School of Life Science and Technology, Tokyo Institute of Technology, 4259-J3-8, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
Research and Development Center, Asahi Group Holdings Ltd., 11-10, 5-chome, Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, 252-0206, Japan.
BMC Microbiol. 2017 Dec 2;17(1):224. doi: 10.1186/s12866-017-1125-0.
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. However, the distributions and regulatory potential of the BCARR in all genes repressed by BCAAs in CM4 remains unclear.
A 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.
Our 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.
在瑞士乳杆菌的蛋白水解基因表达中发现的 BCARR（支链氨基酸响应抑制剂）被认为在存在 BCAAs 的情况下通过结合启动子区域的操纵子位点来负调控转录。然而，BCARR 在 CM4 中所有被 BCAAs 抑制的基因中的分布和调控潜力尚不清楚。
进行了全基因组搜索以阐明 BCARR 盒在瑞士乳杆菌 CM4 中氨基酸代谢调控中的作用。在 CM4 的所有 2174 个基因中，选择了 390 个受氨基酸抑制的基因来搜索 BCARR 盒。在 67 个预测的 BCARR 盒中，有 33 个被注释的基因主要与氨基酸代谢有关。BCARR 盒主要位于启动子的-35 序列附近；然而，不同位置的抑制效果相似。值得注意的是，在高度抑制的基因中观察到的保守的 BCARR 盒基序，5'-A1A2A3A4A5W6N7N8N9W10T11T12W13T14T15-3'，显示出更频繁的 A-T 碱基配对和更低的自由能，比在低抑制基因中观察到的基序更低。MEME 分析也支持在低抑制基因组的 BCARR 盒序列中位置 12、14、13 和 15 处 T 出现的频率较低。这些结果表明，具有更稳定的回文结构的基因可能是 BCARR 结合的更优选靶标，并导致靶基因表达的更高抑制。
我们的全基因组搜索揭示了蛋白酶系统、转运系统和一些转录调节系统参与了瑞士乳杆菌 CM4 中 BCARR 盒的调节。
