Cyanobacterial postgenomic research and systems biology

Trends in Biotechnology

Volumn 21, Issue 11, 2003, Pages 504-511

  Burja, Adam M ^a   Dhamwichukorn, Srisuda ^b   Wright, Phillip C ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CYTOLOGY; GENES; METABOLISM; MICROBIOLOGY; PROTEINS; RESEARCH;

CYANOBACTERIA;

BACTERIA;

BACTERIAL FLORA; BACTERIAL GENETICS; BACTERIAL GENOME; BIOINFORMATICS; BIOREMEDIATION; COMPUTER MODEL; CYANOBACTERIUM; DNA MICROARRAY; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ENGINEERING; GENOMICS; MOLECULAR BIOLOGY; NONHUMAN; PHARMACOGENOMICS; PRIORITY JOURNAL; PROTEOMICS; REVIEW;

BACTERIA (MICROORGANISMS); CYANOBACTERIA;

EID: 0142155254     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2003.08.008     Document Type: Review

References (70)

1. Bernal A., et al. Genomes online database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 29:2001;126-127.
2. Drell D. The department of energy microbial cell project: a 180° paradigm shift for biology. OMICS A Journal of Integrated Biology. 6:2002;3-9.
3. Fleischmann R., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
4. Ideker T., et al. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2:2001;343-372.
5. Kitano H. Systems biology: a brief overview. Science. 295:2002;1662-1664.
6. Ferrero R., Labigne A. Helicobacter pylori vaccine development in the postgenomic era: Can in silico translate to in vivo? Scand. J. Immunol. 53:2001;443-448.
7. Domenech P., et al. Mycobacterium tuberculosis in the postgenomic age. Curr. Opin. Microbiol. 4:2001;28-34.
8. Bowman S., Horrocks P. Assessing the impact of Plasmodium falciparum genome sequencing. Microbes Infect. 2:2000;1479-1487.
9. Goffeau A. Four years of postgenomic life with 6000 yeast genes. FEBS Lett. 480:2000;37-41.
10. Tinsley C., Nassif X. Meningococcal pathogenesis: at the boundary between the pre- and postgenomic eras. Curr. Opin. Microbiol. 4:2001;47-52.
11. Sinchaikul S., et al. Bioinformatics, functional genomics, and proteomics study of Bacillus sp. J. Chromatogr. B. 771:2002;261-287.
12. McGowan S., et al. Ancient blue-green blooms. Limnol. Oceanogr. 44:1999;436-439.
13. Burja A.M., et al. Marine cyanobacteria: a prolific source of natural products. Tetrahedron. 57:2001;9347-9377.
14. Altschul S., et al. Basic local alignment search tools. J. Mol. Biol. 215:1990;403-410.
15. Schena M., et al. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16:1998;301-306.
16. Lemieux B., et al. Overview of DNA chip technology. Mol. Breed. 4:1998;277-289.
17. Cho J.-C., Tiedje J.M. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68:2002;1425-1430.
18. Ye R., et al. Applications of DNA microarrays in microbial systems. J. Microbiol. Methods. 47:2001;257-272.
19. Zhou J., Thompson D. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13:2002;204-207.
20. Kuipers O. Genomics for food biotechnology: prospects of the use of high-throughput technologies for the improvement of food microorganisms. Curr. Opin. Biotechnol. 10:1999;511-516.
21. Schoolnik, G. (2002) Microarray analysis of bacterial pathogenicity. In Advances in Microbial Physiology (Vol. 46) (Poole, R., ed.), pp. 1-45, Academic Press.
22. Read T., et al. Finding drug targets in microbial genomes. Drug Discov. Today. 6:2001;887-892.
23. Beliaev A.S., et al. Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J. Bacteriol. 184:2002;4612-4616.
24. Schut G., et al. DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a new type of sulfur-reducing enzyme complex. J. Bacteriol. 183:2001;7027-7036.
25. Nakamura Y., et al. CyanoBase, the genome database for Synechocystis sp. strain PCC 6803: status for the year 2000. Nucleic Acids Res. 28:2000;72.
26. Hihara Y., et al. DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell. 13:2001;793-806.
27. Huang L., et al. Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light. J. Bacteriol. 184:2002;6845-6858.
28. Hihara Y., et al. DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J. Bacteriol. 185:2003;1719-1725.
29. Allakhverdiev S., et al. Salt stress inhibits the repair of photodamaged photosystem II by suppressing the transcription and translation of psbA genes in Synechocystis. Plant Physiol. 130:2002;1443-1453.
30. Kanesaki Y., et al. Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803. Biochem. Biophys. Res. Commun. 290:2002;339-348.
31. Gill R., et al. Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC 6803. J. Bacteriol. 184:2002;3671-3681.
32. Heffelfinger G., et al. Carbon sequestration in Synechococcus sp.: from molecular machines to hierarchical modelling. OMICS A Journal of Integrated Biology. 6:2002;305-330.
