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Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum.

Takayesu, A ; Mahoney, BJ ; et al.
In: Proteins, 2024-04-10
Online academicJournal

Titel:
Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum.
Autor/in / Beteiligte Person: Takayesu, A ; Mahoney, BJ ; Goring, AK ; Jessup, T ; Ogorzalek Loo, RR ; Loo, JA ; Clubb, RT
Link:
Zeitschrift: Proteins, 2024-04-10
Veröffentlichung: Ahead of Print, 2024
Medientyp: academicJournal
ISSN: 1097-0134 (electronic)
DOI: 10.1002/prot.26690
Sonstiges:
  • Nachgewiesen in: MEDLINE
  • Sprachen: English
  • Publication Type: Journal Article
  • Language: English
  • [Proteins] 2024 Apr 10. <i>Date of Electronic Publication: </i>2024 Apr 10.
  • References: IEA. World Energy Outlook 2022. International Energy Agency (IEA); 2022. ; Bar‐On YM, Phillips R, Milo R. The biomass distribution on earth. Proc Natl Acad Sci USA. 2018;115(25):6506‐6511. ; Nassar HN, Nour Gendy WI. Sustainable ecofriendly recruitment of bioethanol fermentation lignocellulosic spent waste biomass for the safe reuse and discharge of petroleum production produced water via biosorption and solid biofuel production. J Hazard Mater. 2022;422(15):126845. ; Johnson EA, Sakajoh M, Halliwell G, Madia A, Demain AL. Saccharification of complex cellulosic substrates by the Cellulase system from Clostridium thermocellum. Appl Environ Microbiol. 1982;43(5):1125‐1132. ; Seo H, Singh P, Wyman CE, Cai CM, Trinh CT. Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short‐chain esters. Bioresour Technol. 2023;384:129263. ; Lu Y, Zhang Y‐HP, Lynd LR. Enzyme‐microbe synergy during cellulose hydrolysis by Clostridium thermocellum. Proc Natl Acad Sci USA. 2006;103(44):16165‐16169. ; Alves VD, Fontes C, Bule P. Cellulosomes: highly efficient cellulolytic complexes. Subcell Biochem. 2021;96:323‐354. ; Artzi L, Bayer EA, Morais S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol. 2017;15(2):83‐95. ; Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli DK, Puri M. Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion. Int J Biol Macromol. 2021;168:572‐590. ; Smith SP, Bayer EA, Czjzek M. Continually emerging mechanistic complexity of the multi‐enzyme cellulosome complex. Curr Opin Struct Biol. 2017;44:151‐160. ; Leibovitz E, Ohayon H, Gounon P, Béguin P. Characterization and subcellular localization of the Clostridium thermocellum scaffoldin dockerin binding protein SdbA. J Bacteriol. 1997;179(8):2519‐2523. ; Doi RH, Kosugi A, Murashima K, Tamaru Y, Han SO. Cellulosomes from mesophilic bacteria. J Bacteriol. 2003;185(20):5907‐5914. ; Dassa B, Borovok I, Lombard V, et al. Pan‐cellulosomics of mesophilic clostridia: variations on a theme. Microorganisms. 2017;5(4):74. ; Dassa B, Borovok I, Lamed R, et al. Genome‐wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics. 2012;13:210. ; Artzi L, Morag E, Barak Y, Lamed R, Bayer EA. Clostridium clariflavum: key cellulosome players are revealed by proteomic analysis. MBio. 2015;6(3):e00411‐e00415. ; Nataf Y, Bahari L, Kahel‐Raifer H, et al. Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors. Proc Natl Acad Sci USA. 2010;107(43):18646‐18651. ; Kahel‐Raifer H, Jindou S, Bahari L, et al. The unique set of putative membrane‐associated anti‐sigma factors in Clostridium thermocellum suggests a novel extracellular carbohydrate‐sensing mechanism involved in gene regulation. FEMS Microbiol Lett. 2010;308(1):84‐93. ; Sand A et al. Three cellulosomal xylanase genes in Clostridium thermocellum are regulated by both vegetative SigA (sigma(a)) and alternative SigI6 (sigma(I6)) factors. FEBS Lett. 2015;589(20):3133‐3140. ; Munoz‐Gutierrez I et al. Decoding biomass‐sensing regulons of Clostridium thermocellum alternative sigma‐I factors in a heterologous Bacillus subtilis host system. PloS One. 2016;11(1):e0146316. ; Grinberg IR, Yaniv O, De Ora LO, et al. Distinctive ligand‐binding specificities of tandem PA14 biomass‐sensory elements from Clostridium thermocellum and clostridium clariflavum. Proteins. 