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

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2023 Feb 24

PMID 36823556

Authors

Tianshu Wang

Xiyun Zhao

Xinyuan Wu

Sanfeng Chen

Affiliations

Soon will be listed here.

Abstract

Background: Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N-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.

Results: In 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.

Conclusion: This study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.

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