RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription

Sukhodolets, Maxim V.; Cabrera, Julio E.; Zhi, Huijun; Jin, Ding Jun

doi:10.1101/gad.936701

Cited by 76 publications

(133 citation statements)

References 45 publications

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“…The ATPase motor has been shown to engage with nucleosomal DNA approximately two helical turns from the nucleosome dyad (superhelical location 2), and ATP hydrolysis is essential for driving the nucleosome sliding reaction (8 -10). Interestingly, the SWI2/SNF2-type ATPase motor is also found in proteins that do not slide nucleosomes but disrupt other protein-DNA complexes, such as bacterial RapA and eukaryotic Rad54 (11,12). The conservation of the SWI2/SNF2-type ATPase motor outside the chromatin remodeler subfamilies suggests that remodelers possess additional elements that direct action of the ATPase motor to nucleosomes.…”

mentioning

confidence: 99%

Identification of Residues in Chromodomain Helicase DNA-Binding Protein 1 (Chd1) Required for Coupling ATP Hydrolysis to Nucleosome Sliding

Patel

McKnight

Genzor

et al. 2011

Journal of Biological Chemistry

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Background: Chromatin remodelers slide nucleosomes in an ATP-dependent manner. Results: Residues between the ATPase motor and DNA-binding domain of chromodomain helicase DNA-binding protein 1 (Chd1) are required for sliding but not nucleosome-stimulated ATP hydrolysis. Conclusion: Residues outside the conserved ATPase core are required for efficiently utilizing the energy of ATP hydrolysis for sliding. Significance: Understanding the role of ATPase-coupling residues will be critical for revealing nucleosome sliding mechanisms.

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mentioning

confidence: 99%

Identification of Residues in Chromodomain Helicase DNA-Binding Protein 1 (Chd1) Required for Coupling ATP Hydrolysis to Nucleosome Sliding

Patel

McKnight

Genzor

et al. 2011

Journal of Biological Chemistry

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“…At near equimolar Escherichia coli RNA polymerase/template DNA ratioseven with relatively strong E. coli promoters such as tac and rrnBP1-in vitro transcription reactions typically produce an average of one to two catalytic turnovers under most experimental conditions (for example, see Sukhodolets et al 2001). Inhibitory RNA polymerase-transcript interactions present a potential obstacle for continuous transcriptional cycling, with each individual cycle including transcript initiation, elongation, and termination.…”

Section: Introductionmentioning

confidence: 99%

Ribosomal protein S1 promotes transcriptional cycling

Sukhodolets

Garges²,

Adhya³

2006

RNA

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Prokaryotic RNA polymerases are capable of efficient, continuous synthesis of RNA in vivo, yet purified polymerase-DNA model systems for RNA synthesis typically produce only a limited number of catalytic turnovers. Here, we report that the ribosomal protein S1-which plays critical roles in translation initiation and elongation in Escherichia coli and is believed to stabilize mRNA on the ribosome-is a potent activator of transcriptional cycling in vitro. Deletion of the two C-terminal RNA-binding modules-out of a total of six loosely homologous RNA-binding modules present in S1-resulted in a near-loss of the ability of S1 to enhance transcription, whereas disruption of the very last C-terminal RNA-binding module had only a mild effect. We propose that, in vivo, cooperative interaction of multiple RNA-binding modules in S1 may enhance the transcript release from RNA polymerase, alleviating its inhibitory effect and enabling the core enzyme for continuous reinitiation of transcription.

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“…DksA acts at the transcription initiation stage by potentiating both the inhibitory effect of the 'alarmone' ppGpp at rRNA promoters and its positive effect at amino acid biosynthetic promoters (Paul et al ., 2004;Perederina et al ., 2004). Other RNAP-binding factors in E. coli include RapA, an ATPase that stimulates transcription, particularly on supercoiled templates in the presence of high concentrations of salt (Sukhodolets et al ., 2001), and 6S RNA, which accumulates in stationary phase and associates with RNAP containing the vegetative σ factor, σ 70 (Wassarman and Storz, 2000). Unrelated RNAP binding proteins have also been described in other bacteria.…”

Section: Introductionmentioning

confidence: 99%

The RNA polymerase‐binding protein RbpA confers basal levels of rifampicin resistance on Streptomyces coelicolor

Newell

Thomas

Brekasis

et al. 2006

Molecular Microbiology

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SummaryRbpA is an RNA polymerase-binding protein that occurs in the actinomycete family of bacteria and is regulated by the disulphide stress-response sigma factor, σ σ σ σ R , in Streptomyces coelicolor . Here we demonstrate that rbpA null mutants exhibit a slow-growth phenotype and are particularly sensitive to the transcription inhibitor rifampicin. Strikingly, transcription mapping experiments revealed that rbpA expression is induced upon exposure of S. coelicolor to rifampicin and that this, in part, involves an increase in the activity of σ σ σ σ R . In contrast, the ribosomal RNA operon promoter rrnDp3 , which is recognized by the vegetative sigma factor σ σ σ σ HrdB , was strongly inhibited by rifampicin. Reconstitution of RNAP from an rbpA null mutant with purified RbpA revealed that RbpA stimulates transcription from rrnDp3 , even in the presence of rifampicin. The data presented suggest that RbpA confers basal levels of rifampicin resistance and is a novel regulator of rRNA synthesis in S. coelicolor .

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RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription

Cited by 76 publications

References 45 publications

Identification of Residues in Chromodomain Helicase DNA-Binding Protein 1 (Chd1) Required for Coupling ATP Hydrolysis to Nucleosome Sliding

Identification of Residues in Chromodomain Helicase DNA-Binding Protein 1 (Chd1) Required for Coupling ATP Hydrolysis to Nucleosome Sliding

Ribosomal protein S1 promotes transcriptional cycling

The RNA polymerase‐binding protein RbpA confers basal levels of rifampicin resistance on Streptomyces coelicolor

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