Duplicate divergence of two bacterial small heat shock proteins reduces the demand for Hsp70 in refolding of substrates

English version

Autoři: Igor Obuchowski ^aff001; Artur Piróg ^aff001; Milena Stolarska ^aff001; Bartłomiej Tomiczek ^aff001; Krzysztof Liberek ^aff001
Působiště autorů: Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Gdansk, Poland ^aff001
Vyšlo v časopise: Duplicate divergence of two bacterial small heat shock proteins reduces the demand for Hsp70 in refolding of substrates. PLoS Genet 15(10): e32767. doi:10.1371/journal.pgen.1008479
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008479

Souhrn

Small heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones that bind to aggregation-prone polypeptides at stress conditions. sHsps encage these polypeptides in assemblies, shielding them from further aggregation. To facilitate their subsequent solubilization and refolding by Hsp70 (DnaK) and Hsp100 (ClpB) chaperones, first, sHsps need to dissociate from the assemblies. In most γ-proteobacteria, these functions are fulfilled by a single sHsp (IbpA), but in a subset of Enterobacterales, a two-protein sHsp (IbpA and IbpB) system has evolved. To gain insight into the emergence of complexity within this chaperone system, we reconstructed the phylogeny of γ-proteobacteria and their sHsps. We selected proteins representative of systems comprising either one or two sHsps and analysed their ability to form sHsps-substrate assemblies. All the tested IbpA proteins, but not IbpB, stably interact with an aggregating substrate. Moreover, in Escherichia coli cells, ibpA but not ibpB suppress the growth defect associated with low DnaK level, which points to the major protective role of IbpA during the breakdown of protein quality control. We also examined how sHsps affect the association of Hsp70 with the assemblies at the initial phase of disaggregation and how they affect protein recovery after stress. Our results suggest that a single gene duplication event has given rise to the sHsp system consisting of a strong canonical binder, IbpA, and its non-canonical paralog IbpB that enhances sHsps dissociation from the assemblies. The cooperation between the sHsps reduces the demand for Hsp70 needed to outcompete them from the assemblies by promoting sHsps dissociation without compromising assembly formation at heat shock. This potentially increases the robustness and elasticity of sHsps protection against irreversible aggregation.

Klíčová slova:

Binding analysis – Evolutionary genetics – Glycerol – Heat shock response – Luciferase – Phylogenetics – Sedimentation – Polypeptides

Zdroje

1. Ostankovitch M, Buchner J. The network of molecular chaperones: insights in the cellular proteostasis machinery. J Mol Biol. 2015;427(18):2899–903. Epub 2015/09/14. doi: 10.1016/j.jmb.2015.08.010 26363891.

2. Hartl FU, Bracher A, Hayer-Hartl M. Molecular chaperones in protein folding and proteostasis. Nature. 2011;475(7356):324–32. Epub 2011/07/22. doi: 10.1038/nature10317 21776078.

3. Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU. Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem. 2013;82 : 323–55. Epub 2013/06/12. doi: 10.1146/annurev-biochem-060208-092442 23746257.

4. Mogk A, Deuerling E, Vorderwulbecke S, Vierling E, Bukau B. Small heat shock proteins, ClpB and the DnaK system form a functional triade in reversing protein aggregation. Mol Microbiol. 2003;50(2):585–95. doi: 10.1046/j.1365-2958.2003.03710.x 14617181.

5. Liberek K, Lewandowska A, Zietkiewicz S. Chaperones in control of protein disaggregation. Embo Journal. 2008;27(2):328–35. doi: 10.1038/sj.emboj.7601970 WOS:000253408600004. 18216875

6. Cheng G, Basha E, Wysocki VH, Vierling E. Insights into small heat shock protein and substrate structure during chaperone action derived from hydrogen/deuterium exchange and mass spectrometry. J Biol Chem. 2008;283(39):26634–42. Epub 2008/07/16. doi: 10.1074/jbc.M802946200 18621732; PubMed Central PMCID: PMC2546550.

7. Ungelenk S, Moayed F, Ho CT, Grousl T, Scharf A, Mashaghi A, et al. Small heat shock proteins sequester misfolding proteins in near-native conformation for cellular protection and efficient refolding. Nat Commun. 2016;7. doi: ARTN 13673 doi: 10.1038/ncomms13673 WOS:000388800600001.

8. Stengel F, Baldwin AJ, Painter AJ, Jaya N, Basha E, Kay LE, et al. Quaternary dynamics and plasticity underlie small heat shock protein chaperone function. Proc Natl Acad Sci U S A. 2010;107(5):2007–12. doi: 10.1073/pnas.0910126107 20133845; PubMed Central PMCID: PMC2836621.

