[en] Beside bioreactor modeling studies, the molecular characterization of life-support organisms appeared to be essential to complete their global behavior picture, in particular, culture conditions. Using a combination of LC-MS/MS approaches with gel-free and gel-based peptides fractionation steps, we identified 932 proteins from the a-proteobacterium Rhodospirillum rubrum S1H. In addition, abundance data were retrieved using the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. This work has also allowed identification of new and specific proteins for the Rhodospirillaceae family.
Mergeay, M.; Verstraete, W.; Dubertret, G.; Lefort-Tran, M.; Chipaux, C.; Binot R. A. 'MELiSSA' -A Micro-Organisms-Based Model for 'CELSS' Development. Proceedings at the 3rd European Symposium on Space Thermal Control & Life Support Systems; Noordwijk: The Netherlands, 1988; pp 65-68.
Hendrickx, L.; De Wever, H.; Hermans, V.; Mastroleo, F.; Morin, N.; Wilmotte, A.; Janssen, P.; Mergeay, M. Microbial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): Reinventing and compartimentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions. Res. Microbiol. 2006, 157 , 77-86.
Farges, B.; Poughon, L.; Creuly, C.; Cornet, J. F.; Dussap, C. G.; Lasseur, C. Dynamic aspects and controllability of the MELiSSA project: a bioregenerative system to provide life support in space. Appl. Biochem. Biotechnol. 2008, 151 , 686-699.
Hendrickx, L.; Mergeay, M. From the deep sea to the stars: human life support through minimal communities. Curr. Opin. Microbiol. 2007, 10 , 231-237.
Favier-Teodorescu, L.; Cornet, J. F.; Dussap, C. G. Modelling continuous cultures of Rhodospirillum rubrum in a photobiore- actor under light limited conditions. Biotechnol. Lett. 2003, 25 , 359-364.
Montras, A.; Pycke, B.; Boon, N.; Godia, F.; Mergeay, M.; Hendrickx, L.; Perez, J. Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling. Water Res. 2008, 42 , 1700-1714.
Rossi, N.; Derouiniot-Chaplain, M.; Jaouen, P.; Legentilhomme, P.; Petit, I. Arthrospira platensis harvesting with membranes: fouling phenomenon with limiting and critical flux. Bioresour. Technol. 2008, 99 , 6162-6167.
Christophe, G.; Guiavarch, E.; Creuly, C.; Dussap, C. G. Growth monitoring of Fibrobacter succinogenes by pressure measurement. Bioprocess Biosyst. Eng. 2009, 32 , 123-128.
Canas, B; Pineiro, C; Calvo, E.; Lopez-Ferrer, D.; Gallardo, J. M. Trends in sample preparation for classical and second generation proteomics. J. Chromatogr., A. 2007, 1153 , 235-258.
Cargile, B. J.; Bundy, J. L.; Freeman, T. W.; Stephenson, J. L., Jr. Gel based isoelectric focusing of peptides and the utility of isoelectric point in protein identification. J. Proteome Res. 2004, 3 , 112-119.
Cargile, B. J.; Talley, D. L.; Stephenson, J. L., Jr. Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 2004, 25 , 936-945.
Gan, C. S.; Reardon, K. F.; Wright, P. C. Comparison of protein and peptide prefractionation methods for the shotgun proteomic analysis of Synechocystis sp. PCC 6803. Proteomics 2005, 5 , 2468-2478.
Selao, T. T.; Nordlund, S.; Noren, A. Comparative proteomic studies in Rhodospirillum rubrum grown under different nitrogen conditions. J. Proteome Res. 2008, 7 , 3267-3275.
Sistrom, W. R. A requirement for sodium in the growth medium of Rhodopseudomonas sphaeroides. J. Gen. Microbiol. I960, 22 , 77-85.
Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2 , 667-675.
Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72 , 248-254.
Wang, J.; Sung, W. K.; Krishnan, A.; Li, K. B. Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines. BMC Bioinf. 2005, 6 , 174.
Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4 , 1265-1272.
Bjellqvist, B.; Hughes, G. J.; Pasquali, C.; Paquet, N.; Ravier, F.; Sanchez, J.-C.; Frutiger, S.; Hochstrasser, D. F. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14 , 1023-1031.
Schwartz, R.; Ting, C. S.; King, J. Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. Genome Res. 2001, 11 , 703-709.
Kihara, D.; Kanehisa, M. Tandem clusters of membrane proteins in complete genome sequences. Genome Res. 2000, 10 , 731-743.
Vallenet, D.; Labarre, L.; Rouy, Z.; Barbe, V.; Bocs, S.; Cruveiller, S.; Lajus, A.; Pascal, G.; Scarpelli, C.; Medigue, C. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 2006, 34 , 53-65.
