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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
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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
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Journal Article
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
2023
Overview
Background
Paenibacillus polymyxa
WLY78 is a Gram-positive, endospore-forming and N
2
-fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the
nif
(
ni
trogen
f
ixation) 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.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Analysis
/ Animal Genetics and Genomics
/ Bacteria
/ Bacterial Proteins - genetics
/ Bacterial Proteins - metabolism
/ Binding sites (Biochemistry)
/ Biomedical and Life Sciences
/ Carbon
/ Fixation
/ Gene Expression Regulation, Bacterial
/ Genes
/ Genomes
/ Genomics
/ GlnR
/ Methods
/ Microbial Genetics and Genomics
/ Nitrogen
/ Nitrogen-fixing microorganisms
/ Operons
/ Paenibacillus polymyxa - genetics
