Membrane proteome of the green sulfur bacterium Chlorobium tepidum (syn. Chlorobaculum tepidum) analyzed by gel-based and gel-free methods

Photosynthesis Research

Volumn 104, Issue 2, 2010, Pages 153-162

  Kouyianou, Kalliopi ^a   Aivaliotis, Michalis ^a,e   Gevaert, Kris ^b,c   Karas, Michael ^d   Tsiotis, Georgios ^a  

^a UNIVERSITY OF CRETE   (Greece)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c GHENT UNIVERSITY   (Belgium)

^d GOETHE UNIVERSITY   (Germany)

^e INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

Author keywords

Blue native; Chlorobium tepidum; Chlorosome; COFRADIC; Green sulfur bacteria; Inner membrane; Mass spectrometric identification; Membrane proteins; Outer membrane; Photosynthesis; Two dimensional polyacryamide gel electrophoresis

Indexed keywords

BACTERIAL PROTEIN; DETERGENT; MEMBRANE PROTEIN; PROTEOME;

CELL MEMBRANE; CHLOROBIUM; CYTOLOGY; DRUG EFFECT; METABOLISM; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEOMICS; REVIEW; SOLUBILITY;

BACTERIAL PROTEINS; CELL MEMBRANE; CHLOROBIUM; DETERGENTS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MEMBRANE PROTEINS; PROTEOME; PROTEOMICS; SOLUBILITY;

BACTERIA (MICROORGANISMS); CHLOROBACULUM TEPIDUM; CHLOROBI; CHLOROBIA; CHLOROBIUM; NEGIBACTERIA;

EID: 77953650538     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11120-010-9544-x     Document Type: Review

References (46)

