Structural basis for λN-dependent processive transcription antitermination

Nat Microbiol. 2017 Apr 28:2:17062. doi: 10.1038/nmicrobiol.2017.62.

Abstract

λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The structural basis of the process has so far remained elusive. Here we describe a crystal structure of a λN-NusA-NusB-NusE-nut site complex and an electron cryo-microscopic structure of a complete transcription antitermination complex, comprising RNA polymerase, DNA, nut site RNA, all Nus factors and λN, validated by crosslinking/mass spectrometry. Due to intrinsic disorder, λN can act as a multiprotein/RNA interaction hub, which, together with nut site RNA, arranges NusA, NusB and NusE into a triangular complex. This complex docks via the NusA N-terminal domain and the λN C-terminus next to the RNA exit channel on RNA polymerase. Based on the structures, comparative crosslinking analyses and structure-guided mutagenesis, we hypothesize that λN mounts a multipronged strategy to reprogram the transcriptional machinery, which may include (1) the λN C terminus clamping the RNA exit channel, thus stabilizing the DNA:RNA hybrid; (2) repositioning of NusA and RNAP elements, thus redirecting nascent RNA and sequestering the upstream branch of a terminator hairpin; and (3) hindering RNA engagement of termination factor ρ and/or obstructing ρ translocation on the transcript.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Binding Sites
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / genetics
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Gene Expression Regulation
  • RNA / chemistry
  • RNA-Binding Proteins / chemistry*
  • Rho Factor
  • Ribosomal Proteins / genetics
  • Terminator Regions, Genetic*
  • Transcription Factors / chemistry
  • Transcription, Genetic*

Substances

  • Bacterial Proteins
  • Escherichia coli Proteins
  • RNA-Binding Proteins
  • Rho Factor
  • Ribosomal Proteins
  • Transcription Factors
  • antiterminator proteins, Bacteria
  • RNA
  • DNA-Directed RNA Polymerases