AplA, a member of a new class of phycobiliproteins lacking a traditional role in photosynthetic light harvesting

Journal of Bacteriology

Volumn 186, Issue 21, 2004, Pages 7420-7428

  Montgomery, Beronda L ^a   Casey, Elena Silva ^b   Grossman, Arthur R ^c   Kehoe, David M ^a  

^a INDIANA UNIVERSITY   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c GEOPHYSICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOPHYCOCYANIN; AMINO ACID; DIMER; PHYCOBILIPROTEIN; PROTEIN APLA; UNCLASSIFIED DRUG;

ALPHA CHAIN; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; BETA CHAIN; CELLULAR DISTRIBUTION; CHROMATOPHORE; CONTROLLED STUDY; CYANOBACTERIUM; DIMERIZATION; FREMYELLA DIPLOSIPHON; LIGHT HARVESTING SYSTEM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTORECEPTOR; PHOTOSYNTHESIS; PHYCOBILISOME; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FAMILY; PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; RED ALGA;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CYANOBACTERIA; LIGHT; LIGHT-HARVESTING PROTEIN COMPLEXES; MOLECULAR SEQUENCE DATA; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; PHYCOBILISOMES; PHYCOCYANIN; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

ALGAE; BACTERIA (MICROORGANISMS); CYANOBACTERIA; FREMYELLA DIPLOSIPHON; NEGIBACTERIA; PROKARYOTA; RHODOPHYTA;

EID: 6044223542     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.21.7420-7428.2004     Document Type: Article

References (53)

