Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components

English version

Autoři: Luis F. Garcia-Alles ^aff001; Katharina Root ^aff002; Laurent Maveyraud ^aff003; Nathalie Aubry ^aff001; Eric Lesniewska ^aff004; Lionel Mourey ^aff003; Renato Zenobi ^aff002; Gilles Truan ^aff001
Působiště autorů: Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France ^aff001; Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland ^aff002; Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France ^aff003; ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France ^aff004
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0223877

Souhrn

The carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted the localization of interactions that would favor formation of CcmK3/K4 hetero-hexamers. The crystallization of these CcmK3/K4 associations conducted to the elucidation of a structure corresponding to the CcmK4 homo-hexamer. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed within the context of reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.

Klíčová slova:

Crystal structure – Crystallization – Electrostatics – Monomers – Signal processing – Stoichiometry – Operons – Macromolecular engineering

Zdroje

1. Kerfeld CA, Aussignargues C, Zarzycki J, Cai F, Sutter M. Bacterial microcompartments. Nat Rev Microbiol. 2018;16(5):277–90. Epub 2018/03/05. doi: 10.1038/nrmicro.2018.10 29503457.

2. Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. Diverse bacterial microcompartment organelles. Microbiol Mol Biol Rev. 2014;78(3):438–68. doi: 10.1128/MMBR.00009-14 25184561.

3. Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol. 2014;10(10):e1003898. Epub 2014/10/23. doi: 10.1371/journal.pcbi.1003898 25340524.

4. Kinney J, Salmeen A, Cai F, Kerfeld C. Elucidating Essential Role of Conserved Carboxysomal Protein CcmN Reveals Common Feature of Bacterial Microcompartment Assembly. Journal of Biological Chemistry. 2012;287(21):17729–36. doi: 10.1074/jbc.M112.355305 22461622

5. Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, et al. Short N-terminal sequences package proteins into bacterial microcompartments. Proc Natl Acad Sci U S A. 2010;107(16):7509–14. doi: 10.1073/pnas.0913199107

6. Lawrence AD, Frank S, Newnham S, Lee MJ, Brown IR, Xue WF, et al. Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synth Biol. 2014;3(7):454–65. Epub 2014/02/24. doi: 10.1021/sb4001118 24933391.

7. Cai F, Sutter M, Bernstein SL, Kinney JN, Kerfeld CA. Engineering bacterial microcompartment shells: chimeric shell proteins and chimeric carboxysome shells. ACS Synth Biol. 2015;4(4):444–53. Epub 2014/08/27. doi: 10.1021/sb500226j 25117559.

8. Slininger Lee MF, Jakobson CM, Tullman-Ercek D. Evidence for Improved Encapsulated Pathway Behavior in a Bacterial Microcompartment through Shell Protein Engineering. ACS Synth Biol. 2017;6(10):1880–91. Epub 2017/06/21. doi: 10.1021/acssynbio.7b00042 28585808.

9. Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, et al. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci U S A. 2012;109(2):478–83. doi: 10.1073/pnas.1108557109 22184212.

10. Cai F, Bernstein SL, Wilson SC, Kerfeld CA. Production and Characterization of Synthetic Carboxysome Shells with Incorporated Luminal Proteins. Plant Physiol. 2016;170(3):1868–77. Epub 2016/01/20. 26792123.

11. Parsons JB, Dinesh SD, Deery E, Leech HK, Brindley AA, Heldt D, et al. Biochemical and structural insights into bacterial organelle form and biogenesis. J Biol Chem. 2008;283(21):14366–75. doi: 10.1074/jbc.M709214200 18332146.

12. Fang Y, Huang F, Faulkner M, Jiang Q, Dykes GF, Yang M, et al. Engineering and Modulating Functional Cyanobacterial CO. Front Plant Sci. 2018;9:739. Epub 2018/06/05. doi: 10.3389/fpls.2018.00739 29922315.

13. Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, et al. Protein structures forming the shell of primitive bacterial organelles. Science. 2005;309(5736):936–8. doi: 10.1126/science.1113397 16081736.

14. Tanaka S, Sawaya MR, Yeates TO. Structure and mechanisms of a protein-based organelle in Escherichia coli. Science. 2010;327(5961):81–4. doi: 10.1126/science.1179513 20044574.

15. Samborska B, Kimber MS. A dodecameric CcmK2 structure suggests β-carboxysomal shell facets have a double-layered organization. Structure. 2012;20(8):1353–62. doi: 10.1016/j.str.2012.05.013 22748766.

16. Crowley CS, Sawaya MR, Bobik TA, Yeates TO. Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure. 2008;16(9):1324–32. doi: 10.1016/j.str.2008.05.013 18786396.

17. Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. PLoS One. 2012;7(10):e48360. Epub 2012/10/29. doi: 10.1371/journal.pone.0048360 23144756.

18. Mallette E, Kimber MS. A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport. J Biol Chem. 2017;292(4):1197–210. Epub 2016/12/06. doi: 10.1074/jbc.M116.754093 27927988.

19. Cai F, Sutter M, Cameron JC, Stanley DN, Kinney JN, Kerfeld CA. The structure of CcmP, a tandem bacterial microcompartment domain protein from the β-carboxysome, forms a subcompartment within a microcompartment. J Biol Chem. 2013;288(22):16055–63. doi: 10.1074/jbc.M113.456897 23572529.

20. Heldt D, Frank S, Seyedarabi A, Ladikis D, Parsons JB, Warren MJ, et al. Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri. Biochem J. 2009;423(2):199–207. Epub 2009/09/25. doi: 10.1042/BJ20090780 19635047.

21. Dryden K, Crowley C, Tanaka S, Yeates T, Yeager M. Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals. Protein Science. 2009;18(12):2629–35. doi: 10.1002/pro.272 19844993

22. Sutter M, Faulkner M, Aussignargues C, Paasch BC, Barrett S, Kerfeld CA, et al. Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy. Nano Lett. 2016;16(3):1590–5. Epub 2015/12/07. doi: 10.1021/acs.nanolett.5b04259 26617073.

23. Garcia-Alles LF, Lesniewska E, Root K, Aubry N, Pocholle N, Mendoza CI, et al. Spontaneous non-canonical assembly of CcmK hexameric components from β-carboxysome shells of cyanobacteria. PLoS One. 2017;12(9):e0185109. Epub 2017/09/21. doi: 10.1371/journal.pone.0185109 28934279.

24. Iancu CV, Ding HJ, Morris DM, Dias DP, Gonzales AD, Martino A, et al. The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography. J Mol Biol. 2007;372(3):764–73. Epub 2007/06/29. doi: 10.1016/j.jmb.2007.06.059 17669419.

25. Schmid MF, Paredes AM, Khant HA, Soyer F, Aldrich HC, Chiu W, et al. Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J Mol Biol. 2006;364(3):526–35. Epub 2006/09/14. doi: 10.1016/j.jmb.2006.09.024 17028023.

26. Kaneko Y, Danev R, Nagayama K, Nakamoto H. Intact carboxysomes in a cyanobacterial cell visualized by hilbert differential contrast transmission electron microscopy. J Bacteriol. 2006;188(2):805–8. doi: 10.1128/JB.188.2.805-808.2006 16385071.

27. Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, et al. Atomic-level models of the bacterial carboxysome shell. Science. 2008;319(5866):1083–6. doi: 10.1126/science.1151458 18292340.

28. Wheatley NM, Gidaniyan SD, Liu Y, Cascio D, Yeates TO. Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins. Protein Sci. 2013;22(5):660–5. Epub 2013/04/08. doi: 10.1002/pro.2246 23456886.

29. Forouhar F, Kuzin A, Seetharaman J, Lee I, Zhou W, Abashidze M, et al. Functional insights from structural genomics. J Struct Funct Genomics. 2007;8(2–3):37–44. Epub 2007/06/23. doi: 10.1007/s10969-007-9018-3 17588214.

30. Sutter M, Greber B, Aussignargues C, Kerfeld CA. Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell. Science. 2017;356(6344):1293–7. doi: 10.1126/science.aan3289 28642439.

31. Pang A, Frank S, Brown I, Warren MJ, Pickersgill RW. Structural insights into higher order assembly and function of the bacterial microcompartment protein PduA. J Biol Chem. 2014;289(32):22377–84. Epub 2014/05/29. doi: 10.1074/jbc.M114.569285 24873823.

32. Young EJ, Burton R, Mahalik JP, Sumpter BG, Fuentes-Cabrera M, Kerfeld CA, et al. Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications. Front Microbiol. 2017;8:1441. Epub 2017/07/31. doi: 10.3389/fmicb.2017.01441 28824573.

33. Yeates T, Kerfeld C, Heinhorst S, Cannon G, Shively J. Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nature Reviews Microbiology. 2008;6(9):681–91. doi: 10.1038/nrmicro1913 18679172

34. Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, et al. Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells. Plant Physiol. 2019;179(1):156–67. Epub 2018/11/02. doi: 10.1104/pp.18.01190 30389783.

35. Studier FW. Protein production by auto-induction in high density shaking cultures. Protein Expr Purif. 2005;41(1):207–34. 15915565.

