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Transcription factors modulate RNA polymerase conformational equilibrium.

Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-André C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A
Nat Commun 13 1546 (2022)
Related entries: 7py0, 7py1, 7py3, 7py5, 7py7, 7py8, 7pyj, 7pyk, 7q0j, 7q0k

Cited: 8 times
EuropePMC logo PMID: 35318334

Abstract

RNA polymerase (RNAP) frequently pauses during the transcription of DNA to RNA to regulate gene expression. Transcription factors NusA and NusG modulate pausing, have opposing roles, but can bind RNAP simultaneously. Here we report cryo-EM reconstructions of Escherichia coli RNAP bound to NusG, or NusA, or both. RNAP conformational changes, referred to as swivelling, correlate with transcriptional pausing. NusA facilitates RNAP swivelling to further increase pausing, while NusG counteracts this role. Their structural effects are consistent with biochemical results on two categories of transcriptional pauses. In addition, the structures suggest a cooperative mechanism of NusA and NusG during Rho-mediated transcription termination. Our results provide a structural rationale for the stochastic nature of pausing and termination and how NusA and NusG can modulate it.

Articles citing this publication (8)

  1. Structural basis for intrinsic transcription termination. You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y. Nature 613 783-789 (2023)
  2. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. Cell 186 1244-1262.e34 (2023)
  3. An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options. Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R. Proc Natl Acad Sci U S A 120 e2215945120 (2023)
  4. In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH. Proc Natl Acad Sci U S A 119 e2205278119 (2022)
  5. Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS. Proc Natl Acad Sci U S A 120 e2218516120 (2023)
  6. Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG. Yakhnin AV, Bubunenko M, Mandell ZF, Lubkowska L, Husher S, Babitzke P, Kashlev M. Proc Natl Acad Sci U S A 120 e2221114120 (2023)
  7. Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis. Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R. Mol Cell 83 1474-1488.e8 (2023)
  8. Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand. Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG. Nat Struct Mol Biol (2023)


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