1. Adachi, J., and M. Hasegawa. 1996. ProtML 2.3b3: maximum likelihood inference of protein phylogeny. Institute of Statistical Mathematics, Tokyo, Japan.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Apt, K. E., J. L. Collier, and A. R. Grossman. 1995. Evolution of the phycobiliproteins. J. Mol. Biol. 248:79-96.
4. Balabas, B. E., B. L. Montgomery, L. E. Ong, and D. M. Kehoe. 2003. CotB is essential for complete activation of green light-induced genes during complementary chromatic adaptation in Fremyella diplosiphon. Mol. Microbiol. 50:781-793.
5. Bateman, A., E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. L. Sonnhammer. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-280.
6. Betz, M. 1997. One century of protein crystallography, the phycobiliproteins. Biol. Chem. 378:167-176.
7. Bickel, P. J., K. J. Kechris, P. C. Spector, G. J. Wedemayer, and A. N. Glazer. 2002. Finding important sites in protein sequences. Proc. Natl. Acad. Sci. USA 99:14764-14771.
8. Black, T. A., Y. P. Cai, and C. P. Wolk. 1993. Spatial expression and auto-regulation of hetR. a gene involved in the control of heterocyst development in Anabaena. Mol. Microbiol. 9:77-84.
9. Brejc, K., R. Ficner, R. Huber, and S. Steinbacher. 1995. Isolation, crystallization, crystal-structure analysis and refinement of allophycocyanin from the cyanobacterium Spindina platensis at 2.3 Å resolution. J. Mol. Biol. 249:424-40.
10. Cai, Y., and C. P. Wolk. 1990. Use of a conditionally lethal gene in Anabaena sp. strain PCC 7120 to select for double recombinants and to entrap insertion sequences. J. Bacteriol. 172:3138-3145.
11. Casey, E. S., D. M. Kehoe, and A. R. Grossman. 1997. Suppression of mutants aberrant in light intensity responses of complementary chromatic adaptation. J. Bacteriol. 179:4599-4606.
12. Cobley, J. G., A. C. Clark, S. Weerasurya, F. A. Queseda, J. Y. Xiao, N. Bandrapali, I. D'Silva, M. Thounaojam, J. F. Oda, T. Sumiyoshi, and M. H. Chu. 2002. CpeR is an activator required for expression of the phycoerythrin operon (cpeBA) in the cyanobacterium fremyella diplosiphon and is encoded in the phycoerythrin linker-polypeptide operon (cpeCDESTR). Mol. Microbiol. 44:1517-1531.
13. Cobley, J. G., and R. D. Miranda. 1993. Construction of shuttle plasmids which can be efficiently mobilized from Escherichia coli into the chromatically adapting cyanobacterium, Fremyella diplosiphon. Plasmid 30:90-105.
14. Collier, J. L., and A. R. Grossman. 1992. Chlorosis induced by nutrient deprivation in Synechococcus sp. strain PCC 7942: not all bleaching is the same. J. Bacteriol. 174:4718-4726.
15. Dodd, I. B., and J. B. Egan. 1990. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18:5019-5026.
16. Federspiel, N. A., and L. Scott. 1992. Characterization of a light-regulated gene encoding a new phycoerythrin-associated linker protein from the cyanobacterium Fremyella diplosiphon. J. Bacteriol. 174:5994-5998.
17. Fischer, D. 2000. Hybrid fold recognition: combining sequence derived properties with evolutionary information, p. 119-130. In Proceedings of the Pacific Symposium on Biocomputing 2000. World Scientific, Honolulu, Hawaii.
18. Fischer, D., and D. Eisenberg. 1996. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:947-955.
19. Gantt, E. 1981. Phycobilisomes. Annu. Rev. Plant Physiol. 32:327-347.
20. Gindt, Y. M., J. H. Zhou, D. A. Bryant, and K. Sauer. 1992. Core mutations of Synechococcus sp. PCC 7002 phycobilisomes: a spectroscopic study. J. Photochem. Photobiol. B 15:75-89.
21. Gingrich, J. C., D. J. Lundell, and A. N. Glazer. 1983. Core substructure in cyanobacterial phycobilisomes. J. Cell. Biochem. 22:1-14.
22. Glauser, M., W. A. Sidler, K. W. Graham, D. A. Bryant, G. Frank, E. Wehrli, and H. Zuber. 1992. Three C-phycoerythrin-associated linker polypeptides in the phycobilisome of green-light-grown Calothrix sp. PCC 7601 (cyanobacteria). FEES Lett. 297:19-23.
23. Glazer, A. N. 1984. Phycobilisome. A macromolecular complex optimized for light energy transfer. Biochim. Biophys. Acta 768:29-51.
24. max 671,618 nm). A new cyanobacterial phycobiliprotein. Arch. Microbiol. 104:15-22.
25. Grossman, A. R., D, Bhaya, K. E. Apt, and D. M. Kehoe. 1995. Light-harvesting complexes in oxygenic photosynthesis: diversity, control, and evolution. Annu. Rev. Genet. 291:231-288.
26. Hess, W. R., F. Partensky, G. W. M. van der Staay, J. M. Garcia-Fernandez, T. Börner, and D. Vaulot. 1996. Coexistence of phycoerythrin and a chlorophyll a/b antenna in a marine prokaryote. Proc. Natl. Acad. Sci. USA 93:11126-11130.