36. Kröner F, Hubbuch J. Systematic generation of buffer systems for pH gradient ion exchange chromatography and their application. J Chromatogr A. 2013;1285:78–87. Epub 2013/02/14. doi: 10.1016/j.chroma.2013.02.017 23489486.

37. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr. 2007;40(Pt 4):658–74. Epub 2007/07/13. doi: 10.1107/S0021889807021206 19461840.

38. Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2011;67(Pt 4):355–67. Epub 2011/03/18. doi: 10.1107/S0907444911001314 21460454.

39. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010;66(Pt 4):486–501. Epub 2010/03/24. doi: 10.1107/S0907444910007493 20383002.

40. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr. 2011;67(Pt 4):235–42. Epub 2011/03/18. doi: 10.1107/S0907444910045749 21460441.

41. Tanaka S, Sawaya MR, Phillips M, Yeates TO. Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein Sci. 2009;18(1):108–20. doi: 10.1002/pro.14 19177356.

42. Kopf M, Klähn S, Scholz I, Matthiessen JK, Hess WR, Voß B. Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803. DNA Res. 2014;21(5):527–39. Epub 2014/06/16. doi: 10.1093/dnares/dsu018 24935866.

43. Sommer M, Cai F, Melnicki M, Kerfeld CA. β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. J Exp Bot. 2017;68(14):3841–55. doi: 10.1093/jxb/erx115 28419380.

44. Root K. Doctoral Thesis: Dissecting Non-covalent Interactions in Oligomeric Protein Complexes by Native Mass Spectrometry. ETH Zurich2018.

45. Abdul-Rahman F, Petit E, Blanchard JL. The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly. Journal of Phylogenetics and Evolutionary Biology. 2013;1:118. doi: 10.4172/2329-9002.1000118

46. Sturms R, Streauslin NA, Cheng S, Bobik TA. In Salmonella enterica, Ethanolamine Utilization Is Repressed by 1,2-Propanediol To Prevent Detrimental Mixing of Components of Two Different Bacterial Microcompartments. J Bacteriol. 2015;197(14):2412–21. Epub 2015/05/11. doi: 10.1128/JB.00215-15 25962913.

47. Lidón-Moya MC, Barrera FN, Bueno M, Pérez-Jiménez R, Sancho J, Mateu MG, et al. An extensive thermodynamic characterization of the dimerization domain of the HIV-1 capsid protein. Protein Sci. 2005;14(9):2387–404. doi: 10.1110/ps.041324305 16131662.

48. Rae BD, Long BM, Badger MR, Price GD. Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL. PLoS One. 2012;7(8):e43871. doi: 10.1371/journal.pone.0043871 22928045.

49. Zhang S, Laborde SM, Frankel LK, Bricker TM. Four novel genes required for optimal photoautotrophic growth of the cyanobacterium Synechocystis sp. strain PCC 6803 identified by in vitro transposon mutagenesis. J Bacteriol. 2004;186(3):875–9. doi: 10.1128/JB.186.3.875-879.2004 14729717.

50. Sun Y, Wollman AJM, Huang F, Leake MC, Liu LN. Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment. Plant Cell. 2019;31(7):1648–64. Epub 2019/05/02. doi: 10.1105/tpc.18.00787 31048338.

51. Faulkner M, Rodriguez-Ramos J, Dykes GF, Owen SV, Casella S, Simpson DM, et al. Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes. Nanoscale. 2017;9(30):10662–73. doi: 10.1039/c7nr02524f 28616951.

52. Sinha S, Cheng S, Sung YW, McNamara DE, Sawaya MR, Yeates TO, et al. Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment. J Mol Biol. 2014;426(12):2328–45. Epub 2014/04/18. doi: 10.1016/j.jmb.2014.04.012 24747050.

53. Cameron JC, Wilson SC, Bernstein SL, Kerfeld CA. Biogenesis of a bacterial organelle: the carboxysome assembly pathway. Cell. 2013;155(5):1131–40. doi: 10.1016/j.cell.2013.10.044 24267892.

54. Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS One. 2013;8(9):e76127. doi: 10.1371/journal.pone.0076127 24023971.

55. MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, et al. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. Elife. 2018;7. Epub 2018/12/06. doi: 10.7554/eLife.39723 30520729.

56. Hagen AR, Plegaria JS, Sloan N, Ferlez B, Aussignargues C, Burton R, et al. In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures. Nano Lett. 2018;18(11):7030–7. Epub 2018/10/31. doi: 10.1021/acs.nanolett.8b02991 30346795.

Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components

Souhrn

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