2019;87(11):917‐930. ; Bahari L, Gilad Y, Borovok I, et al. Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum. J Ind Microbiol Biotechnol. 2011;38(7):825‐832. ; Mahoney BJ, Takayesu A, Zhou A, Cascio D, Clubb RT. The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing. Proteins. 2022;90(7):1457‐1467. ; Marcos‐Torres FJ, Moraleda‐Muñoz A, Contreras‐Moreno FJ, Muñoz‐Dorado J, Pérez J. Mechanisms of action of non‐canonical ECF sigma factors. Int J Mol Sci. 2022;23(7):3601. ; Asai K. Anti‐sigma factor‐mediated cell surface stress responses in Bacillus subtilis. Genes Genet Syst. 2018;92(5):223‐234. ; Brunet YR, Habib C, Brogan AP, Artzi L, Rudner DZ. Intrinsically disordered protein regions are required for cell wall homeostasis in Bacillus subtilis. Genes Dev. 2022;36(17–18):970‐984. ; Brogan AP, Habib C, Hobbs SJ, Kranzusch PJ, Rudner DZ. Bacterial SEAL domains undergo autoproteolysis and function in regulated intramembrane proteolysis. Proc Natl Acad Sci USA. 2023;120(40):e2310862120. ; Chen C, Dong S, Yu Z, et al. Essential autoproteolysis of bacterial anti‐σ factor RsgI for transmembrane signal transduction. Sci Adv. 2023;9(27):eadg4846. ; Cavanagh J. Protein NMR Spectroscopy: Principles and Practice. 2nd ed. Elsevier Academic Press; 2007:885. ; Shen Y, Delaglio F, Cornilescu G, Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR. 2009;44(4):213‐223. ; Kay LE, Torchia DA, Bax A. Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry. 1989;28(23):8972‐8979. ; Stetz MA et al. Characterization of internal protein dynamics and conformational entropy by NMR relaxation. Methods Enzymol. 2019;615:237‐284. ; Laskowski RA, Rullmannn JA, MacArthur M, Kaptein R, Thornton JM. AQUA and PROCHECK‐NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR. 1996;8(4):477‐486. ; Madeira F, Pearce M, Tivey ARN, et al. Search and sequence analysis tools services from EMBL‐EBI in 2022. Nucleic Acids Res. 2022;50(W1):W276‐W279. ; Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583‐589. ; Chen VB, Arendall WB III, Headd JJ, et al. MolProbity: all‐atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010;66(1):12‐21. ; Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC. New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters”, and NGL viewer to recapture online 3D graphics. Protein Sci. 2020;29(1):315‐329. ; Huang J, MacKerell AD. CHARMM36 all‐atom additive protein force field: validation based on comparison to NMR data. J Comput Chem. 2013;34(25):2135‐2145. ; Guan C, Cui T, Rao V, et al. Activation of glycosylasparaginase. Formation of active N‐terminal threonine by intramolecular autoproteolysis. J Biol Chem. 1996;271(3):1732‐1737. ; Johansson DG et al. Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N –> O acyl shift reaction. J Am Chem Soc. 2009;131(27):9475‐9477. ; Voorter CE, de Haard‐Hoekman WA, Van Den Oetelaar PJ, Bloemendal H, de Jong WW. Spontaneous peptide bond cleavage in aging alpha‐crystallin through a succinimide intermediate. J Biol Chem. 1988;263(35):19020‐19023. ; Boon L, Ugarte‐Berzal E, Vandooren J, Opdenakker G. Protease propeptide structures, mechanisms of activation, and functions. Crit Rev Biochem Mol Biol. 2020;55(2):111‐165. ; Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. Biochim Biophys Acta Proteins Proteomics. 