27. Hess, W. R., G. Rocap, C. S. Ting, F. Larimer, S. Stilwagen, J. Lamerdin, and S. W. Chisholm. 2001. The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics. Photosynth. Res. 70:53-71.
28. Houmard, J., V. Capuano, T. Coursin, and N. Tandeau de Marsac. 1988. Genes encoding core components of the phycobilisome in the cyanobacterium Calothrix sp. strain PCC 7601: occurrence of a multigene family. J. Bacteriol. 170:5512-5521.
29. Houmard, J., V. Capuano, T. Coursin, and N. Tandeau de Marsac. 1988. Isolation and molecular characterization of the gene encoding allophycocyanin B, a terminal energy acceptor in cyanobacterial phycobilisomes. Mol. Microbiol. 2:101-107.
30. Kehoe, D. M., and A. R. Grossman. 1994. Complementary chromatic adaptation: photoperception to gene regulation. Semin. Cell Biol. 5:303-313.
31. Kehoe, D. M., and A. R. Grossman. 1997. New classes of mutants in complementary chromatic adaptation provide evidence for a novel four-step phosphorelay system. J. Bacteriol. 179:3914-3921.
32. Kehoe, D. M., and A. R. Grossman. 1996. Similarity of a chromatic adaptation sensor to phytochrome and ethylene receptors. Science 273:1409-1412.
33. Kehoe, D. M., and A. R. Grossman. 1998. Use of molecular genetics to investigate complementary chromatic adaptation: advances in transformation and complementation. Methods Enzymol. 297:279-290.
34. Laemmli, U. K. 1970. Cleavage of structural protein during the assembly of the head of bacteriophage T4. Nature 227:680-685.
35. Li, L., and J. C. Lagarias. 1992. Phytochrome assembly. Defining chromophore structural requirements for covalent attachment and photoreversibility. J. Biol. Chem. 267:19204-19210.
36. Lundell, D. J., and A. N. Glazer. 1981. Allophycocyanin B. J. Biol. Chem. 256:12600-12606.
37. Lundell, D. J., and A. N. Glazer. 1983. Molecular architecture of a light-harvesting antenna. Core substructure in Synechococcus 6301 phycobilisomes: two new allophycocyanin and allophycocyanin B complexes. J. Biol. Chem. 258:902-908.
38. Lundell, D. J., and A. N. Glazer. 1983. Molecular architecture of a light-harvesting antenna. Structure of the 18 S core-rod subassembly of the Synechococcus 6301 phycobilisome. J. Biol. Chem. 258:894-901.
39. Maxson, P., K. Sauer, J. H. Zhou, D. A. Bryant, and A. N. Glazer. 1989. Spectroscopic studies of cyanobacterial phycobilisomes lacking core polypeptides. Biochim. Biophys. Acta 977:40-51.
40. Mizuguchi, K., C. M. Deane, T. L. Blundell, and J. P. Overington. 1998. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7:2469-2471.
41. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
42. Seib, L. O., and D. M. Kehoe. 2002. A turquoise mutant genetically separates expression of genes encoding phycoerythrin and its associated linker peptides. J. Bacteriol. 184:962-970.
43. Shi, J. Y., T. L. Blundell, and K. Mizuguchi. 2001. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310:243-257.
44. Sidler, W. A. 1994. Phycobilisome and phycobiliprotein structures, p. 139-216. In D. A. Bryant (ed.), The molecular biology of cyanobacteria. Kluwer, Dordrecht, The Netherlands.
45. Steglich, C., A. F. Post, and W. R. Hess. 2003. Analysis of natural populations of Prochlorococcus spp. in the northern Red Sea using phycoerythrin gene sequences. Environ. Microbiol. 5:681-690.
46. Suter, F., P. Fuglistaller, D. J. Lundell, A. N. Glazer, and H. Zuber. 1987. Amino acid sequences of α-allophycocyanin B from Synechococcus 6301 and Mastigodadus laminosus. FEBS Lett. 217:279-282.
47. Tandeau de Marsac, N. 1977. Occurrence and nature of chromatic adaptation in cyanobacteria. J. Bacteriol. 130:82-91.
48. Tandeau de Marsac, N. 1983. Phycobilisomes and complementary chromatic adaptation in cyanobacteria. Bull. Inst. Pasteur 81:201-254.
49. Tandeau de Marsac, N., and G. Cohen-Bazire. 1977. Molecular composition of cyanobacterial phycobilisomes. Proc. Natl. Acad. Sci. USA 74:1635-1639.
50. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
51. Yamanaka, G., D. J. Lundell, and A. N. Glazer. 1982. Molecular architecture of a light-harvesting antenna. Isolation and characterization of phycobilisome subassembly particles. J. Biol. Chem. 257:4077-4086.
52. Zhao, J., J. Zhou, and D. Bryant. 1992. Energy transfer process in phycobilisomes as deduced from analyses of mutants of Synechococcus sp. PCC 7002, p. 25-32. In N. Murata (ed.), Research in photosynthesis, vol. I. Kluwer, Dordrecht, The Netherlands.
53. Zhao, K.-H., and H. Scheer. 1995. Type I and type II reversible photochemistry of phycoerythrocyanin α-subunit from Mastigocladus laminosus both involve Z, E isomerization of phycoviolobilin chromophore and are controlled by sulfhydryls in apoprotein. Biochim. Biophys. Acta Bioenergetics 1228:244-253.