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

Naoyuki Yamamoto,Taketo Wakai

doi:10.1186/s12866-017-1125-0

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.

Highlights

A branched chain amino acid responsive repressor (BCARR) 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 branched chain amino acids (BCAAs)
The production of the antihypertensive peptides by L. helveticus CM4 was repressed by amino acids that accumulated in fermented milk because of the down-regulation of genes, such as pepO2, pepCE and pepE, that most likely encode enzymes involved in the processing of active peptides [7, 9]
We investigated the impact of the BCARR system on amino acid metabolism, which plays a crucial role in cell growth in milk and other metabolism throughout the selection of the downregulated genes by amino acids

Summary

Introduction

A 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. the distributions and regulatory potential of the BCARR in all genes repressed by BCAAs in CM4 remains unclear. The CBS domain protein binds to a specific DNA sequence present at the promoter regions of the repressed proteolytic genes in response to intracellular BCAAs [10]. From a comparative sequence analysis of the promoter regions of the proteolytic genes, a gel shift assay and a footprinting analysis, a palindromic AT-rich motif, 5′-AAAAANNCTWTTATT-3′, was predicted as the consensus DNA motif for the branched chain amino acid responsive repressor (BCARR) protein binding box (BCARR-box). No CodY and no regulatory system of the proteolytic enzyme have been reported

Methods

Results

Conclusion