Advertisement

Photosynthesis Research

, Volume 118, Issue 1–2, pp 9–16 | Cite as

Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species

  • Markus Sutter
  • Steven C. Wilson
  • Samuel Deutsch
  • Cheryl A. KerfeldEmail author
Regular Paper

Abstract

Cyanobacteria have evolved a unique carbon fixation organelle known as the carboxysome that compartmentalizes the enzymes RuBisCO and carbonic anhydrase. This effectively increases the local CO2 concentration at the active site of RuBisCO and decreases its relatively unproductive side reaction with oxygen. Carboxysomes consist of a protein shell composed of hexameric and pentameric proteins arranged in icosahedral symmetry. Facets composed of hexameric proteins are connected at the vertices by pentameric proteins. Structurally homologous pentamers and hexamers are also found in heterotrophic bacteria where they form architecturally related microcompartments such as the Eut and Pdu organelles for the metabolism of ethanolamine and propanediol, respectively. Here we describe two new high-resolution structures of the pentameric shell protein CcmL from the cyanobacteria Thermosynechococcus elongatus and Gloeobacter violaceus and provide detailed analysis of their characteristics and comparison with related shell proteins.

Keywords

Cyanobacteria Microcompartment Carboxysome CcmL 

Notes

Acknowledgments

We would like to thank the entire staff at the Advanced Light Source, Lawrence Berkeley National Laboratory, which is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. CAK and SCW are supported by the NSF (EF1105897). MS was supported by a Swiss National Science Foundation Postdoctoral Fellowship.

Supplementary material

11120_2013_9909_MOESM1_ESM.doc (155 kb)
Supplementary material 1 (DOC 155 kb)