Pan, C.; Oda, Y.; Lankford, P. K.; Zhang, B.; Samatova, N. F.; Pelletier, D. A.; Harwood, C. S.; Hettich, R. L. Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palus- tris by integrating transcriptomics and quantitative proteomics. Mol. Cell. Proteomics 2008, 7 , 938-948.
Ishihama, Y.; Schmidt, T.; Rappsilber, J.; Mann, M.; Hartl, F. U.; Kerner, M. J.; Frishman, D. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 2008, 9 , 102.
Assiddiq, B. F.; Snijders, A. P.; Chong, P. K.; Wright, P. C.; Dickman, M. J. Identification and characterization of Sulfolobus solfataricus P2 proteome using multidimensional liquid phase protein separations. J. Proteome Res. 2008, 7 , 2253-2261.
Rohmer, L.; Guina, T.; Chen, J.; Gallis, B.; Taylor, G. K.; Shaffer, S. A.; Miller, S. I.; Brittnacher, M. J.; Goodlett, D. R. Determination and comparison of the Francisella tularensis subsp.novicida U112 proteome to other bacterial proteomes. J. Proteome Res. 2008, 7 , 2016-2024.
Kolker, E.; Purvine, S.; Galperin, M. Y.; Stolyar, S.; Goodlett, D. R.; Nesvizhskii, A. I.; Keller, A.; Xie, T.; Eng, J. K.; Yi, E.; Hood, L.; Picone, A. F.; Cherny, T.; Tjaden, B. C.; Siegel, A. F.; Reilly, T. J.; Makarova, K. S.; Palsson, B. O.; Smith, A. L. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J. Bacteriol. 2003, 185 , 4593-4602.
Corbin, R. W.; Paliy, O.; Yang, F.; Shabanowitz, J.; Platt, M.; Lyons, C. E., Jr.; Root, K.; McAuliffe, J.; Jordan, M. I.; Kustu, S.; Soupene, E.; Hunt, D. F. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 , 9232-9237.
Jaffe, J. D.; Berg, H. C.; Church, G. M. Proteogenomic mapping as a complementary method to perform genome annotation. Pro- teomics 2004, 4 , 59-77.
Elias, D. A.; Monroe, M. E.; Smith, R. D.; Fredrickson, J. K.; Lipton, M. S. Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. J. Microbiol. Methods 2006, 66 , 223-233.
VerBerkmoes, N. C.; Shah, M. B.; Lankford, P. K.; Pelletier, D. A.; Strader, M. B.; Tabb, D. L.; McDonald, W. H.; Barton, J. W.; Hurst, G. B.; Hauser, L.; Davison, B. H.; Beatty, J. T.; Harwood, C. S.; Tabita, F. R.; Hettich, R. L.; Larimer, F. W. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J. Proteome Res. 2006, 5 , 287-298.
Zhang, W.; Gritsenko, M. A.; Moore, R. J.; Culley, D. E.; Nie, L.; Petritis, K.; Strittmatter, E. F.; Camp, D. G., II; Smith, R. D.; Brockman, F. J. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. Proteomics 2006, 6 , 4286-4299.
Laukel, M.; Rossignol, M.; Borderies, G.; Volker, U.; Vorholt, J. A. Comparison of the proteome of Methylobacterium extorquens AM1 grown under methylotrophic and nonmethylotrophic conditions. Proteomics 2004, 4 , 1247-1264.
Bosch, G.; Skovran, E.; Xia, Q.; Wang, T.; Taub, F.; Miller, J. A.; Lidstrom, M. E.; Hackett, M. Comprehensive proteomics of Me- thylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions. Proteomics 2008, 8 , 3494-3505.
Berard, J.; Belanger, G.; Gingras, G. Mapping of the puh messenger RNAs from Rhodospirillum rubrum. Evidence for tandem promoters. J. Biol. Chem. 1989, 18 , 10897-10903.
Hendrickson, E. L.; Xia, Q.; Wang, T.; Leigh, J. A.; Hackett, M. Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics. Analyst 2006, 131 , 1335-1341.
Gupta, R. S.; Mok, A. Phylogenomics and signature proteins for the alpha proteobacteria and its main groups. BMC Microbiol. 2007, 7, 106.
Fermin, D.; Allen, B. B.; Blackwell, T. W.; Menon, R.; Adamski, M.; Xu, Y.; Ulintz, P.; Omenn, G. S.; States, D. J. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 2006, 7 , R35.
Ansong, C.; Purvine, S. O.; Adkins, J. N.; Lipton, M. S.; Smith, R. D. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings Funct. Genomic Proteomic 2008, 7, 50-62.
