De novo sequence analysis and Intact mass Measurements for characterization of phycocyanin subunit isoforms from the blue-green alga Aphanizomenon flos-aquae

Journal of Mass Spectrometry

Volumn 44, Issue 4, 2009, Pages 503-515

  Rinalducci, Sara ^a   Roepstorff, Peter ^b   Zoiia, Lello ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

4 sulfophenyl isothiocyanate; Charge derivatization; De novo sequencing; Homology search; Phycocyanin; Protein isoforms

Indexed keywords

4-SULFOPHENYL ISOTHIOCYANATE; CHARGE DERIVATIZATION; DE NOVO SEQUENCING; HOMOLOGY SEARCH; PHYCOCYANIN; PROTEIN ISOFORMS;

AMINO ACIDS; MASS SPECTROMETRY; ORGANIC ACIDS; PEPTIDES;

AMINES;

4 SULFOPHENYL ISOTHIOCYANATE; ALPHA PHYCOCYANIN POLYPEPTIDE; AMINO ACID; BETA PHYCOCYANIN POLYPEPTIDE; ISOPROTEIN; ISOTHIOCYANIC ACID DERIVATIVE; PEPTIDE; PHYCOCYANIN; POLYPEPTIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANIMAL EXPERIMENT; APHANIZOMENON; APHANIZOMENON FLOS AQUAE; ARTICLE; BACTERIUM DETECTION; BLUE GREEN ALGA; CHEMICAL STRUCTURE; CYANOBACTERIUM; DE NOVO SEQUENCING; DERIVATIZATION; DNA FINGERPRINTING; ELECTROSPRAY MASS SPECTROMETRY; EVOLUTIONARY ADAPTATION; GENETIC TRAIT; INTACT MASS MEASUREMENT; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEASUREMENT; NONHUMAN; OPERON; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES DIVERSITY; SULFONATION; TIME OF FLIGHT MASS SPECTROMETRY;

AMINO ACID SEQUENCE; APHANIZOMENON; BACTERIAL PROTEINS; BENZENESULFONATES; ISOTHIOCYANATES; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PHYCOCYANIN; PROTEIN ISOFORMS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

APHANIZOMENON FLOS-AQUAE; CYANOBACTERIA;

EID: 65649104112     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.1526     Document Type: Article

References (64)