References

  1. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D 68:352–367. doi: 10.1107/S0907444912001308 PubMedCrossRefGoogle Scholar
  2. Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, Keasling JD (2010) BglBricks: a flexible standard for biological part assembly. J Biol Eng 4(1):1PubMedCrossRefGoogle Scholar
  3. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98(18):10037–10041. doi: 10.1073/pnas.181342398 PubMedCrossRefGoogle Scholar
  4. Bobik TA, Havemann GD, Busch RJ, Williams DS, Aldrich HC (1999) The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B12-dependent 1,2-propanediol degradation. J Bacteriol 181(19):5967–5975PubMedGoogle Scholar
  5. Cai F, Menon BB, Cannon GC, Curry KJ, Shively JM, Heinhorst S (2009) The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier. PLoS One 4(10):e7521PubMedCrossRefGoogle Scholar
  6. Cai F, Sutter M, Cameron JC, Stanley DN, Kinney JN, Kerfeld CA (2013) The structure of CcmP, a tandem bacterial microcompartment domain protein from the beta-carboxysome, forms a subcompartment within a microcompartment. J Biol Chem 288(22):16055–16063. doi: 10.1074/jbc.M113.456897 PubMedCrossRefGoogle Scholar
  7. Cot SS, So AK, Espie GS (2008) A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria. J Bacteriol 190(3):936–945PubMedCrossRefGoogle Scholar
  8. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60(Pt 12 Pt 1):2126–2132. doi: 10.1107/S0907444904019158 PubMedCrossRefGoogle Scholar
  9. Forouhar F, Kuzin A, Seetharaman J, Lee I, Zhou W, Abashidze M, Chen Y, Yong W, Janjua H, Fang Y, Wang D, Cunningham K, Xiao R, Acton TB, Pichersky E, Klessig DF, Porter CW, Montelione GT, Tong L (2007) Functional insights from structural genomics. J Struct Funct Genomics 8(2–3):37–44. doi: 10.1007/s10969-007-9018-3 PubMedCrossRefGoogle Scholar
  10. Hess WR, Rocap G, Ting CS, Larimer F, Stilwagen S, Lamerdin J, Chisholm SW (2001) The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics. Photosynth Res 70(1):53–71. doi: 10.1023/A:1013835924610 PubMedCrossRefGoogle Scholar
  11. Iancu CV, Morris DM, Dou Z, Heinhorst S, Cannon GC, Jensen GJ (2010) Organization, structure, and assembly of alpha-carboxysomes determined by electron cryotomography of intact cells. J Mol Biol 396(1):105–117PubMedCrossRefGoogle Scholar
  12. Karplus PA, Diederichs K (2012) Linking crystallographic model and data quality. Science 336(6084):1030–1033. doi: 10.1126/science.1218231 Google Scholar
  13. Kerfeld CA, Sawaya, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO (2005) Protein structures forming the shell of primitive bacterial organelles. Science 309(5736):936–938PubMedCrossRefGoogle Scholar
  14. Kerfeld CA, Heinhorst S, Cannon GC (2010) Bacterial microcompartments. Annu Rev Microbiol 64:391–408PubMedCrossRefGoogle Scholar
  15. Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA (2009) Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392(2):319–333PubMedCrossRefGoogle Scholar
  16. Kofoid E, Rappleye C, Stojiljkovic I, Roth J (1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181(17):5317–5329PubMedGoogle Scholar
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948. doi: 10.1093/bioinformatics/btm404 PubMedCrossRefGoogle Scholar
  18. Li Y, Conway JF, Cheng N, Steven AC, Hendrix RW, Duda RL (2005) Control of virus assembly: HK97 “whiffleball” mutant capsids without pentons. J Mol Biol 348(1):167–182. doi: 10.1016/j.jmb.2005.02.045 PubMedCrossRefGoogle Scholar
  19. Long BM, Badger MR, Whitney SM, Price GD (2007) Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple RuBisCO complexes with carboxysomal proteins CcmM and CcaA. J Biol Chem 282(40):29323–29335PubMedCrossRefGoogle Scholar
  20. Price GD, Badger MR (1989) Isolation and characterization of high CO(2)-requiring-mutants of the cyanobacterium Synechococcus PCC7942: two phenotypes that accumulate inorganic carbon but are apparently unable to generate CO(2) within the carboxysome. Plant Physiol 91(2):514–525PubMedCrossRefGoogle Scholar
  21. Price GD, Howitt SM, Harrison K, Badger MR (1993) Analysis of a genomic DNA region from the cyanobacterium Synechococcus sp. strain PCC7942 involved in carboxysome assembly and function. J Bacteriol 175(10):2871–2879PubMedGoogle Scholar
  22. Quan J, Saaem I, Tang N, Ma S, Negre N, Gong H, White KP, Tian J (2011) Parallel on-chip gene synthesis and application to optimization of protein expression. Nat Biotechnol 29(5):449–452. doi: 10.1038/nbt.1847 PubMedCrossRefGoogle Scholar
  23. Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD (2006) GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res 16(4):550–556. doi: 10.1101/gr.4431306 PubMedCrossRefGoogle Scholar
  24. Samborska B, Kimber MS (2012) A dodecameric CcmK2 structure suggests beta-carboxysomal shell facets have a double-layered organization. Structure 20(8):1353–1362. doi: 10.1016/j.str.2012.05.013 PubMedCrossRefGoogle Scholar
  25. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18(20):6097–6100PubMedCrossRefGoogle Scholar
  26. Smart OS, Goodfellow JM, Wallace BA (1993) The pore dimensions of gramicidin A. Biophys J 65(6):2455–2460. doi: 10.1016/S0006-3495(93)81293-1 PubMedCrossRefGoogle Scholar
  27. Smith HO, Hutchison CA 3rd, Pfannkoch C, Venter JC (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA 100(26):15440–15445. doi: 10.1073/pnas.2237126100 PubMedCrossRefGoogle Scholar
  28. Tanaka S, Kerfeld CA, Sawaya, Cai F, Heinhorst S, Cannon GC, Yeates TO (2008) Atomic-level models of the bacterial carboxysome shell. Science 319(5866):1083–1086PubMedCrossRefGoogle Scholar
  29. Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO (2007) Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol 5(6):e144PubMedCrossRefGoogle Scholar
  30. Wheatley NM, Gidaniyan SD, Liu Y, Cascio D, Yeates TO (2013) Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins. Protein Sci. doi: 10.1002/pro.2246 Google Scholar
  31. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67(Pt 4):235–242. doi: 10.1107/S0907444910045749 PubMedCrossRefGoogle Scholar
  32. Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6(9):681–691PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Markus Sutter
    • 1
  • Steven C. Wilson
    • 2
  • Samuel Deutsch
    • 1
  • Cheryl A. Kerfeld
    • 1
    • 2
    • 3
    Email author
  1. 1.United States Department of Energy – Joint Genome InstituteWalnut CreekUSA
  2. 2.Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyUSA
  3. 3.Berkeley Synthetic Biology InstituteBerkeleyUSA

Personalised recommendations