A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity

Amr Elghondakly; Chih Hao Wu; Steven Klupt; Jonathan Goodson; Wade C Winkler

doi:10.1016/j.jmb.2021.167100

A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity

J Mol Biol. 2021 Jul 23;433(15):167100. doi: 10.1016/j.jmb.2021.167100. Epub 2021 Jun 11.

Authors

Amr Elghondakly¹, Chih Hao Wu², Steven Klupt², Jonathan Goodson², Wade C Winkler³

Affiliations

¹ The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States.
² The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States.
³ The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States; The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States. Electronic address: wwinkler@umd.edu.

PMID: 34119489
DOI: 10.1016/j.jmb.2021.167100

Abstract

Bacterial NusG associates with RNA polymerase (RNAP) through its N-terminal domain, while the C-terminal domain (CTD) forms dynamic interactions with Rho, S10, NusB and NusA to affect transcription elongation. While virtually all bacteria encode for a core NusG, many also synthesize paralogs that transiently bind RNAP to alter expression of targeted genes. Yet, despite the importance of the genes they regulate, most of the subfamilies of NusG paralogs (e.g., UpxY, TaA, ActX and LoaP) have not been investigated in depth. Herein, we discover that LoaP requires a small RNA hairpin located within the 5' leader region of its targeted operons. LoaP binds the RNA element with nanomolar affinity and high specificity, in contrast to other NusG proteins, which have not been shown to exhibit RNA-binding activity. These data reveal a sequence feature that can be used to identify LoaP-regulated operons. This discovery also expands the repertoire of macromolecular interactions exhibited by the NusG CTD during transcription elongation to include an RNA ligand.

Keywords: KOW domain; NusG; UNCG tetraloop hairpin; processive antitermination; transcription elongation.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

5' Untranslated Regions
Bacillus / genetics*
Bacillus / metabolism
Bacterial Proteins / chemistry*
Bacterial Proteins / metabolism*
DNA-Directed RNA Polymerases / metabolism
Molecular Conformation
Operon
Protein Domains
RNA, Bacterial / chemistry
RNA, Bacterial / metabolism*
RNA-Binding Proteins / chemistry*
RNA-Binding Proteins / metabolism*

Substances

5' Untranslated Regions
Bacterial Proteins
RNA, Bacterial
RNA-Binding Proteins
antiterminator proteins, Bacteria
DNA-Directed RNA Polymerases

Supplementary concepts

Bacillus velezensis