PXD041877

PXD041877 is an original dataset announced via ProteomeXchange.

Title	Sigma E of Streptomyces coelicolor can function both as a direct activator or repressor of transcription
Description	Sigma factors are key components of the bacterial transcriptional apparatus that are essential for promoter recognition and transcription initiation. These factors are considered as positive regulators of gene expression. Here, we reveal the opposite, inhibitory role of these proteins. We used a combination of ChIP-seq, transcriptomic time series data, promoter sequence analysis, and computational modeling of gene expression to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. Kinetic modeling of gene expression then allowed to cluster respective genes into groups, based on the type of their control. Importantly, this analysis indicated that σE might act not only as an activator of gene expression but also as its repressor. The direct repressor function of σE was then demonstrated by experimental analysis of selected promoter regions in vivo, showing that σE binds to promoter-like sequences, forming roadblocks for transcription initiated upstream. Finally, the σE interactome was defined, allowing the identification of ApgA as its potential anti- factor. Taken together, the results characterize σE, its regulation, regulon, and reveal its direct inhibitory function in gene expression, a so far unknown phenomenon that may be common also to other  factors and organisms.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_10:42:22.656.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD041877
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Martin Hubalek
SpeciesList	scientific name: Streptomyces coelicolor; NCBI TaxID: 1902;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-28 09:04:38	ID requested
⏵ 1	2024-01-26 10:42:23	announced

10.6019/PXD041877;

10.1038/s42003-023-05716-y;

Posp, í, š, il J, Schwarz M, Zikov, á A, V, í, tovsk, á D, Hradilov, á M, Kol, á, ř M, K, ř, enkov, á A, Hub, á, lek M, Kr, á, sn, ý L, Vohradsk, ý J, of Streptomyces coelicolor can function both as a direct activator or repressor of transcription. Commun Biol, 7(1):46(2024) [pubmed]

submitter keyword: SigmaE, bacterial transcriptional apparatus

Martin Hubálek
contact affiliation	Institute of Organic Chemistry and Biochemistry
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. PXD041877
     1. Label: PRIDE project
     2. Name: Sigma E of Streptomyces coelicolor can function both as a direct activator or repressor of transcription