1. Aivaliotis M, Samolis P, Neofotistou E, Remigy H, Rizos A, Tsiotis G (2003) Molecular size determination of a membrane protein in surfactants by light scattering. Biochimica Et Biophysica Acta 1615: 69-76.
2. Aivaliotis M, Corvey C, Tsirogianni I, Karas M, Tsiotis G (2004a) Membrane proteome analysis of the green-sulfur bacterium Chlorobium tepidum. Electrophoresis 25: 3468-3474.
3. Aivaliotis M, Neofotistou E, Remigy H-W, Tsimpinos G, Lustig A, Lottspeich F, Tsiotis G (2004b) Isolation and characterization of an outer membrane protein of Chlorobium tepidum. Photosynth Res 79: 161-166.
4. Aivaliotis M, Karas M, Tsiotis G (2006a) High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of cytoplasmatic protein complexes from Chlorobium tepidum. Photosynth Res 88: 143-157.
5. Aivaliotis M, Haase W, Karas M, Tsiotis G (2006b) Proteomic analysis of chlorosome-depleted membranes of the green sulfur bacterium Chlorobium tepidum. Proteomics 6: 217-232.
6. Aivaliotis M, Karas M, Tsiotis G (2007) An alternative strategy for the membrane proteome analysis of the green sulfur bacterium Chlorobium tepidum using Blue Native PAGE and 2-D PAGE on purified membranes. J Proteome Res 6: 1048-1058.
7. Bernstein HD (2000) The biogenesis and assembly of bacterial membrane proteins. Curr Opin Microbiol 3: 203-209.
8. Brookes PS, Pinner A, Ramachandran A, Coward L, Barnes S, Kim H, Darley-Usmar VM (2002) High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of mitochondria and signaling complexes. Proteomics 2: 969-977.
9. Cavalier-Smith T (2001) Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol 53: 555-595.
10. Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (2002) The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci USA 99: 9509-9514.
11. Evans MC, Buchanan BB, Arnon DI (1966) A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc Natl Acad Sci USA 55: 928-934.
12. Feiler U, Nitschke W, Michel H (1992) Characterization of an improved reaction center preparation from the photosynthetic green sulfur bacterium Chlorobium containing the FeS centers FA and FB and a bound cytochrome subunit. Biochemistry 31: 2608-2614.
13. Frigaard NU, Gomez Maqueo Chew A, Li H, Maresca JA, Bryant DA (2003) Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth Res 78: 93-117.
14. Gevaert K, Damme PV, Martens L, Vandekerckhove J (2005) Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics? Anal Biochem 345: 18-29.
15. Gevaert K, Vandekerckhove J, Julio EC (2006) Nongel-based proteomics: selective reversed-phase chromatographic isolation of methionine-containing peptides from complex peptide mixtures. In: Cell biology, 3rd edn. Academic Press, Burlington, pp 451-455.
16. Golbeck JH (1993) Shared thematic elements in photochemical reaction centers. Proc Natl Acad Sci USA 90: 1642-1646.
17. Hager-Braun C, Xie DL, Jarosch U, Herold E, Buttner M, Zimmermann R, Deutzmann R, Hauska G, Nelson N (1995) Stable photobleaching of P840 in Chlorobium reaction center preparations: presence of the 42-kDa bacteriochlorophyll a protein and a 17-kDa polypeptide. Biochemistry 34: 9617-9624.
18. Hauska G, Schoedl T, Remigy H, Tsiotis G (2001) The reaction center of green sulfur bacteria. Biochim Biophys Acta 1507: 260-277.
19. Hille JM, Freed AL, Wätzig H (2001) Possibilities to improve automation, speed and precision of proteome analysis: a comparison of two-dimensional electrophoresis and alternatives. Electrophoresis 22: 4035-4052.
20. Hofmann K, Stoffel W (1993) TMbase-a database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 374: 166.
21. Hohmann-Marriott MF, Blankenship RE, Roberson RW (2005) The ultrastructure of Chlorobium tepidum chlorosomes revealed by electron microscopy. Photosynth Res 86: 145-154.
22. Kantzilakis K, Aivaliotis M, Kotakis C, Krasanakis F, Rizos AK, Kotzabasis K, Tsiotis G (2007) A comparative approach towards thylakoid membrane proteome analysis of unicellular green alga Scenedesmus obliquus. Biochim Biophys Acta 1768: 2271-2279.
23. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
24. Lelwala-Guruge J, Nilsson I, Ljungh A, Wadstrom T (1992) Cell surface proteins of Helicobacter pylori as antigens in an ELISA and a comparison with three commercial ELISA. Scand J Infect Dis 24: 457-465.
25. Molloy MP, Herbert BR, Slade MB, Rabilloud T, Nouwens AS, Williams KL, Gooley AA (2000) Proteomic analysis of the Escherichia coli outer membrane. Eur J Biochem 267: 2871-2881.
26. Nijtmans LGJ, Henderson NS, Holt IJ (2002) Blue native electrophoresis to study mitochondrial and other protein complexes. Methods 26: 327-334.
27. Nouwens AS, Cordwell SJ, Larsen MR, Molloy MP, Gillings M, Willcox MD, Walsh BJ (2000) Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1. Electrophoresis 21: 3797-3809.
28. Oda Y, Nagasu T, Chait BT (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19: 379-382.
29. Okuyama T, Satake K (1960) On the preparation and properties of 2, 4, 6-trinitrophenyl-amino acids and -peptides. J Biochem 47: 454-466.
30. Olson JM, Giddings TH, Shaw EK (1976) An enriched reaction center preparation from green photosynthetic bacteria. Biochim Biophys Acta 449: 197-208.
31. Orlowski J, Grinstein S (1997) Na+/H+ exchangers of mammalian cells. J Biol Chem 272: 22373-22376.
32. Overmann J (2000) The family Chlorobiaceae. In: Dworkin M III, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes: an evolving electronic resource for the microbiological community. Springer Verlag, New York.
33. Remigy H, Fotiadis D, Wolpensinger B, Mueller SA, Engel A, Tsiotis G (1998) Evidence for the association of three FMO subunits per reaction center of Chlorobium tepidum by scanning transmission electron microscopy. In: Garab G (ed) Photosynthesis: mechanisms and effects, vol I. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 531-534.
34. Remigy HW, Stahlberg H, Fotiadis D, Muller SA, Wolpensinger B, Engel A, Hauska G, Tsiotis G (1999) The reaction center complex from the green sulfur bacterium Chlorobium tepidum: a structural analysis by scanning transmission electron microscopy. J Mol Biol 290: 851-858.
35. Rietschel B, Arrey T, Meyer B, Bornemann S, Schuerken M, Karas M, Poetsch A (2009) Elastase digests: new ammunition for shotgun membrane proteomics. Mol Cell Proteomics 8: 1029-1043.
36. Santoni V, Rabilloud T, Doumas P, Rouquie D, Mansion M, Kieffer S, Garin J, Rossignol M (1999) Towards the recovery of hydrophobic proteins on two-dimensional electrophoresis gels. Electrophoresis 20: 705-711.
37. Schaegger H, von Jagow G (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199: 223-231.
38. Schmidt K (1980) A comparative study on the composition of chlorosomes (Chlorobium vesicles) and the cytoplasmatic membrane from Chloroflexus aurantiacus strain OK-70-fl and Chlorobium limicola f. thiosulfatophilum strain 6230. Arch Microbiol 124: 21-31.
39. Sonnhammer ELL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In: Glasgow J, Major TLF, Lathrop R, Sankoff D, Sensen C (eds) Proceedings of sixth international conference on intelligent systems for molecular biology. AAAI Press, Menlo Park, pp 175-182.
40. Staehelin LA, Golecki JR, Drews G (1980) Supramolecular organization of chlorosomes (chlorobium vesicles) and of their membrane attachment sites in Chlorobium limicola. Biochim Biophys Acta 589: 30-45.
41. Struyve M, Moons M, Tommassen J (1991) Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. J Mol Biol 218: 141-148.
42. Wallin E, von-Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7: 1029-1038.
43. Wang S, Regnier FE (2001) Proteomics based on selecting and quantifying cysteine containing peptides by covalent chromatography. J Chromatogr A 924: 345-357.
44. Washburn MP, Wolters D, Yates JRI (2001) Large-scale analysis of the yeast proteome via multidimensional protein identification technology. Nat Biotechnol 19: 242-247.
45. Wu CC, Yates JR III (2003) The application of mass spectrometry to membrane proteomics. Nat Biotechnol 21: 262-267.
46. Wu CC, MacCoss MJ, Howell KE, Yates JR III (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21: 532-538.