9. Zwirowski S, Klosowska A, Obuchowski I, Nillegoda NB, Pirog A, Zieztkiewicz S, et al. Hsp70 displaces small heat shock proteins from aggregates to initiate protein refolding. Embo Journal. 2017;36(6):783–96. doi: 10.15252/embj.201593378 WOS:000397293500008. 28219929

10. Zietkiewicz S, Krzewska J, Liberek K. Successive and synergistic action of the Hsp70 and Hsp100 chaperones in protein disaggregation. J Biol Chem. 2004;279(43):44376–83. doi: 10.1074/jbc.M402405200 15302880.

11. Weibezahn J, Tessarz P, Schlieker C, Zahn R, Maglica Z, Lee S, et al. Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB. Cell. 2004;119(5):653–65. doi: 10.1016/j.cell.2004.11.027 15550247.

12. Glover JR, Lindquist S. Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues previously aggregated proteins. Cell. 1998;94(1):73–82. doi: 10.1016/s0092-8674(00)81223-4 9674429.

13. Haslbeck M, Vierling E. A first line of stress defense: small heat shock proteins and their function in protein homeostasis. J Mol Biol. 2015;427(7):1537–48. doi: 10.1016/j.jmb.2015.02.002 25681016; PubMed Central PMCID: PMC4360138.

14. Lentze N, Aquilina JA, Lindbauer M, Robinson CV, Narberhaus F. Temperature and concentration-controlled dynamics of rhizobial small heat shock proteins. Eur J Biochem. 2004;271(12):2494–503. doi: 10.1111/j.1432-1033.2004.04180.x 15182365.

15. Painter AJ, Jaya N, Basha E, Vierling E, Robinson CV, Benesch JL. Real-time monitoring of protein complexes reveals their quaternary organization and dynamics. Chem Biol. 2008;15(3):246–53. Epub 2008/03/22. doi: 10.1016/j.chembiol.2008.01.009 18355724.

16. Benesch JL, Aquilina JA, Baldwin AJ, Rekas A, Stengel F, Lindner RA, et al. The quaternary organization and dynamics of the molecular chaperone HSP26 are thermally regulated. Chem Biol. 2010;17(9):1008–17. Epub 2010/09/21. doi: 10.1016/j.chembiol.2010.06.016 20851350; PubMed Central PMCID: PMC3388541.

17. Peschek J, Braun N, Rohrberg J, Back KC, Kriehuber T, Kastenmuller A, et al. Regulated structural transitions unleash the chaperone activity of alphaB-crystallin. Proc Natl Acad Sci U S A. 2013;110(40):E3780–9. Epub 2013/09/18. doi: 10.1073/pnas.1308898110 24043785; PubMed Central PMCID: PMC3791731.

18. Treweek TM, Meehan S, Ecroyd H, Carver JA. Small heat-shock proteins: important players in regulating cellular proteostasis. Cell Mol Life Sci. 2015;72(3):429–51. doi: 10.1007/s00018-014-1754-5 25352169.

19. Jaya N, Garcia V, Vierling E. Substrate binding site flexibility of the small heat shock protein molecular chaperones. Proc Natl Acad Sci U S A. 2009;106(37):15604–9. doi: 10.1073/pnas.0902177106 19717454; PubMed Central PMCID: PMC2773522.

20. Kuczynska-Wisnik D, Kedzierska S, Matuszewska E, Lund P, Taylor A, Lipinska B, et al. The Escherichia coli small heat-shock proteins IbpA and IbpB prevent the aggregation of endogenous proteins denatured in vivo during extreme heat shock. Microbiology. 2002;148(Pt 6):1757–65. doi: 10.1099/00221287-148-6-1757 12055295.

21. Plesofsky-Vig N, Brambl R. Disruption of the gene for hsp30, an alpha-crystallin-related heat shock protein of Neurospora crassa, causes defects in thermotolerance. Proc Natl Acad Sci U S A. 1995;92(11):5032–6. doi: 10.1073/pnas.92.11.5032 7761443; PubMed Central PMCID: PMC41842.

22. Lee S, Owen HA, Prochaska DJ, Barnum SR. HSP16.6 is involved in the development of thermotolerance and thylakoid stability in the unicellular cyanobacterium, Synechocystis sp. PCC 6803. Curr Microbiol. 2000;40(4):283–7. 10688700.

23. Ratajczak E, Zietkiewicz S, Liberek K. Distinct activities of Escherichia coli small heat shock proteins IbpA and IbpB promote efficient protein disaggregation. J Mol Biol. 2009;386(1):178–89. doi: 10.1016/j.jmb.2008.12.009 19101567.

