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RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Corynebacterium glutamicum

ABSTRACT: 6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In mycobacteria, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. Ms1 has been predicted in many actinobacterial species, except of corynebacteria. To identify RNAs that have a similar function as Ms1 or 6S RNA in Corynebacterium glutamicum, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A. We also sequenced total RNA isolated from the lysate (input sample). We expect that Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A samples compared to the inputs. The experiment was performed in exponential and stationary phase of growth.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Corynebacterium glutamicum ATCC 13032

SUBMITTER:

PROVIDER: E-MTAB-13608 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-12351

REPOSITORIES: biostudies-arrayexpress

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RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Corynebacterium glutamicum

Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In mycobacteria, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. Ms1 has been predicted in many actinobacterial species, except of corynebacteria. To identify RNAs that have a similar function as Ms1 or 6S RNA in Corynebacterium glutamicum, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A. We also sequenced total RNA isolated from the lysate (input sample). We expect that Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A samples compared to the inputs. The experiment was performed in exponential and stationary phase of growth.

2024-02-09 | E-MTAB-12351 | biostudies-arrayexpress

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2024-02-09 | E-MTAB-13584 | biostudies-arrayexpress

RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor HrdB in Streptomyces coelicolor

Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In mycobacteria, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. It is unclear if S. coelicolor has any 6S RNA or Ms1 RNA. To identify putative Ms1/6S RNA or any other similar RNAs in Streptomycetes, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor HrdB. We also sequenced total RNA isolated from the lysate (input sample). We expect that putative Ms1/6S-like RNAs are enriched in RNA polymerase or sigma A samples compared to the inputs. The experiment was performed 42 hrs and 66 hrs after germination.

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Proteins of anti-sigma70 and anti-RNAP immunoprecipitates in bacteria

Project description:As part of the project aimed at the interaction of RNA with RNA polymerase and primary sigma factor in bacteria we analyzed anti-σ70 antibody immunoprecipitates from Mycobacterium smegmatis stationary phase to identify proteins in σA complex in non-treated cells. We performed mass spectrometry analysis of anti-σ70 antibody and anti-RNAP immunoprecipitates from Corynebacterium glutamicum stationary phase to identify proteins present in σA and RNAP complexes.

2024-03-06 | PXD047705 | Pride

RNA-seq of wild type Mycobacterium smegmatis mc2 155 (exponential and stationary phase) and Ms1 deletion strain (exponential and stationary phase)

Project description:Ms1 RNA is ~300 nt sRNA that is highly expressed in stationary phase of growth and binds to the RNA polymerase (RNAP) core. We assume that by binding to RNAP, Ms1 could regulate transcription. Our aim was to reveal the most prominent changes in the transcriptome upon entry into stationary phase that might be dependent on Ms1. We performed RNA-seq data to characterize exponential (Ms_WT_exp) and stationary phase (Ms_WT_stat) transcriptome in M. smegmatis in wild type cells. In addition, we compared the transcriptome of the Ms1 knockout cells (Ms_KO_stat) with wild type cells in stationary phase and in exponential phase (Ms_KO_exp).

2018-11-12 | E-MTAB-7004 | biostudies-arrayexpress

MoaB2 binds to SigA in Mycobacterium smegmatis and modulates its activity and biological stability

Project description:In mycobacteria, SigA is the primary sigma factor. This essential protein binds to RNA polymerase (RNAP) and is responsible for initiating transcription of housekeeping genes. Our knowledge about this factor in medicinally important mycobacteria is limited. Here, we performed an unbiased search for interacting partners of Mycobacterium smegmatis SigA. The search revealed a number of proteins; prominent among them was MoaB2. The SigA-MoaB2 interaction was validated and characterized by several approaches, revealing that it does not require RNAP and is highly specific, as alternative sigma factors did not interact with MoaB2. The structure of MoaB2 was solved by crystallography and the unique, unstructured N-terminal domain of SigA was identified to play a role in the SigA-MoaB2 interaction. Functional experiments showed that MoaB2 inhibits SigA-dependent transcription and increases biological stability of SigA. We propose that MoaB2, by sequestering SigA, exerts a dual effect on the transcription apparatus, and has the potential to modulate gene expression. In summary, this study has uncovered a new binding partner of mycobacterial SigA, paving the way for future research of this phenomenon.

2024-11-11 | PXD039468 | Pride

Molecular insights into RNA polymerase recycling by mycobacterial HelD

Project description:Mycobacterial HelD is a transcription factor that binds RNA polymerase (RNAP) and thereby rescues it from stalled transcription complexes. HelD also protects RNAP against the antibiotic rifampicin. HelD, however, must be released from the rescued RNAP to participate in the next round of the transcription cycle. The exact mechanism of this release is unknown. Here we show that HelD from Mycobacterium smegmatis can form a complex with RNAP, together with σA primary sigma factor, and RbpA, but not CarD, transcription factors. Using cryo-EM, we solved a series of RNAP-σA-RbpA-HelD structures with or without promoter DNA. These snapshots capture the involvement of HelD in transcription initiation, describes mechanistic aspects of HelD release, and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding/hydrolysis to/by HelD in the process, and functionally confirms the rifampicin-protective effect of HelD. Taken together, HelD assists an alternative pathway of transcription initiation.

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