PXD058166-1

PXD058166 is an original dataset announced via ProteomeXchange.

Title	Expanding the CarD interaction network: CrsL is a novel transcription factor in Mycobacterium smegmatis
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.
HostingRepository	PRIDE
AnnounceDate	2025-12-22
AnnouncementXML	Submission_2025-12-21_16:15:11.014.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martin Hubalek
SpeciesList	scientific name: Mycobacterium smegmatis; NCBI TaxID: NEWT:1772;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-22 02:56:18	ID requested
⏵ 1	2025-12-21 16:15:12	announced

10.1093/nar/gkaf1342;

Shoman M, Č, ern, ý M, Jir, á, t Mat, ě, j, č, kov, á J, Schwarz M, Borah N, Va, ň, kov, á, Hausnerov, á V, Neva S, Š, ikov, á M, Š, anderov, á H, Halada P, Hub, á, lek M, Dvo, ř, á, kov, á V, P, ř, evorovsk, ý M, Holubov, á J, Stan, ě, k O, Kr, á, sn, ý L, Ž, í, dek L, Hnilicov, á J, Expanding the CarD interaction network: CrsL is a novel transcription regulator in actinobacteria. Nucleic Acids Res, 53(22):(2025) [pubmed]

submitter keyword: MSMEG_5890, RNAP, actinobacterial transcription factors,Mycobacterium smegmatis, CarD interaction partners, CrsL, ApeB, MSMEG_5828

Martin Hubálek
contact affiliation	Institute of Organic Chemistry and Biochemistry CAS
contact email	hubalek@uochb.cas.cz
lab head
Martin Hubalek
contact affiliation	Institute of Organic Chemistry and Biochemistry, Czech Academy of Science
contact email	hubalek@uochb.cas.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD058166
     1. Label: PRIDE project
     2. Name: Expanding the CarD interaction network: CrsL is a novel transcription factor in Mycobacterium smegmatis