Genome-wide mapping of GlnR-binding sites reveals the global regulatory role of GlnR in controlling the metabolism of nitrogen and carbon in Paenibacillus polymyxa WLY78

BMC Genomics

Research

Xiyun Zhao¹  Xinyuan Wu¹  Sanfeng Chen¹  Tianshu Wang² 

[1]State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, People’s Republic of China

[2]State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Key Laboratory of Soil Microbiology of Agriculture Ministry, China Agricultural University, Beijing, People’s Republic of China

[3]Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China

关键词: Paenibacillus polymyxa;    GlnR;    GlnR-binding site;    Transcriptional regulator;    Nitrogen fixation;   

DOI  :  10.1186/s12864-023-09147-1

 received in 2022-10-27, accepted in 2023-01-23,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundPaenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N2-fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) according to nitrogen availability, which is achieved by binding to the two GlnR-binding sites located in the nif promoter region. However, further study on the GlnR-mediated global regulation in this bacterium is still needed.ResultsIn this study, global identification of the genes directly under GlnR control is determined by using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assays (EMSA). Our results reveal that GlnR directly regulates the transcription of 17 genes/operons, including a nif operon, 14 nitrogen metabolism genes/operons (glnRA, amtBglnK, glnA1, glnK1, glnQHMP, nasA, nasD1, nasD2EF, gcvH, ansZ, pucR, oppABC, appABCDF and dppABC) and 2 carbon metabolism genes (ldh3 and maeA1). Except for the glnRA and nif operon, the other 15 genes/operons are newly identified targets of GlnR. Furthermore, genome-wide transcription analyses reveal that GlnR not only directly regulates the expression of these 17 genes/operons, but also indirectly controls the expression of some other genes/operons involved in nitrogen fixation and the metabolisms of nitrogen and carbon.ConclusionThis study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.

【 授权许可】

CC BY   
© The Author(s) 2023

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