Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D

Journal of Bacteriology

Volumn 194, Issue 4, 2012, Pages 787-795

  Roberts, Evan W ^a   Cai, Fei ^b   Kerfeld, Cheryl A ^b,c   Cannon, Gordon C ^a   Heinhorst, Sabine ^a  

^a The University of Southern Mississippi   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARBOXYSOME; CSOS1D PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIUM ISOLATION; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; PROCHLOROCOCCUS; PROCHLOROCOCCUS MARINUS; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN PURIFICATION;

BACTERIAL PROTEINS; CARBONIC ANHYDRASES; CYTOPLASMIC STRUCTURES; PROCHLOROCOCCUS; RIBULOSE-BISPHOSPHATE CARBOXYLASE;

CYANOBACTERIA; PROCHLOROCOCCUS; PROCHLOROCOCCUS MARINUS;

EID: 84857065808     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.06444-11     Document Type: Article

References (45)

1. 2 concentrating mechanisms in cyanobacteria. Funct. Plant Biol. 29: 161-173.
2. Beller HR, et al. 2006. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J. Bacteriol. 188:1473-1488.
3. Cai F, Heinhorst S, Shively J, Cannon G. 2008. Transcript analysis of the Halothiobacillus neapolitanus cso operon. Arch. Microbiol. 189:141-150.
4. 2 leakage barrier. PLoS One 4:e7521.
5. Cannon GC, et al. 2003. Organization of carboxysome genes in the thiobacilli. Curr. Microbiol. 46:115-119.
6. Cannon GC, Heinhorst S, Bradburne CE, Shively JM. 2002. Carboxysome genomics: a status report. Funct. Plant Biol. 29:175-182.
7. 2 fixation. Biochim. Biophys. Acta. 1804:382-392.
8. Cannon GC, Shively JM. 1983. Characterization of a homogenous preparation of carboxysomes from Thiobacillus neapolitanus. Arch. Microbiol. 134:52-59.
9. Chen X, et al. 2004. Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. Nucleic Acids Res. 32:2147-2157.
10. Dereeper A, et al. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36:W465-W469.
11. 2. J. Biol. Chem. 283:10377-10384.
12. Golden JS, Harrison SC. 1982. Proteolytic dissection of turnip crinkle virus subunit in solution. Biochemistry 21:3862-3866.
13. 2-concentrating mechanism in the open-ocean cyanobacterium Synechococcus WH8102. Can. J. Bot. 83:735-745.
14. 2 specificity determination and identification of side products. Anal. Biochem. 209: 367-374.
15. Heinhorst S, Cannon GC, Shively JM. 2006. Carboxysomes and carboxysome-like inclusions, p 141-164. In Shively (ed), J. M. Complex intracellular structures in prokaryotes, vol 2. Springer, Berlin, Germany.
16. Heinhorst S, et al. 2006. Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus. J. Bacteriol. 188: 8087-8094.
17. Huson D, et al. 2007. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 8:460.
18. Iancu CV, et al. 2010. Organization, structure, and assembly of [alpha]-carboxysomes determined by electron cryotomography of intact cells. J. Mol. Biol. 396:105-117.
19. Jacob E, Sasikumar R, Nair KNR. 2005. A fuzzy guided genetic algorithm for operon prediction. Bioinformatics 21:1403-1407.
20. 2 concentrating mechanisms in photosynthetic microorganisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 539-570.
21. Khalifah RG. 1971. The carbon dioxide hydration activity of carbonic anhydrase. I. Stop-flow kinetic studies on the native human isoenzymes B and C. J. Biol. Chem. 246:2561-2573.
22. Klein MG, et al. 2009. Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J. Mol. Biol. 392:319-333.
23. Maeda S, Badger MR, Price GD. 2002. Novel gene products associated with NdhD3/D4-containing NDH-1 complexes are involved in photosynthetic CO2 hydration in the cyanobacterium, Synechococcus sp. PCC7942. Mol. Microbiol. 43:425-435.
24. Moore LR, et al. 2007. Culturing the marine cyanobacterium Prochlorococcus. Limnol. Oceanogr. Methods 5:353-362.
25. Mueller-Cajar O, et al. 2011. Structure and function of the AAA+protein CbbX, a red-type Rubisco activase. Nature 479:194-199.
26. Notredame C, Higgins DG, Jheringa. 2000. T-COFFEE: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
27. Partensky F, Hess WR, Vaulot D. 1999. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63:106-127.
28. 2-concentrating-mechanism (CCM): functional components, Ci transporters, diversity, genetic regulation and prospects for engineering into plants. J. Exp. Bot. 59:1441-1461.
29. Price GD, Coleman JR, Badger MR. 1992. Association of carbonic anhydrase activity with carboxysomes isolated from the cyanobacterium Synechococcus PCC7942. Plant Physiol. 100:784-793.
30. Price GD, Woodger FJ, Badger MR, Howitt SM, Tucker L. 2004. Identification of a SulP-type bicarbonate transporter in marine cyanobacteria. Proc. Natl. Acad. Sci. U. S. A. 101:18228-18233.
31. Price MN, Huang KH, Alm EJ, Arkin AP. 2005. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33:880-892.
32. Rocap G, et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042-1047.
33. Rodriguez-Buey ML, Marco E, Orus MI. 2005. Isolation of Synechococcus PCC7942 carboxysomes. Ann. Microbiol. 55:81-84.
34. Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J. 2000. Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl. Acad. Sci. U. S. A. 97:6652-6657.
35. Scott KM, et al. 2007. Kinetic isotope effect and biochemical characterization of form IA RubisCO from the marine cyanobacterium Prochlorococcus marinus MIT9313. Limnol. Oceanogr. 52:2199-2204.
36. Shibata M, et al. 2002. Genes essential to sodium-dependent bicarbonate transport in cyanobacteria: function and phylogenetic analysis. J. Biol. Chem. 277:18658-18664.
37. Shively JM, English RS. 1991. The carboxysome, a prokaryotic organelle: a mini review. Can. J. Bot. 69:957-962.
38. Smith KS, Ferry JG. 2000. Prokaryotic carbonic anhydrases. FEMS Microbiol. Rev. 24:335-366.
39. So AK-C, et al. 2004. A novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell. J. Bacteriol. 186: 623-630.
40. Suck D, Ficner R. 1996. Structure and function of PCD/DCoH, an enzyme with regulatory properties. FEBS Lett. 389:35-39.
41. Ting CS, Hsieh C, Sundararaman S, Mannella C, Marko M. 2007. Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium. J. Bacteriol. 189:4485-4493.
42. Wang H-L, Postier BL, Burnap RL. 2004. Alterations in global patterns of gene expression in Synechocystis sp. PCC 6803 in response to inorganic carbon limitation and the inactivation of ndhR, a LysR family regulator. J. Biol. Chem. 279:5739-5751.
43. Wu M, Eisen J. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9:R151.
44. Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM. 2008. Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat. Rev. Microbiol. 6:681-691.
45. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S. 2002. Computational identification of operons in microbial genomes. Genome Res. 12:1221-1230.