دورية أكاديمية
A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.
العنوان: | A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. |
---|---|
المؤلفون: | Takada H; Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan.; Department of Biotechnology, Toyama Prefectural University,5180 Kurokawa, Imizu, Toyama 939-0398, Japan.; Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden., Paternoga H; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany., Fujiwara K; Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan., Nakamoto JA; Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden., Park EN; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Dimitrova-Paternoga L; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany., Beckert B; Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland., Saarma M; University of Tartu, Institute of Technology, 50411 Tartu, Estonia., Tenson T; University of Tartu, Institute of Technology, 50411 Tartu, Estonia., Buskirk AR; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Atkinson GC; Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.; Virus Centre, Lund University, Lund, Sweden., Chiba S; Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan., Wilson DN; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany., Hauryliuk V; Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.; Virus Centre, Lund University, Lund, Sweden.; Science for Life Laboratory, Lund, Sweden. |
المصدر: | Nucleic acids research [Nucleic Acids Res] 2024 Aug 12; Vol. 52 (14), pp. 8483-8499. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE |
أسماء مطبوعة: | Publication: 1992- : Oxford : Oxford University Press Original Publication: London, Information Retrieval ltd. |
مواضيع طبية MeSH: | Bacillus subtilis*/genetics , Bacillus subtilis*/metabolism , Bacterial Proteins*/metabolism , Bacterial Proteins*/genetics , Ribosomes*/metabolism , Protein Biosynthesis*, Protein Domains ; Cryoelectron Microscopy ; Protein Binding ; RNA-Binding Proteins/metabolism ; RNA-Binding Proteins/genetics ; Models, Molecular ; RNA, Transfer, Amino Acyl |
مستخلص: | Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC. (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.) |
References: | Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10584-9. (PMID: 11535833) Nucleic Acids Res. 2024 May 8;52(8):4111-4123. (PMID: 38554105) Elife. 2019 Jun 20;8:. (PMID: 31219035) Genes Cells. 2000 Aug;5(8):627-35. (PMID: 10947848) Nat Struct Mol Biol. 2022 Feb;29(2):152-161. (PMID: 35165455) Acta Crystallogr D Struct Biol. 2021 Oct 1;77(Pt 10):1282-1291. (PMID: 34605431) Annu Rev Biochem. 2020 Jun 20;89:417-442. (PMID: 32569528) Nucleic Acids Res. 2021 Feb 22;49(3):1550-1566. (PMID: 33503266) Nucleic Acids Res. 2022 Nov 28;50(21):12515-12526. (PMID: 36370110) Nucleic Acids Res. 2021 Aug 20;49(14):8355-8369. (PMID: 34255840) Cold Spring Harb Perspect Biol. 2018 Oct 1;10(10):. (PMID: 29735640) Bioinformatics. 2017 Sep 01;33(17):2781-2783. (PMID: 28498899) Nat Biotechnol. 2014 Mar;32(3):223-6. (PMID: 24727771) Mol Cell. 2023 Feb 16;83(4):607-621.e4. (PMID: 36804914) Genome Biol. 2009;10(3):R25. (PMID: 19261174) Mol Microbiol. 