Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation.
| Title: | Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation. |
|---|---|
| Authors: | Said N; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany.; Finazzo M; The Ohio State University, Department of Microbiology and Center for RNA Biology, Columbus, OH, USA.; Hilal T; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany.; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy and Core Facility BioSupraMol, Fabeckstr. 36a, 14195 Berlin, Germany.; Wang B; The Ohio State University, Department of Microbiology and Center for RNA Biology, Columbus, OH, USA.; Selinger TL; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany.; Gjorgjevikj D; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany.; Artsimovitch I; The Ohio State University, Department of Microbiology and Center for RNA Biology, Columbus, OH, USA.; Wahl MC; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany.; Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany. |
| Source: | BioRxiv : the preprint server for biology [bioRxiv] 2023 Aug 31. Date of Electronic Publication: 2023 Aug 31. |
| Publication Type: | Preprint; Journal Article |
| Language: | English |
| Journal Info: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| Abstract: | Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Our electron microscopic structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions, and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirmed that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses revealed that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ would be lethal. |
| Competing Interests: | Competing Interest Statement The authors declare no competing interests. |
| Comments: | Update in: Nat Commun. 2024 Apr 15;15(1):3186. doi: 10.1038/s41467-024-47439-6.. (PMID: 38622114) |
| References: | Science. 2008 May 16;320(5878):935-8. (PMID: 18487194); Nat Commun. 2024 Apr 8;15(1):3040. (PMID: 38589445); Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7691-E7700. (PMID: 27856760); Mol Syst Biol. 2021 May;17(5):e9536. (PMID: 34032011); Genome Res. 2004 Jun;14(6):1188-90. (PMID: 15173120); Nucleic Acids Res. 2022 Jan 7;50(D1):D785-D794. (PMID: 34520557); Biochemistry. 1992 Jan 14;31(1):111-21. (PMID: 1370623); Nat Commun. 2022 Nov 15;13(1):6968. (PMID: 36379955); BMC Genomics. 2018 Jan 16;19(1):52. (PMID: 29338696); Bioinformatics. 2006 Jul 1;22(13):1658-9. (PMID: 16731699); Mol Cell. 2018 Sep 20;71(6):911-922.e4. (PMID: 30122535); PLoS Genet. 2019 Oct 7;15(10):e1008425. (PMID: 31589608); Sci Adv. 2023 Feb 10;9(6):eade7093. (PMID: 36753546); Science. 2021 Jan 1;371(6524):. (PMID: 33243850); J Biol Chem. 2007 Aug 10;282(32):23348-53. (PMID: 17565995); Mol Microbiol. 1998 Aug;29(3):859-69. (PMID: 9723924); mBio. 2017 May 30;8(3):. (PMID: 28559482); Science. 2020 Sep 11;369(6509):1359-1365. (PMID: 32820061); Cell. 2003 Jul 11;114(1):135-46. (PMID: 12859904); Nat Methods. 2017 Mar;14(3):290-296. (PMID: 28165473); Mol Cell. 2022 Oct 20;82(20):3885-3900.e10. (PMID: 36220101); Front Microbiol. 2014 Apr 10;5:156. (PMID: 24782844); Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13714-13719. (PMID: 27821776); Genes Dev. 1997 May 1;11(9):1169-82. (PMID: 9159398); Nucleic Acids Res. 2013 Jul;41(12):e121. (PMID: 23598997); J Biol Chem. 1993 Jul 5;268(19):13947-55. (PMID: 8314761); Cell. 2016 Sep 22;167(1):111-121.e13. (PMID: 27662085); J Bacteriol. 2019 Apr 24;201(10):. (PMID: 30833359); Mol Cell. 2019 Apr 4;74(1):143-157.e5. (PMID: 30795892); Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14414-9. (PMID: 23940369); Nucleic Acids Res. 2013 Aug;41(14):6839-56. (PMID: 23703205); J Mol Biol. 2019 Dec 6;431(24):4749-4766. (PMID: 31628950); J Biol Chem. 2006 Nov 3;281(44):33697-703. (PMID: 16908525); Cell. 2009 Oct 30;139(3):523-34. (PMID: 19879839); Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844); Science. 2020 Sep 11;369(6509):1355-1359. (PMID: 32820062); Mol Cell. 2021 Jan 21;81(2):281-292.e8. (PMID: 33296676); Mol Gen Genet. 1984;193(2):210-3. (PMID: 6363877); Mol Cell. 2020 Sep 17;79(6):1024-1036.e5. (PMID: 32871103); Protein Sci. 2021 Jan;30(1):70-82. (PMID: 32881101); Mol Cell. 2011 Jul 22;43(2):253-62. (PMID: 21777814); EMBO J. 2011 Jun 14;30(14):2805-16. (PMID: 21673658); mBio. 2022 Oct 13;13(6):e0237122. (PMID: 36226957); BMC Microbiol. 2014 Jun 26;14:171. (PMID: 24964927); Mol Biol Evol. 2018 Dec 1;35(12):3041-3043. (PMID: 30351396); Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. (PMID: 22505256); Nucleic Acids Res. 2023 Apr 11;51(6):2778-2789. (PMID: 36762473); Nat Commun. 2022 Mar 29;13(1):1663. (PMID: 35351884); Protein Sci. 2020 Apr;29(4):1069-1078. (PMID: 31730249); Nucleic Acids Res. 2019 May 21;47(9):4442-4448. (PMID: 31081040); Acta Crystallogr F Struct Biol Commun. 2020 Sep 1;76(Pt 9):398-405. (PMID: 32880587); Science. 2006 May 19;312(5776):1044-6. (PMID: 16645050); mBio. 2016 Sep 13;7(5):. (PMID: 27624127); Cell. 2006 Nov 3;127(3):553-64. (PMID: 17081977); J Mol Biol. 2007 Aug 24;371(4):855-72. (PMID: 17599352); mBio. 2021 Oct 26;12(5):e0256121. (PMID: 34634934); Mol Cell. 2009 Jan 16;33(1):97-108. (PMID: 19150431); iScience. 2022 Nov 02;25(12):105483. (PMID: 36387024); J Mol Biol. 2011 Jan 14;405(2):497-518. (PMID: 21059356); Nature. 2023 Feb;614(7947):367-374. (PMID: 36697824); Biochemistry. 2011 Jun 28;50(25):5799-805. (PMID: 21619030); Nat Commun. 2022 Aug 15;13(1):4668. (PMID: 35970830); Annu Rev Genet. 2022 Nov 30;56:187-205. (PMID: 36055649) |
| Grant Information: | R01 GM067153 United States GM NIGMS NIH HHS |
| Entry Date(s): | Date Created: 20230911 Latest Revision: 20240924 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC10491184 |
| DOI: | 10.1101/2023.08.30.555460 |
| PMID: | 37693585 |
| Database: | MEDLINE |
Preprint; Journal Article