24. Matuszewska M, Kuczynska-Wisnik D, Laskowska E, Liberek K. The small heat shock protein IbpA of Escherichia coli cooperates with IbpB in stabilization of thermally aggregated proteins in a disaggregation competent state. J Biol Chem. 2005;280(13):12292–8. doi: 10.1074/jbc.M412706200 15665332.

25. Rosenzweig R, Moradi S, Zarrine-Afsar A, Glover JR, Kay LE. Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction. Science. 2013;339(6123):1080–3. Epub 2013/02/09. doi: 10.1126/science.1233066 23393091.

26. Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, et al. A tightly regulated molecular toggle controls AAA+ disaggregase. Nat Struct Mol Biol. 2012;19(12):1338–46. doi: 10.1038/nsmb.2441 23160353.

27. Seyffer F, Kummer E, Oguchi Y, Winkler J, Kumar M, Zahn R, et al. Hsp70 proteins bind Hsp100 regulatory M domains to activate AAA+ disaggregase at aggregate surfaces. Nat Struct Mol Biol. 2012;19(12):1347–55. doi: 10.1038/nsmb.2442 23160352.

28. Miot M, Reidy M, Doyle SM, Hoskins JR, Johnston DM, Genest O, et al. Species-specific collaboration of heat shock proteins (Hsp) 70 and 100 in thermotolerance and protein disaggregation. Proc Natl Acad Sci U S A. 2011;108(17):6915–20. doi: 10.1073/pnas.1102828108 21474779; PubMed Central PMCID: PMC3084080.

29. Allen SP, Polazzi JO, Gierse JK, Easton AM. Two novel heat shock genes encoding proteins produced in response to heterologous protein expression in Escherichia coli. J Bacteriol. 1992;174(21):6938–47. doi: 10.1128/jb.174.21.6938-6947.1992 1356969; PubMed Central PMCID: PMC207373.

30. Laskowska E, Wawrzynow A, Taylor A. IbpA and IbpB, the new heat-shock proteins, bind to endogenous Escherichia coli proteins aggregated intracellularly by heat shock. Biochimie. 1996;78(2):117–22. doi: 10.1016/0300-9084(96)82643-5 WOS:A1996UT23000009. 8818220

31. Kitagawa M, Miyakawa M, Matsumura Y, Tsuchido T. Escherichia coli small heat shock proteins, IbpA and IbpB, protect enzymes from inactivation by heat and oxidants. European Journal of Biochemistry. 2002;269(12):2907–17. doi: 10.1046/j.1432-1033.2002.02958.x WOS:000176298700011. 12071954

32. Mogk A, Schlieker C, Friedrich KL, Schonfeld HJ, Vierling E, Bukau B. Refolding of substrates bound to small Hsps relies on a disaggregation reaction mediated most efficiently by ClpB/DnaK. J Biol Chem. 2003;278(33):31033–42. doi: 10.1074/jbc.M303587200 12788951.

33. Shearstone JR, Baneyx F. Biochemical characterization of the small heat shock protein IbpB from Escherichia coli. J Biol Chem. 1999;274(15):9937–45. doi: 10.1074/jbc.274.15.9937 10187768.

34. Lerat E, Daubin V, Moran NA. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol. 2003;1(1):E19. doi: 10.1371/journal.pbio.0000019 12975657; PubMed Central PMCID: PMC193605.

35. Williams KP, Gillespie JJ, Sobral BWS, Nordberg EK, Snyder EE, Shallom JM, et al. Phylogeny of Gammaproteobacteria. J Bacteriol. 2010;192(9):2305–14. doi: 10.1128/JB.01480-09 WOS:000276685800003. 20207755

36. Gao B, Mohan R, Gupta RS. Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol Micr. 2009;59 : 234–47. doi: 10.1099/ijs.0.002741–0 WOS:000263576500006.

37. De Maayer P, Cowan DA. Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae. BMC Genomics. 2016;17 : 377. doi: 10.1186/s12864-016-2735-x 27206480; PubMed Central PMCID: PMC4875605.

38. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Micr. 2016;66 : 5575–99. doi: 10.1099/ijsem.0.001485 WOS:000393357900103. 27620848

39. Tao J, Sang Y, Teng Q, Ni J, Yang Y, Tsui SK, et al. Heat shock proteins IbpA and IbpB are required for NlpI-participated cell division in Escherichia coli. Front Microbiol. 2015;6 : 51. doi: 10.3389/fmicb.2015.00051 25699035; PubMed Central PMCID: PMC4316790.

