Journal Article

Probing the structure of Nun transcription arrest factor bound to RNA polymerase

Vitiello, Christal L., Gottesman, Max E., Mustaev, Arkady

2016

Overview

The coliphage HK022 protein Nun transcription elongation arrest factor inhibits RNA polymerase translocation. In vivo, Nun acts specifically to block transcription of the coliphage λ chromosome. Using in vitro assays, we demonstrate that Nun cross-links RNA in an RNA:DNA hybrid within a ternary elongation complex (TEC). Both the 5′ and the 3′ ends of the RNA cross-link Nun, implying that Nun contacts RNA polymerase both at the upstream edge of the RNA:DNA hybrid and in the vicinity of the catalytic center. This finding suggests that Nun may inhibit translocation by more than one mechanism. Transcription elongation factor GreA efficiently blocked Nun cross-linking to the 3′ end of the transcript, whereas the highly homologous GreB factor did not. Surprisingly, both factors strongly suppressed Nun cross-linking to the 5′ end of the RNA, suggesting that GreA and GreB can enter the RNA exit channel as well as the secondary channel, where they are known to bind. These findings extend the known action mechanism for these ubiquitous cellular factors.

• Publisher: National Academy of Sciences
• Subject: Amino Acid Sequence / Bacteriophage HK022 - genetics / Bacteriophage HK022 - metabolism / Bioassays / Biocatalysts / Biochemistry / Biological Sciences / Chromosomes / Deoxyribonucleic acid / DNA / DNA-Directed RNA Polymerases - chemistry / DNA-Directed RNA Polymerases - metabolism / Gene Expression Regulation, Viral / Gram-negative bacteria / Models, Molecular / Nucleic Acid Conformation / Protein Binding / Protein Domains / RNA polymerase / RNA, Viral - chemistry / RNA, Viral - genetics / RNA, Viral - metabolism / RNA-protein interactions / Transcription Factors - chemistry / Transcription Factors - genetics / Transcription Factors - metabolism / Transcription, Genetic / Transcriptional Elongation Factors - chemistry / Transcriptional Elongation Factors - metabolism / Translocation / Viral Proteins - chemistry / Viral Proteins - genetics / Viral Proteins - metabolism