-forming routes based on the genomic information stored in the public data- bases is the inconsistency in the functional annotation for many of the relevant genes. These genes are mostly members of larger protein families. Moreover, even when the functional annotation in databases is appropriate, it sometimes reflects only part of the protein's full functional potential, since broad substrate specificities are often not taken into consideration in the annotation. We have now improved the functional annotation of the key enzymes in the formation of flavor compounds from amino acids by applying comparative genomics approaches that have been developed within our group to specify the annotation of homologous proteins, by combining phylogeny, gene context, and experimental evidence (32). We focused especially on the enzymes involved in the metabolism of sulfur-containing amino acids since these are known to be precursors of many flavor compounds in dairy fermentations. Comparative analy- sis of the various sequenced LAB species and strains resulted in an overall view of differences in their flavor-forming capac- ities. IN SILICO ANALYSES OF LAB GENOMES