2010 Nov;78(4):796-808. (PMID: 21062370) Cell Rep. 2020 Mar 31;30(13):4321-4331.e4. (PMID: 32234470) Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690) Trends Biochem Sci. 2021 Sep;46(9):731-743. (PMID: 33966939) J Struct Biol. 2015 Nov;192(2):216-21. (PMID: 26278980) EMBO J. 2024 Feb;43(4):484-506. (PMID: 38177497) Nature. 2018 May;557(7705):446-451. (PMID: 29632312) Nat Biotechnol. 2018 Nov;36(10):996-1004. (PMID: 30148503) Commun Biol. 2020 Feb 11;3(1):61. (PMID: 32047248) Bioinformatics. 2021 Jun 9;37(9):1312-1314. (PMID: 32956448) J Bacteriol. 2021 Jan 11;203(3):. (PMID: 32900832) J Bacteriol. 2003 Oct;185(20):6209-14. (PMID: 14526035) Cell. 2019 Jun 27;178(1):76-90.e22. (PMID: 31155236) Nature. 2024 Feb;626(8001):1133-1140. (PMID: 38326618) Science. 1996 Feb 16;271(5251):990-3. (PMID: 8584937) IUCrJ. 2019 Jan 01;6(Pt 1):5-17. (PMID: 30713699) Nat Commun. 2018 Jun 6;9(1):2197. (PMID: 29875445) mBio. 2018 Dec 18;9(6):. (PMID: 30563899) Microorganisms. 2021 Dec 21;10(1):. (PMID: 35056452) Mol Microbiol. 2011 May;80(3):772-85. (PMID: 21418110) Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844) Genes Cells. 2002 Jul;7(7):629-38. (PMID: 12081641) Curr Protoc Microbiol. 2015 Feb 02;36:1E.3.1-1E.3.24. (PMID: 25641100) Nucleic Acids Res. 2022 Jan 7;50(D1):D439-D444. (PMID: 34791371) Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296. (PMID: 33885785) Protein Sci. 2021 Jan;30(1):70-82. (PMID: 32881101) Crit Rev Biochem Mol Biol. 2021 Dec;56(6):603-620. (PMID: 34233554) Bioessays. 2022 Aug;44(8):e2200046. (PMID: 35719031) Nucleic Acids Res. 2011 Mar;39(5):1739-48. (PMID: 21051357) Front Microbiol. 2021 Mar 18;12:652980. (PMID: 33815344) Nature. 2022 Mar;603(7901):503-508. (PMID: 35264790) RNA Biol. 2005 Apr;2(2):70-4. (PMID: 17132943) Protein Sci. 2023 Jan;32(1):e4519. (PMID: 36419248) Mol Cell. 2021 Jan 7;81(1):104-114.e6. (PMID: 33259811) Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):. (PMID: 34453003) Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. (PMID: 20383002) EMBO J. 2019 Mar 1;38(5):. (PMID: 30609991) PLoS One. 2016 Oct 5;11(10):e0163962. (PMID: 27706213) RNA Biol. 2014;11(4):360-72. (PMID: 24646681) Nucleic Acids Res. 2022 Jul 22;50(13):7669-7679. (PMID: 35766409) Cell Syst. 2017 Mar 22;4(3):291-305.e7. (PMID: 28189581) PLoS Comput Biol. 2011 Oct;7(10):e1002195. (PMID: 22039361) Mol Microbiol. 2012 Oct;86(1):37-50. (PMID: 22857598) Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):215-227. (PMID: 29533229) Chembiochem. 2023 Oct 17;24(20):e202300264. (PMID: 37382189) Biochemistry. 2011 Jan 25;50(3):329-39. (PMID: 21141807) Nat Struct Mol Biol. 2015 Apr;22(4):342-344. (PMID: 25775268) Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877. (PMID: 31588918) J Bacteriol. 2002 Sep;184(17):4881-90. (PMID: 12169614) Genes Dev. 1998 May 1;12(9):1338-47. (PMID: 9573050) J Bacteriol. 1979 Jan;137(1):694-6. (PMID: 368041) Bioinformatics. 2009 May 1;25(9):1189-91. (PMID: 19151095) Elife. 