Ancient Transcription Factors in the News

Abstract

In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In Escherichia coli, NusG stimulates silencing of horizontally acquired genes, while its paralog RfaH counters NusG action by activating a subset of these genes. Acting alone or as part of regulatory complexes, NusG factors can promote uninterrupted RNA synthesis, bring about transcription pausing or premature termination, modulate RNA processing, and facilitate translation. Recent structural and mechanistic studies of NusG homologs from all domains of life reveal molecular details of multifaceted interactions that underpin their unexpectedly diverse regulatory roles. NusG proteins share conserved binding sites on RNA polymerase and many effects on the transcription elongation complex but differ in their mechanisms of recruitment, interactions with nucleic acids and secondary partners, and regulatory outcomes. Strikingly, some can alternate between autoinhibited and activated states that possess dramatically different secondary structures to achieve exquisite target specificity.

Origins and Molecular Evolution of the NusG Paralog RfaH

“…Consistently with their common evolutionary origin and function, NGNs of NusG homologs from archaea, bacteria, and eukaryotes bind to the same sites on the elongating RNAP ( 4 – 6 ), composed of the clamp helix (CH) domain in the largest RNAP subunit (β′ in Bacteria ) and the gate loop in the second-largest subunit (β in Bacteria ). Once bound, NusG proteins (or their NGNs alone) promote processive, pause-free RNA synthesis ( 7 ), a function thought to be particularly important for the synthesis of very long RNAs. Recent structural studies revealed a common molecular basis for antipausing activity among all NusG-like proteins ( 4 , 5 , 8 ).…”

“…S1 ). Within a given cell, NusG and its paralogs can be viewed as alternative transcription elongation factors which compete for binding to RNAP, similarly to σ initiation factors ( 7 ). This analogy is strengthened by the fact that NusG and σ (or Spt5 and TFE in Archaea ) share the binding site on RNAP ( 18 , 19 ).…”

“…Yet if RNA is useless or potentially harmful, as is the case with many xenogenes, the NusG-KOW domain interacts with the termination factor Rho to induce its early release from RNAP ( 23 ); in fact, silencing of xenogenes constitutes an essential function of E. coli NusG ( 24 ). RfaH plays an opposite role; it activates expression of xenogenes ( 7 ), many of which encode virulence factors, and is required for virulence in enteric pathogens ( 7 ).…”

“…An emerging view is that specialized NusG paralogs (NusG SP s) function as dedicated antiterminators of long, difficult-to-express gene clusters required for adaptation to diverse environments, including human hosts. Bacterial genes shown to be dependent on NusG SP s for expression encode adhesins, capsular polysaccharides, conjugation machinery, polyketide antibiotics, and toxins ( 7 ). While RfaH is recruited to ops sites in the leader regions of several unlinked chromosomal targets ( 20 ), some NusG SP s are encoded within the operons that they regulate ( 32 , 33 ) and their modes of recruitment are unknown.…”

NusA directly interacts with antitermination factor Q from phage λ

“…1a) 22 . NusG-NTD has a mixed α/β topology and binds to the β' clamp helices of RNAP, increasing its processivity, whereas NusG-CTD forms a five-stranded β-barrel that can interact with different binding partners (reviewed in 23 ). For example, NusG-CTD is able to bind termination factor Rho, resulting in stimulation of Rho-dependent termination [24][25][26] , or to ribosomal protein S10 so that NusG serves as physical linker between RNAP and the ribosome to couple transcription and translation 24 .…”