1. G. S. Jensen, D. I. Ginsberg, P. Huerta, M. Citton, C. Drapeau. Consumption of Aphanizomenon flos-aquae has rapid effects on the circulation and function of immune cells in humans. Journal of the American NutraceuticalAssociation 2000, 2, 50.
2. G. S. Jensen, D. I. Ginsberg, C. Drapeau. Blue-green algae as an immuno-enhancer and biomodulator. Journal of the American NutraceuticalAssociation 2001, 3, 24.
3. V. B. Bhat, K. M. Madyastha. C-phycocyanin: a potent peroxyl radical scavenger in vivo and in vitro. Biochemical and Biophysical Research Communications 2000, 275, 20. (Pubitemid 30663622)
4. C. Romay, R. Gonzalez. Phycocyanin is an antioxidant protector of human erythrocytes against lysis by peroxyl radicals. Journal of Pharmacy and Pharmacology 2000, 52, 367. (Pubitemid 30223676)
5. V. B. Bhat, K. M. Madyastha. Scavenging of peroxynitrite by phycocyanin and phycocyanobilin from Spirulina platensis: protection against oxidative damage to DNA. Biochemical and Biophysical Research Communications 2001, 285, 262. (Pubitemid 32918063)
6. C. Romay, J. Armesto, D. Remirez, R. Gonzalez, N. Ledon, I. Garcia. Antioxidant and anti-inflammatory properties of C-phycocyanin from blue-green algae, inflammation Research 1998, 47, 36. (Pubitemid 28048114)
7. A. N. Glazer. Phycobiliproteins. Methods in Enzymology 1988, 167, 291.
8. A. K. Padyana, V. B. Bhat, K. M. Madyastha, K. R. Rajashankar, S. Ramakumar. Crystal structure of a light-harvesting protein C-phycocyanin from Spirulina platensis. Biochemical and Biophysical Research Communications 2001, 282, 893. (Pubitemid 32924578)
9. S. Benedetti, S. Rinalducci, F. Benvenuti, S. Francogli, S. Pagliarani, L Giorgi, M. Micheloni, G. M. D'Amici, L. Zolla, F. Canestrari. Purification and characterization of phycocyanin from the blue-green alga Aphanizomenon flos-aquae. Journal of chromatography B, Analytical Technologies in the Biomedical and Life Sciences 2006, 833, 12.
10. A. Shevchenko, A. Loboda, A. Shevchenko, W. Ens, K. G. Standing. MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Analytical Chemistry 2000, 72, 2132. (Pubitemid 30316592)
11. A. Shevchenko, S. Sunyaev, A. Loboda, A. Shevchenko, P. Bork, W. Ens, K. G. Standing. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Analytical Chemistry 2001, 73, 1917. (Pubitemid 32862395)
12. A. Wattenberg, A. J. Organ, K. Schneider, R. Tyldesley, R. Bordoli, R. H. Bateman. Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) mass spectrometry and its implications for protein identification. Journal of the American Society for Mass Spectrometry 2002, 13, 772. (Pubitemid 36871611)
13. W. Zhang, A. N. Krutchinsky, B. T. Chait. "De novo" peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: a preliminary study. Journal of the American Society for Mass Spectrometry 2003, 14, 1012. (Pubitemid 37040762)
14. D. Arnott, W. J. Henzel, J. T. Stults. Rapid identification of comigrating gel-isolated proteins by ion trap-mass spectrometry. Electrophoresis 1998, 19, 968. (Pubitemid 28239966)
15. D. M. Horn, R. A. Zubarev, F. W. McLafferty. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 2000, 97, 10 313.
16. A. L. Yergey, J. R. Coorssen, P. S. Backlund Jr, P. S. Blank, G. A. Humphrey, J. Zimmerberg, J. M. Campbell, M. L. Vestal. De novo sequencing of peptides using MALDI/TOF-TOF. Journal of the American Society for Mass Spectrometry 2002, 13, 784. (Pubitemid 36871612)
17. P. Roepstorff, J. Fohlman. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomedical Mass Spectrometry 1984, 11, 601.
18. K. D. Roth, Z. H. Huang, N. Sadagopan, J. T. Watson. Charge derivatization of peptides for analysis by mass spectrometry. Mass Spectrometry Reviews 1998, 17, 255. (Pubitemid 128631223)
19. T. Keough, R. S. Youngquist, M. P. Lacey. A method for high-sensitivity peptide sequencing using post-source decay matrix-assisted laser desorption ionization mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 1999, 96, 7131. (Pubitemid 29299627)
20. M. D. Bauer, Y. Sun, T. Keough, M. P. Lacey. Sequencing of sulfonic acid derivatized peptides by electrospray mass spectrometry. Rapid Communications in Mass Spectrometry 2000, 14, 924. (Pubitemid 30367584)
21. C. Gu, G. Tsaprailis, L. Breci, V. H. Wysocki. Selective gas-phase cleavage at the peptide bond C-terminal to aspartic acid in fixed-charge derivatives of Asp-containing peptides. Analytical Chemistry 2000, 72, 5804. (Pubitemid 32002334)
22. M. Munchbach, M. Quadroni, G. Miotto, P. James. Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Analytical Chemistry 2000, 72, 4047.
