ChIP-seq identification of CarD (MSMEG_6077) binding sites in Mycobacterium smegmatis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 550
ORGANISM(S): Mycolicibacterium smegmatis MC2 155
SUBMITTER:
PROVIDER: E-MTAB-11828 | biostudies-arrayexpress |
SECONDARY ACCESSION(S): E-MTAB-7004
REPOSITORIES: biostudies-arrayexpress
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Project description:CarD is an essential transcription factor for Mycobacterium smegmatis. We identified a new interaction partner of CarD and named it CrsL (MSMEG_5890). To address the genome-wide effect of CrsL, we generated knockdown strains for both carD (MSMEG_6077) and crsL (MSMEG_5890) genes in Mycobacterium smegmatis. We aimed to compare the differentially expressed genes of crsL knockdown and correlate them with the ones of carD knockdown to describe the role of CrsL in transcription.
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Project description:Bacterial transcription is a tightly regulated process critical for gene expression, adaptation and cell survival. CarD is an essential transcription factor in mycobacteria involved in regulation of gene expression. Here, we searched for CarD interaction partners in the model organism Mycobacterium smegmatis and identified two candidate proteins: ApeB (MSMEG_5828) and an uncharacterized protein, which we named CrsL (MSMEG_5890). While ApeB interacted with CarD only when CarD was overexpressed, CrsL associated with CarD at its physiological levels. We therefore focused on CrsL. It is a small protein of 5.7 kDa that we show by NMR to be intrinsically disordered. Genes encoding CrsL homologs are present in Actinobacteria including pathogenic species such as Mycobacterium tuberculosis. We demonstrate that CrsL directly interacts with CarD and both proteins bind to RNAP. Moreover, we show by ChIP-seq that CrsL associates with promoter regions of actively transcribed genes and ~75 % of these regions are associated also with CarD. By RNA-seq experiments with crsL and carD knockdown strains, we reveal ~50 % and ~66 % overlap between differentially expressed genes in the two strains in exponential and stationary phase, respectively. CrsL represses the expression of DesA desaturase and RNA helicase MSMEG_1930 gene, which are important for adaptation to cold stress. Furthermore, CrsL promotes the growth of M. smegmatis at elevated temperature. In summary, this study identifies CrsL as a novel actinobacterial transcription factor and provides a basis for its further investigation.
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