2021;1869(1):140557. ; Perler FB, Xu MQ, Paulus H. Protein splicing and autoproteolysis mechanisms. Curr Opin Chem Biol. 1997;1(3):292‐299. ; Bastiaansen KC, Van Ulsen P, Wijtmans M, Bitter W, Llamas MA. Self‐cleavage of the Pseudomonas aeruginosa cell‐surface signaling anti‐sigma factor FoxR occurs through an N‐O acyl rearrangement. J Biol Chem. 2015;290(19):12237‐12246. ; Araç D, Boucard AA, Bolliger MF, et al. A novel evolutionarily conserved domain of cell‐adhesion GPCRs mediates autoproteolysis. EMBO J. 2012;31(6):1364‐1378. ; Hsu M‐F, Kuo CJ, Chang KT, et al. Mechanism of the maturation process of SARS‐CoV 3CL protease. J Biol Chem. 2005;280(35):31257‐31266. ; Ball LE, Garland DL, Crouch RK, Schey KL. Post‐translational modifications of aquaporin 0 (AQP0) in the normal human lens: spatial and temporal occurrence. Biochemistry. 2004;43(30):9856‐9865. ; Ferris HU, Furukawa Y, Minamino T, et al. FlhB regulates ordered export of flagellar components via autocleavage mechanism. J Biol Chem. 2005;280(50):41236‐41242. ; Monjarás Feria JV, Lefebre MD, Stierhof YD, Galán JE, Wagner S. Role of autocleavage in the function of a type III secretion specificity switch protein in Salmonella enterica serovar Typhimurium. MBio. 2015;6(5):e01415‐e01459. ; Kato K, Nakayoshi T, Ishikawa Y, Kurimoto E, Oda A. Computational analysis of the mechanism of nonenzymatic peptide bond cleavage at the C‐terminal side of an asparagine residue. ACS Omega. 2021;6(44):30078‐30084. ; Robinson NE, Robinson AB. Molecular clocks. Proc Natl Acad Sci USA. 2001;98(3):944‐949. ; Geiger T, Clarke S. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide‐linked reactions that contribute to protein degradation. J Biol Chem. 1987;262(2):785‐794. ; Tarelli E, Corran PH. Ammonia cleaves polypeptides at asparagine proline bonds. J Peptide Res Off J Am Peptide Soc. 2003;62(6):245‐251. ; Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995;6(3):277‐293. ; Garrett DS, Cai M, Clore GM. XIPP: multi‐dimensional NMR analysis software. J Biomol NMR. 2020;74(1):9‐25. ; Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol. 2002;319(1):209‐227. ; Lee W, Tonelli M, Markley JL. NMRFAM‐SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015;31(8):1325‐1327. ; Shen Y, Bax A. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR. 2013;56(3):227‐241. ; Schwieters CD, Bermejo GA, Clore GM. Xplor‐NIH for molecular structure determination from NMR and other data sources. Prot Sci Publ Prot Soc. 2018;27(1):26‐40. ; Schwieters CD, Kuszewski JJ, Tjandra N, Marius Clore G. The Xplor‐NIH NMR molecular structure determination package. J Magn Reson. 2003;160(1):65‐73. ; Koradi R, Billeter M, Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph. 1996;14(1):51‐55. ; Lam WWT, Siu SWI. PyMOL mControl: manipulating molecular visualization with mobile devices. Biochem Mol Biol Educ. 2017;45(1):76‐83. ; Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33‐38. ; Turner PJ. Celiac disease associated with epilepsy and intracranial calcifications: report of two patients. Center for Coastal and Land‐Margin Research, Oregon Graduate Institute of Science and Technology; 2005. ; Rappsilber J, Mann M, Ishihama Y. Protocol for micro‐purification, enrichment, pre‐fractionation and storage of peptides for proteomics using StageTips. Nat Protoc. 2007;2(8):1896‐1906.
  • Grant Information: S10OD025073 United States NH NIH HHS; S10OD016336 United States NH NIH HHS; R01-AI052217 United States NH NIH HHS; T90-DE030860 United States DE NIDCR NIH HHS
  • Contributed Indexing: Keywords: Clostridium thermocellum; RsgI; anti‐sigma factor; autoproteolysis; cellulosome; conserved RsgI extracellular domain; periplasmic domain
  • Entry Date(s): Date Created: 20240410 Latest Revision: 20240410
  • Update Code: 20240410

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