23. T. Keough, M. P. Lacey, R. S. Youngquist. Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry. Rapid Communications in Mass Spectrometry 2000, 14, 2348. (Pubitemid 32001088)
24. T. Keough, M. P. Lacey, R. S. Youngquist. Solid-phase derivatization of tryptic peptides for rapid protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Communications in Mass Spectrometry 2002, 16, 1003. (Pubitemid 34555900)
25. K. Gevaert, H. Demol, L. Martens, B. Hoorelbeke, M. Puype, M. Goethals, J. V. Damme, S. D. Boeck, J. Vandekerckhove. Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry. Electrophoresis 2001, 22, 1645.
26. L. N. Marekov, P. M. Steinert. Charge derivatization by 4-sulfophenyl isothiocyanate enhances peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Journal of Mass Spectrometry 2003, 38, 373. (Pubitemid 36582214)
27. D. Wang, S. R. Kalb, R. J. Cotter. Improved procedures for N-terminal sulfonation of peptides for matrix-assisted laser desorption/ionization post-source decay peptide sequencing. Rapid Communications in Mass Spectrometry 2004, 18, 96. (Pubitemid 38031423)
28. P. Chen, S. Nie, W. Mi, X. C. Wang, S. P. Liang. De novo sequencing of tryptic peptides sulfonated by 4-sulfophenyl isothiocyanate for unambiguous protein identification using post-source decay matrix-assisted laser desorption/ionization mass spectrometry. Rapid Communications in Mass Spectrometry 2004, 18, 191. (Pubitemid 38160355)
29. B. Samyn, K. Sergeant, S. Memmi, G. Debyser, B. Devreese, J. Van Beeumen. MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE- separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome. Electrophoresis 2006, 27, 2702 (Pubitemid 44069409)
30. B. Samyn, K. Sergeant, S. Carpentier, G. Debyser, B. Panis, R. Swennen, J. Van Beeumen. Functional proteome analysis of the banana plant (Musa spp.) using de novo sequence analysis of derivatized peptides. Journal of Proteome Research 2007, 6, 70. (Pubitemid 46173660)
31. I. R. León, A. G. Neves-Ferreira, R. H. Valente, E. M. Mota, H. L. Lenzi, J, Perales. Improved protein identification efficiency by mass spectrometry using N-terminal chemical derivatization of peptides from Angiostrongylus costaricensis, a nematode with unknown genome. Journal of Mass Spectrometry 2007, 42, 781. (Pubitemid 46984140)
32. S. W. Hunsucker, K. Klage, S. M. Slaughter, M. Potts, R. F. Helm. A preliminary investigation of the Nostoc punctiforme proteome. Biochemical and Biophysical Research Communications 2004, 317, 1121. (Pubitemid 38496426)
33. V. Neuhoff, N. Arold, D. Taube, W. Ehrhardt. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie brilliant blue G-250 and R-250. Electrophoresis 1988, 9, 255. (Pubitemid 18152745)
34. A. Shevchenko, M. Wilm, O. Vorm, M. Mann. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Analytical Chemistry 1996, 68, 850. (Pubitemid 26101214)
35. J. Gobom, E. Nordhoff, E. Mirgorodskaya, R. Ekman, P. Roepstorff. Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. Journal of Mass Spectrometry 1999, 34, 105. (Pubitemid 129500440)
36. M. Kussmann, E. Nordhoff, H. Rahbek-Nielsen, S. Haebel, M. R. Larsen, L Jakobsen, J. Gobom, E. Mirgorodskaya, A. Kroll-Kristensen, L. Palm, P. Roepstorff. Matrix-assisted laser desorption/ionization mass spectrometry sample preparation techniques designed for various peptide and protein analytes. Journal of Mass Spectrometry 1997, 32, 593. (Pubitemid 27273949)
37. L. Zolla, M. Bianchetti. High-performance liquid chromatography coupled on-line with electrospray ionization mass spectrometry for the simultaneous separation and identification of the Synechocystis PCC 6803 phycobilisome proteins. Journal of Chromatography A 2001, 912, 269. (Pubitemid 32234364)
38. M. E. Barrios-Llerena, K. F. Reardon, P. C. Wright. 2-DE proteomic analysis of the model cyanobacterium Anabaena variabilis. Electrophoresis 2007, 28, 1624. (Pubitemid 46852121)
39. Y. H. Lee, M. S. Kim, W. S. Choie, H. K. Min, S. W. Lee. Highly informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry. Proteomics 2004, 4, 1684. (Pubitemid 38738325)
40. V. P. Williams, A. N. Glazer. Structural studies on phycobiliproteins. I. Bilin-containing peptides of C-phycocyanin. Journal of Biological Chemistry 1978, 253, 202.
41. B. Herbert, F. Hopwood, D. Oxley, J. McCarthy, M. Laver, J. Grinyer, A. Goodall, K. Williams, A. Castagna, P. G. Righetti. Beta-elimination: an unexpected artefact in proteome analysis. Proteomics 2003, 3, 826. (Pubitemid 36801668)
42. T. M. Florence. Degradation of protein disulphide bonds in dilute alkali. The Biochemical Journal 1980, 189, 507.
43. J. S. Kim, H. J. Kim. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric observation of a peptide triplet induced by thermal cleavage of cystine. Rapid Communications in Mass Spectrometry 2001, 15, 2296.
44. J. E. Bishop, J. C. Lagarias, J. O. Nagy, R. W. Schoenleber, H. Rapoport, A. V. Klotz, A. N. Glazer. Phycobiliprotein-bilin linkage diversity. I. Structural studies on A- and D-ring-linked phycocyanobilins. Journal of Biological Chemistry 1986, 261, 6790. (Pubitemid 17219444)
45. M. Duerring, R. Huber, W. Bode. The structure of y-N-methyl asparagines in C-phycocyanin from Mastigocladus laminosus and Agmenellum quadruplicatum. FEBS Letters 1988, 236, 167.
46. R. V. Swanson, A. N. Glazer. Phycobiliprotein methylation. Effect of the gamma-N-methylasparagine residue on energy transfer in phycocyanin and the phycobilisome. Journal of Molecular Biology 1990, 214, 787. (Pubitemid 20267852)
47. B. A. Thomas, L. P. McMahon, A. V. Klotz. N5-methylasparagine and energy-transfer efficiency in C-phycocyanin. Biochemistry 1995, 34, 3758.
48. T. Schirmer, W. Bode, R. Huber. Refined three-dimensional structures of two cyanobacterial C-phycocyanins at 2.1 and 2.5 å resolution. A common principle of phycobilin-protein interaction. Journal of Molecular Biology 1987, 196, 677.
49. K. Sergeant, B. Samyn, G. Debyser, J. Van Beeumen. De novo sequence analysis of N-terminal sulfonated peptides after in-gel guanidination. Proteomics 2005, 5, 2369. (Pubitemid 40835406)
50. H. Hara, T. Nishi, T. Kasai. A protein less sensitive to trypsin, guanidinated casein, is a potent stimulator of exocrine pancreas in rats. Proceedings of the Society for Experimental Biology and Medicine 1995, 210, 278. (Pubitemid 26020255)
51. B. Samyn, G. Debyser, K. Sergeant, B. Devreese, J. Van Beeumen. A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry. Journal of the American Society for Mass Spectrometry 2004, 15, 1838. (Pubitemid 39602734)
52. K. E. Apt, J. L. Collier, A. R. Grossman. Evolution of the phycobiliproteins. Journal of Molecular Biology 1995, 248, 79.
53. D. A. Bryant, G. Cohen-Bazire. Effects of chromatic illumination on cyanobacterial phycobilisomes. Evidence for the specific induction of a second pair of phycocyanin subunits in Pseudanabaena 7409 grown in red light. European Journal of'Biochemistry 1981, 119, 415.
54. P. B. Conley, P. G. Lemaux, A. R. Grossman. Cyanobacterial light-harvesting complex subunits are encoded in two red light-induced transcripts. Science 1985, 230, 550. (Pubitemid 16169809)
55. P. B. Conley, P. G. Lemaux, T. L. Lomax, A. R. Grossman. Genes encoding major light harvesting polypeptides are clustered on the cyanobacterial genome of Fremyella diplosiphon. Proceedings of the National Academy of Sciences of the United States of America 1986, 83, 3924. (Pubitemid 16062394)
56. P. B. Conley, P. G. Lemaux, A. R. Grossman. Molecular characterization and evolution of sequences encoding light harvesting components in the chromatically adapting cyanobacterium Fremyella dipiosiphon. Journal of Molecular Biology 1988, 199, 447.
57. M. Duerring, G. B. Schmidt, R. Huber.lsolation, crystallization, crystal structure analysis and refinement of constitutive C-phycocyanin from the chromatically adapting cyanobacterium Fremyella dipiosiphon at 1.66 å resolution. Journal of Molecular Biology 1991, 277, 577. (Pubitemid 121003303)
58. D. Mazel, P. Marliere. Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins. Nature 1989, 341, 245.
59. R. Kalla, L. K. Lind, P. Gustafsson. Genetic-analysis of phycobilisome mutants in the cyanobacterium Synechococcus species PCC-6301. Molecular Microbiology 1989, 3, 339.
60. R. H. Lau, S. D. Blakeley, G. Alvarado-Urbina, J. E. Bailly, J. A. Condie, P. C. Lau. Duplication of the phycocyanin operon in the unicellular cyanobacterium Anacystis nidulans R2. Gene 1989, 80, 375.
61. S. R. Kalla, L. K. Lind, J. Lidholm, P. Gustafsson. Transcriptional organization of the phycocyanin subunit gene clusters of the cyanobacterium Anacystis nidulans UTEX 625. Journal of Bacteriology 1988, 770, 2961.
62. W. R. Belknap, R. Haselkorn. Cloning and light regulation of expression of the phycocyanin operon of the cyanobacterium Anabaena. EMBO Journal 1987, 6, 871.
63. T. R. Johnson, J. I. Haynes II, J. L. Wealand, L. R. Yarbrough, R. Hirschberg. Structure and regulation of genes encoding phycocyanin and allophycocyanin from Anabaena variabilis ATCC 29413. Journal of Bacteriology 1988, 170, 1858.
64. G. L. A. Barker, A. Konopka, B. A. Handley, P. K. Hayes. Genetic variation in Aphanizomenon (cyanobacteria) colonies from the Baltic Sea and North America. Journal of Phycology 2000, 36, 947.