2018 Nov 09;7:. (PMID: 30412051) Nucleic Acids Res. 2016 Sep 6;44(15):7495-508. (PMID: 27402159) Protein Sci. 2020 Apr;29(4):1069-1078. (PMID: 31730249) Nature. 2022 Mar;603(7901):509-514. (PMID: 35264791) Mol Cell. 2024 Feb 15;84(4):715-726.e5. (PMID: 38183984) Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4678-83. (PMID: 12682299) RNA. 2023 Sep;29(9):1339-1354. (PMID: 37221012) Mol Cell. 2003 Mar;11(3):671-83. (PMID: 12667450) Elife. 2020 Sep 14;9:. (PMID: 32924932) Nat Struct Mol Biol. 2015 Apr;22(4):336-41. (PMID: 25775265) Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2487-99. (PMID: 25195761) Biochemistry (Mosc). 2021 Sep;86(9):1107-1121. (PMID: 34565314) J Biol Chem. 1995 Apr 21;270(16):9322-6. (PMID: 7536743) J Mol Evol. 1999 Mar;48(3):291-302. (PMID: 10093218) Nat Commun. 2019 Nov 27;10(1):5397. (PMID: 31776341) Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12150-12155. (PMID: 27791002) Nat Microbiol. 2022 Dec;7(12):2114-2127. (PMID: 36411352) Mol Cell. 2021 Jan 7;81(1):115-126.e7. (PMID: 33259810) J Antimicrob Chemother. 2013 Nov;68(11):2477-81. (PMID: 23812681) Science. 2017 Jul 28;357(6349):414-417. (PMID: 28751611) Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):8978-8983. (PMID: 30126986) Nucleic Acids Res. 2023 Jan 6;51(D1):D418-D427. (PMID: 36350672) Cell Rep. 2020 Oct 13;33(2):108250. (PMID: 33053345) Nat Methods. 2009 Oct;6(10):767-72. (PMID: 19767758) Commun Biol. 2019 Jun 19;2:218. (PMID: 31240256) Nat Methods. 2017 Apr;14(4):331-332. (PMID: 28250466) J Biol Chem. 2015 Apr 24;290(17):11008-20. (PMID: 25759383) Cold Spring Harb Perspect Biol. 2018 Sep 4;10(9):. (PMID: 29661790) Cell Rep. 2021 Jan 5;34(1):108599. (PMID: 33406423) Mol Cell. 2022 Apr 21;82(8):1451-1466. (PMID: 35452614) Nat Methods. 2012 Jul;9(7):671-5. (PMID: 22930834) Bioinformatics. 2004 Jan 22;20(2):289-90. (PMID: 14734327) RNA. 2022 Sep;28(9):1185-1196. (PMID: 35710145) Protein Sci. 2023 Nov;32(11):e4792. (PMID: 37774136) Protein Sci. 2018 Jan;27(1):14-25. (PMID: 28710774) RNA Biol. 2022 Jan;19(1):117-131. (PMID: 34923906) J Mol Biol. 2012 Apr 13;417(5):425-39. (PMID: 22326347) Front Microbiol. 2020 Feb 28;11:277. (PMID: 32184768) Elife. 2020 Oct 22;9:. (PMID: 33089779) |
معلومات مُعتمدة: | G-2021-2-063 Institute for Fermentation, Osaka; 20H05926 JSPS Grants-in-Aid for Scientific Research; R01 GM136960 United States GM NIGMS NIH HHS; 20220562 Crafoord foundation; PRG335 Estonian Research Council; Umeå Centre for Microbial Research; 2020-0037 Knut and Alice Wallenberg Foundation; Universität Hamburg; 20 0872 Pj Cancerfonden; Centre for Structural Systems Biology, Hamburg; WI3285/11-1 Deutsche Forschungsgemeinschaft; 2019-01085 Swedish Research Council; INST 152/772-1 DFG; JP1159335 JST, ACT X, Japan; GM136960 United States GF NIH HHS |
المشرفين على المادة: | 0 (Bacterial Proteins) 0 (RNA-Binding Proteins) 0 (tRNA, peptidyl-) 0 (RNA, Transfer, Amino Acyl) |
تواريخ الأحداث: | Date Created: 20240529 Date Completed: 20240811 Latest Revision: 20240822 |
رمز التحديث: | 20240822 |
مُعرف محوري في PubMed: | PMC11317155 |
DOI: | 10.1093/nar/gkae399 |
PMID: | 38811035 |
قاعدة البيانات: | MEDLINE |
كن أول من يترك تعليقا!