Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux
Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux
复制标题
OdcR通过启动子中的单核苷酸突变精确调控各种分解代谢基因的差异转录确保代谢流的安全
DOI：
10.1128/aem.01182-22
复制
发表时间：
2022-08-29
影响因子：
4.4
通讯作者：
Jiang, Jiandong
中科院分区：
文献类型：
--
作者：
Chen, Kai;Ke, Zhuang;Jiang, Jiandong
分解代谢途径中各种基因表达的协同调控对于微生物在污染环境中的降解、生存和适应至关重要。然而，单个调控因子如何精确调控各种分解代谢基因的差异转录以确保代谢安全在很大程度上仍然未知。在此，由调控基因odcR编码的LysR型转录调控因子（LTTR）OdcR被证实对3,5 - 二溴 - 4 - 羟基苯甲酸酯（DBHB）的分解代谢至关重要，同时激活了一个功能未知的基因orf419以及参与Pigmentiphaga sp.菌株H8中DBHB分解代谢的三个基因odcA、odcB和odcC的转录。OdcB进一步代谢由OdcA从DBHB产生的剧毒中间体2,6 - 二溴对苯二酚。响应DBHB时，odcB的上调转录水平比orf419、odcA或odcC高7到9倍。通过电泳迁移率变动分析和DNase I足迹分析，发现DBHB是效应物，并且对于OdcR结合orf419、odcA、odcB和odcC的所有四个启动子是必需的。与odcA/ orf419（CAT - N - 11 - ATG）和odcC（CAT - N - 11 - ATT）的启动子相比，在odcB启动子的调控结合位点（RBS）（TAT - N - 11 - ATG）中鉴定出一个单核苷酸突变，并且表明该突变使odcB的转录显著提高。OdcR通过启动子中的单核苷酸突变对这些基因的精确调控避免了2,6 - 二溴对苯二酚的积累，确保了DBHB的代谢安全。
重要性：原核生物使用各种机制，包括提高解毒酶的活性，来应对分解代谢过程中产生的有毒中间体。然而，关于细菌如何通过单个调控因子精确调控各种分解代谢基因的差异转录以确保代谢安全的研究很少。这项研究揭示了一种LysR型转录激活因子OdcR，它强烈激活odcB的转录以对有毒中间体2,6 - 二溴对苯二酚进行解毒，并轻微激活其他基因（orf419、odcA和odcC）用于Pigmentiphaga sp.菌株H8中3,5 - 二溴 - 4 - 羟基苯甲酸酯（DBHB）的分解代谢。有趣的是，确保细胞中DBHB代谢安全的这四个基因的差异转录/表达是由四个启动子的调控结合位点中的单核苷酸突变决定的。这项研究描述了一种确保细菌代谢安全的新颖而巧妙的调控模式，扩展了我们对原核生物协同转录调控的理解。原核生物使用各种机制，包括提高解毒酶的活性，来应对分解代谢过程中产生的有毒中间体。然而，关于细菌如何通过单个调控因子精确调控各种分解代谢基因的差异转录以确保代谢安全的研究很少。
Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N-11-ATG), compared to those of odcA/orf419 (CAT-N-11-ATG) and odcC (CAT-N-11-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce.