The coevolution of phycobilisomes: Molecular structure adapting to functional evolution

Comparative and Functional Genomics

Volumn 2011, Issue , 2011, Pages

  Shi, Fei ^a   Qin, Song ^a   Wang, Yin Chu ^a  

^a YANTAI INSTITUTE OF COASTAL ZONE RESEARCH   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOPHYCOCYANIN; PHYCOCYANIN; PHYCOERYTHRIN; POLYPEPTIDE;

ARTHROSPIRA PLATENSIS; ARTICLE; BACTERIAL STRAIN; COEVOLUTION; CONTROLLED STUDY; CROSS LINKING; CYANIDIOSCHYZON MEROLAE; CYANIDIUM CALDARIUM; CYANOBACTERIUM; CYANOTHECE; GLOEOBACTER VIOLACEUS; HYDROPHOBICITY; MICROCYSTIS AERUGINOSA; MOLECULAR WEIGHT; NONHUMAN; NOSTOC PUNCTIFORME; NUCLEOTIDE SEQUENCE; PHYCOBILISOME; PHYSICAL CHEMISTRY; PORPHYRA PURPUREA; PORPHYRA YEZOENSIS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SYNECHOCOCCUS; SYNECHOCOCCUS ELONGATUS; SYNECHOCYSTIS; THERMOSYNECHOCOCCUS ELONGATUS;

CYANOBACTERIA; RHODOPHYTA;

EID: 81555222877     PISSN: 15316912     EISSN: 15326268     Source Type: Journal    
DOI: 10.1155/2011/230236     Document Type: Article

References (48)

1. Grossman A. R., Schaefer M. R., Chiang G. G., Collier J. L., The phycobilisome, a light-harvesting complex responsive to environmental conditions Microbiological Reviews 1993 57 3 725 749 (Pubitemid 23262516)
2. MacColl R., Cyanobacterial phycobilisomes Journal of Structural Biology 1998 124 2-3 311 334 (Pubitemid 29143068)
3. Adir N., Elucidation of the molecular structures of components of the phycobilisome: reconstructing a giant Photosynthesis Research 2005 85 1 15 32 (Pubitemid 40678757)
4. Glazer A. N., Phycobiliproteins Methods in Enzymology 1988 167 291 303
5. Rippka R., Waterbury J., Cohen-Bazire G., A cyanobacterium which lacks thylakoids Archives of Microbiology 1974 100 4 419 436
6. Nakamura Y., Kaneko T., Sato S., Mimuro M., Miyashita H., Tsuchiya T., Sasamoto S., Watanabe A., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Nakazaki N., Shimpo S., Takeuchi C., Yamada M., Tabata S., Complete genome structure of gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids DNA Research 2003 10 4 137 145 (Pubitemid 37288299)
7. Apt K. E., Collier J. L., Grossman A. R., Evolution of the phycobiliproteins Journal of Molecular Biology 1995 248 1 79 96
8. Wang X. Q., Li L. N., Chang W. R., Zhang J. P., Gui L. L., Guo B. J., Liang D. C., Structure of C-phycocyanin from Spirulina platensis at 2.2 resolution: a novel monoclinic crystal form for phycobiliproteins in phycobilisomes Acta Crystallographica Section D 2001 57 6 784 792
9. Padyana A. K., Bhat V. B., Madyastha K. M., Rajashankar K. R., Ramakumar S., Crystal structure of a light-harvesting protein C-phycocyanin from Spirulina platensis Biochemical and Biophysical Research Communications 2001 282 4 893 898 (Pubitemid 32924578)
10. Glazer A. N., Phycobilisome a macromolecular complex optimized for light energy transfer BBA Reviews On Bioenergetics 1984 768 1 29 51
11. Glazer A. N., Light harvesting by phycobilisomes Annual Review of Biophysics and Biophysical Chemistry 1985 14 47 77
12. Zilinskas B. A., Greenwald L. S., Phycobilisome structure and function Photosynthesis Research 1986 10 1-2 7 35
13. Gantt E., Lipschultz C. A., Zilinskas B., Further evidence for a phycobilisome model from selective dissociation, fluorescence emission, immunoprecipitation, and electron microscopy Biochimica et Biophysica Acta 1976 430 2 375 388
14. Jiang T., Zhang J. P., Liang D. C., Structure and function of chromophores in R-Phycoerythrin at 1.9 Resolution Proteins 1999 34 2 224 231 (Pubitemid 29028808)
15. Stec B., Troxler R. F., Teeter M. M., Crystal structure of C-phycocyanin from Cyanidium caldarium provides a new perspective on phycobilisome assembly Biophysical Journal 1999 76 6 2912 2921 (Pubitemid 29269441)
16. Brejc K., Ficner R., Huber R., Steinbacher S., Isolation, crystallization, crystal structure analysis and refinement of allophycocyanin from the cyanobacterium Spirulina platensis at 2.3 resolution Journal of Molecular Biology 1995 249 2 424 440
17. Ficner R., Lobeck K., Schmidt G., Huber R., Isolation, crystallization, crystal structure analysis and refinement of B-phycoerythrin from the red alga Porphyridium sordidum at 2.2 resolution Journal of Molecular Biology 1992 228 3 935 950 (Pubitemid 23017282)
18. Schirmer T., Bode W., Huber R., Sidler W., Zuber H., X-ray crystallographic structure of the light-harvesting biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and its resemblance to globin structures Journal of Molecular Biology 1985 184 2 257 277
19. Guan X., Qin S., Zhao F., Zhang X., Tang X., Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution International Journal of Biological Sciences 2007 3 7 434 445 (Pubitemid 350132787)
20. Partensky F., Hess W. R., Vaulot D., Prochlorococcus, a marine photosynthetic prokaryote of global significance Microbiology and Molecular Biology Reviews 1999 63 1 106 127 (Pubitemid 29116088)
21. Hess W. R., Rocap G., Ting C. S., Larimer F., Stilwagen S., Lamerdin J., Chisholm S. W., The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics Photosynthesis Research 2001 70 1 53 71 (Pubitemid 34128538)
22. Allen J. F., Matthijs H. C. P., Complementary adaptations, photosynthesis and phytochrome Trends in Plant Science 1997 2 2 41 43 (Pubitemid 127740659)
23. Six C., Thomas J. C., Brahamsha B., Lemoine Y., Partensky F., Photophysiology of the marine cyanobacterium Synechococcus sp. WH8102, a new model organism Aquatic Microbial Ecology 2004 35 1 17 29 (Pubitemid 39104242)
24. Codoer F. M., Fares M. A., Why should we care about molecular coevolution? Evolutionary Bioinformatics 2008 4 237 246 (Pubitemid 351419611)
25. Fares M. A., Travers S. A. A., A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses Genetics 2006 173 1 9 23 (Pubitemid 43800180)
26. Gloor G. B., Martin L. C., Wahl L. M., Dunn S. D., Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions Biochemistry 2005 44 19 7156 7165 (Pubitemid 40656660)
27. Atchley W. R., Wollenberg K. R., Fitch W. M., Terhalle W., Dress A. W., Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis Molecular Biology and Evolution 2000 17 1 164 178 (Pubitemid 30057002)
28. Wang Z. O., Pollock D. D., Context dependence and coevolution among amino acid residues in proteins Methods in Enzymology 2005 395 779 790 (Pubitemid 40754397)
29. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G., The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Research 1997 25 24 4876 4882 (Pubitemid 28022245)
30. Larkin M. A., Blackshields G., Brown N. P., Chenna R., Mcgettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., Lopez R., Thompson J. D., Gibson T. J., Higgins D. G., Clustal W and clustal X version 2.0 Bioinformatics 2007 23 21 2947 2948 (Pubitemid 350162903)
31. Edgar R. C., MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research 2004 32 5 1792 1797 (Pubitemid 38832724)
32. Henikoff S., Henikoff J. G., Amino acid substitution matrices from protein blocks Proceedings of the National Academy of Sciences of the United States of America 1992 89 22 10915 10919
33. Fares M. A., McNally D., CAPS: coevolution analysis using protein sequences Bioinformatics 2006 22 22 2821 2822 (Pubitemid 44742405)
34. Gouveia-Oliveira R., Pedersen A. G., Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation Algorithms for Molecular Biology 2007 2 1, article 12
35. Gouveia-Oliveira R., Roque F. S., Wernersson R., Sicheritz-Ponten T., Sackett P. W., Mlgaard A., Pedersen A. G., InterMap3D: predicting and visualizing co-evolving protein residues Bioinformatics 2009 25 15 1963 1965
36. Pollock D. D., Taylor W. R., Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution Protein Engineering 1997 10 6 647 657 (Pubitemid 27332071)
37. Tomii K., Kanehisa M., Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins Protein Engineering 1996 9 1 27 36 (Pubitemid 26099761)
38. Adir N., Lerner N., The crystal structure of a novel unmethylated form of c-phycocyanin, a possible connector between cores and rods in phycobilisomes The Journal of Biological Chemistry 2003 278 28 25926 25932 (Pubitemid 36835355)
39. Yeang C. H., Haussler D., Detecting coevolution in and among protein domains PLoS Computational Biology 2007 3 11 2122 2134 (Pubitemid 350241937)
40. Atchley W. R., Zhao J., Fernandes A. D., Drke T., Solving the protein sequence metric problem Proceedings of the National Academy of Sciences of the United States of America 2005 102 18 6395 6400 (Pubitemid 40617454)
41. Privalov P. L., Gill S. J., Stability of Protein Structure and Hydrophobic Interaction Advances in Protein Chemistry 1988 39 191 234
42. Dill K. A., Dominant forces in protein folding Biochemistry 1990 29 31 7133 7155 (Pubitemid 20230041)
43. Zhao F., Qin S., Evolutionary analysis of phycobiliproteins: implications for their structural and functional relationships Journal of Molecular Evolution 2006 63 3 330 340 (Pubitemid 44440475)
44. Gu X., Statistical methods for testing functional divergence after gene duplication Molecular Biology and Evolution 1999 16 12 1664 1674
45. Agrawal-Gamse C., Lee F. H., Haggarty B., Jordan A. P. O., Yanjie Y., Lee B., Collman R. G., Hoxie J. A., Doms R. W., Laakso M. M., Adaptive mutations in a human immunodeficiency virus type 1 envelope protein with a truncated V3 loop restore function by improving interactions with CD4 Journal of Virology 2009 83 21 11005 11015
46. Tully D. C., Fares M. A., Unravelling selection shifts among foot-and-mouth disease virus serotypes Evolutionary Bioinformatics Online 2006 2 211 225
47. Zhong J., Gastaminza P., Chung J., Stamataki Z., Isogawa M., Cheng G., McKeating J. A., Chisari F. V., Persistent hepatitis C virus infection in vitro: coevolution of virus and host Journal of Virology 2006 80 22 11082 11093 (Pubitemid 44706549)
48. Fares M. A., Computational and statistical methods to explore the various dimensions of protein evolution Current Bioinformatics 2006 1 2 207 217