Dataset Information

Sigma E of Streptomyces coelicolor can function both as a direct activator or repressor of transcription

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Streptomyces Coelicolor

SUBMITTER: Martin Hubalek

LAB HEAD: Martin Hubálek

PROVIDER: PXD041877 | Pride | 2024-01-26

REPOSITORIES: Pride

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σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription.

Pospíšil Jiří J Schwarz Marek M Ziková Alice A Vítovská Dragana D Hradilová Miluše M Kolář Michal M Křenková Alena A Hubálek Martin M Krásný Libor L Vohradský Jiří J

Communications biology 20240106 1

σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. The direct activator/repressor function of σE was then explored by experimental analysis of selected promoter regions in vivo. Additionally, the σE interactom ...[more]

PMID: 38184746

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Project description:Desert locusts (Schistocerca gregaria) show an extreme form of phenotypic plasticity and can transform between a cryptic solitarious phase and a swarming gregarious phase. The two phases differ extensively in behavior, morphology and physiology but very little is known about the molecular basis of these differences. We used our recently generated Expressed Sequence Tag (EST) database derived from S. gregaria central nervous system (CNS) to design oligonucleotide microarrays and compare the expression of thousands of genes in the CNS of long-term gregarious and solitarious adult desert locusts. This identified 214 differentially expressed genes, of which 40% have been annotated to date. These include genes encoding proteins that are associated with CNS development and modeling, sensory perception, stress response and resistance, and fundamental cellular processes. Our microarray analysis has identified genes whose altered expression may enable locusts of either phase to deal with the different challenges they face. Genes for heat shock proteins and proteins which confer protection from infection were upregulated in gregarious locusts, which may allow them to respond to acute physiological challenges. By contrast the longer-lived solitarious locusts appear to be more strongly protected from the slowly accumulating effects of ageing by an upregulation of genes related to anti-oxidant systems, detoxification and anabolic renewal. Gregarious locusts also had a greater abundance of transcripts for proteins involved in sensory processing and in nervous system development and plasticity. Gregarious locusts live in a more complex sensory environment than solitarious locusts and may require a greater turnover of proteins involved in sensory transduction, and possibly greater neuronal plasticity. Two condition experiment: Solitarious central nervous system (CNS) vs gregarious CNS. 6 biological repeats per condition, balanced over 3 male and 3 females samples. The overall experimental design consisted of two identical repeats of an n+2 A-optimal design, organized per sex (n=6 per sex, 3 solitarious - 3 gregarious samples)

Dataset Information

Sigma E of Streptomyces coelicolor can function both as a direct activator or repressor of transcription

Publications

σ<sup>E</sup> of Streptomyces coelicolor can function both as a direct activator or repressor of transcription.

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