40. Butland G, Peregrin-Alvarez JM, Li J, Yang WH, Yang XC, Canadien V, et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005;433(7025):531–7. doi: 10.1038/nature03239 WOS:000226727200051. 15690043

41. Strozecka J, Chrusciel E, Gorna E, Szymanska A, Zietkiewicz S, Liberek K. Importance of N -⁠ and C-terminal regions of IbpA, Escherichia coli small heat shock protein, for chaperone function and oligomerization. J Biol Chem. 2012;287(4):2843–53. doi: 10.1074/jbc.M111.273847 22139842; PubMed Central PMCID: PMC3268442.

42. Shi X, Yan L, Zhang H, Sun K, Chang Z, Fu X. Differential degradation for small heat shock proteins IbpA and IbpB is synchronized in Escherichia coli: implications for their functional cooperation in substrate refolding. Biochem Biophys Res Commun. 2014;452(3):402–7. doi: 10.1016/j.bbrc.2014.08.084 25173932.

43. Bissonnette SA, Rivera-Rivera I, Sauer RT, Baker TA. The IbpA and IbpB small heat-shock proteins are substrates of the AAA plus Lon protease. Molecular Microbiology. 2010;75(6):1539–49. doi: 10.1111/j.1365-2958.2010.07070.x WOS:000275396200016. 20158612

44. Kirschner M, Winkelhaus S, Thierfelder JM, Nover L. Transient expression and heat-stress-induced co-aggregation of endogenous and heterologous small heat-stress proteins in tobacco protoplasts. Plant J. 2000;24(3):397–411. doi: 10.1046/j.1365-313x.2000.00887.x 11069712.

45. Basha E, Jones C, Wysocki V, Vierling E. Mechanistic differences between two conserved classes of small heat shock proteins found in the plant cytosol. J Biol Chem. 2010;285(15):11489–97. doi: 10.1074/jbc.M109.074088 20145254; PubMed Central PMCID: PMC2857027.

46. Arrigo AP. Human small heat shock proteins: Protein interactomes of homo -⁠ and hetero-oligomeric complexes: An update. Febs Lett. 2013;587(13):1959–69. doi: 10.1016/j.febslet.2013.05.011 WOS:000320910300019. 23684648

47. Slingsby C, Wistow GJ, Clark AR. Evolution of crystallins for a role in the vertebrate eye lens. Protein Sci. 2013;22(4):367–+. doi: 10.1002/pro.2229 WOS:000316623900001. 23389822

48. Bepperling A, Alte F, Kriehuber T, Braun N, Weinkauf S, Groll M, et al. Alternative bacterial two-component small heat shock protein systems. Proc Natl Acad Sci U S A. 2012;109(50):20407–12. Epub 2012/11/28. doi: 10.1073/pnas.1209565109 23184973; PubMed Central PMCID: PMC3528540.

49. Specht S, Miller SBM, Mogk A, Bukau B. Hsp42 is required for sequestration of protein aggregates into deposition sites in Saccharomyces cerevisiae. J Cell Biol. 2011;195(4):617–29. doi: 10.1083/jcb.201106037 WOS:000297206400010. 22065637

50. Hochberg GKA, Shepherd DA, Marklund EG, Santhanagoplan I, Degiacomi MT, Laganowsky A, et al. Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science. 2018;359(6378):930–4. doi: 10.1126/science.aam7229 WOS:000425752600048. 29472485

51. Altenhoff AM, Skunca N, Glover N, Train CM, Sueki A, Pilizota I, et al. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res. 2015;43(Database issue):D240–9. doi: 10.1093/nar/gku1158 25399418; PubMed Central PMCID: PMC4383958.

52. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7 : 539. doi: 10.1038/msb.2011.75 21988835; PubMed Central PMCID: PMC3261699.

53. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. doi: 10.1093/bioinformatics/btu033 24451623; PubMed Central PMCID: PMC3998144.

54. Altenhoff AM, Gil M, Gonnet GH, Dessimoz C. Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS One. 2013;8(1):e53786. doi: 10.1371/journal.pone.0053786 23342000; PubMed Central PMCID: PMC3544860.

55. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25(7):1307–20. doi: 10.1093/molbev/msn067 18367465.

56. Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011;27(8):1164–5. doi: 10.1093/bioinformatics/btr088 21335321; PubMed Central PMCID: PMC5215816.

57. Reisch CR, Prather KLJ. The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli. Sci Rep-Uk. 2015;5. ARTN 15096 doi: 10.1038/srep15096 WOS:000362720700001. 26463009