Genome-wide motif predictions of BCARR-box in the amino-acid repressed genes of Lactobacillus helveticus CM4

Abstract

BackgroundA BCARR (branched-chain amino acid responsive repressor) identified in proteolytic gene expressions in Lactobacillus helveticus is considered to negatively control transcriptions by binding to operator sites at the promoter regions in the presence of BCAAs. However, the distributions and regulatory potential of the BCARR in all genes repressed by BCAAs in CM4 remains unclear.ResultsA genome-wide search for the BCARR-box was conducted to clarify the contribution of BCARR in the regulation of amino acid metabolism in L. helveticus CM4. Among all 2174 genes of CM4, 390 genes repressed by amino acids were selected for the search of the BCARR-box. The annotated 33 genes among the 67 predicted BCARR-boxes were mainly linked to amino acid metabolism. The BCARR-boxes were mainly located adjacent to the −35 sequence of the promoter; however, the repressive effects in different locations were similar. Notably, the consensus BCARR-box motif, 5′-A1A2A3A4A5W6N7N8N9W10T11T12W13T14T15–3′, observed in highly repressed genes, revealed more frequent A-T base pairing and a lower free energy than that in lowly repressed genes. A MEME analysis also supported the lower frequency of T at positions 12, 14, 13 and 15 in the BCARR-box sequence of the lowly repressed gene group. These results reveal that genes with a more stable palindromic structure might be preferable targets for BCARR binding and result in higher repressions in the target gene expressions.ConclusionsOur genome-wide search revealed the involvement of the proteolytic system, transporter system and some transcriptional regulator systems in BCARR-box regulation in L. helveticus CM4.Electronic supplementary materialThe online version of this article (10.1186/s12866-017-1125-0) contains supplementary material, which is available to authorized users.

Characteristics of the Proteolytic Enzymes Produced by Lactic Acid Bacteria

“…lactis cells, and the inhibitory potency is modulated in an intracellular environment rich in amino acids such as isoleucine, leucine, and valine [ 89 , 90 ]. While regulating the proteolytic system, the CodY repressor acts as a blocking agent that binds to the CodY operator sequence (AATTTTCWGAAAATT) and prevents RNA polymerase from accessing the promoter sites of individual components of the proteolytic system [ 4 , 91 , 92 , 93 ]. To sum up, when the intracellular concentration of the amino acids isoleucine, leucine, and valine increases, several of these amino acids attach to the allosteric site of the CodY repressor by changing the conformation of this protein in a such way that it allows it to bind to the operator in the DNA; consequently, this combination blocks the transcription of genes responsible for enzyme synthesis.…”