33. Inaba M., et al. Gene-engineered rigidification of membrane lipids enhances the cold inducibility of gene expression in Synechocystis. J. Biol. Chem. 278:2003;12191-12198.
34. Mikami K., et al. The histidine kinase Hik33 perceives osmotic stress and cold stress in Synechocystis sp. PCC 6803. Mol. Microbiol. 46:2002;905-915.
35. Singh A., Sherman L. Identification of iron-responsive, differential gene expression in the cyanobacterium Synechocystis sp. strain PCC 6803 with a customized amplification library. J. Bacteriol. 182:2000;3536-3543.
36. 2+-sensing system negatively regulates expression of the mntCAB operon in Synechocystis. Plant Cell. 14:2002;2901-2913.
37. 2+-sensing two-component system identified by systematic genomic and DNA microarray technology in Synechocystis. Plant Cell Physiol. 43:2002;S200.
38. Rudi K., et al. Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl. Environ. Microbiol. 68:2002;1146-1156.
39. Matsunaga T., et al. Fluorescent detection of cyanobacterial DNA using bacterial magnetic particles on a MAG-microarray. Biotechnol. Bioeng. 73:2001;400-405.
40. Castiglioni B., et al. Application of an universal DNA microarray to cyanobacterial diversity assessment. Minerva Biotechnol. 14:2002;253-257.
41. Taroncher-Oldenburg G., et al. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69:2003;1159-1171.
42. Masayuki O. Analysis of gene expression in the cyanobacterium Anabaena using a microarray. Plant Cell Physiol. 43:2002;S4.
43. Molloy M., et al. Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins. Electrophoresis. 22:2001;1686-1696.
44. Lester P., Hubbard S. Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics. Proteomics. 2:2002;1392-1405.
45. Wolters D., et al. An automated multi-dimensional protein identification technology for shotgun proteomics. Anal. Chem. 73:2001;5683-5690.
46. Link A., et al. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17:1999;676-682.
47. Hancock W., et al. The challenges of developing a sound proteomics strategy. Proteomics. 2:2002;352-359.
48. Shen Y., Smith R. Proteomics based on high-efficiency capillary separations. Electrophoresis. 23:2002;3106-3124.
49. Wang Y., et al. Proteomic study of the peripheral proteins from thylakoid membranes of the cyanobacterium Synechocystis sp. PCC 6803. Electrophoresis. 21:2000;1746-1754.
50. Sazuka T., et al. Cyano2Dbase updated: linkage of 234 protein spots to corresponding genes through N-terminal microsequencing. Electrophoresis. 20:1999;2160-2171.
51. Fulda S., et al. Proteomics of Synechocystis sp. strain PCC 6803. Identification of periplasmic proteins in cells grown at low and high salt concentrations. Eur. J. Biochem. 267:2000;5900-5907.
52. Ehling-Schulz M., et al. The UV-B stimulon of the terrestrial cyanobacterium Nostoc commune comprises early shock proteins and late acclimation proteins. Mol. Microbiol. 46:2002;827-843.
53. Yang C., et al. Integration of the information from gene expression and metabolic fluxes for the analysis of the regulatory mechanisms in Synechocystis. Appl. Microbiol. Biotechnol. 58:2002;813-822.
54. Pruess M., et al. The proteome analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31:2003;414-417.
55. Simon W., et al. Proteomic study of the soluble proteins from the unicellular cyanobacterium Synechocystis sp. PCC 6803 using automated matrix-assisted laser desorption/ionization-time of flight peptide mass fingerprinting. Proteomics. 2:2002;1735-1742.
56. Berman H., et al. The protein data bank. Acta Crystallogr. D. 58:(6):2002;899-907.
57. Oliver S., et al. Systematic functional analysis of the yeast genome. Trends Biotechnol. 16:1998;373-378.
58. Hesketh A., et al. Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor. Mol. Microbiol. 46:2002;917-932.
59. Christiansen G., et al. Nonribosomal peptide synthetase genes occur in most cyanobacterial genera as evidenced by their distribution in axenic strains of the PCC. Arch. Microbiol. 176:2001;452-458.
60. Burja A., Wright P. Look first to nature before invention: industrial applications for marine cyanobacteria. SIM News. 53:2003;4-9.
61. Hatzimanikatis V., Lee K. Dynamical analysis of gene networks requires both mRNA and protein expression information. Metab. Eng. 1:1999;275-281.
62. Graves P., Haystead T. Molecular biologist's guide to proteomics. Microbiol. Mol. Biol. Rev. 66:2002;39-63.
63. Frey K.M., et al. Technical-scale production of cyanophycin with recombinant strains of Escherichia coli. Appl. Environ. Microbiol. 68:2002;3377-3384.
64. Dittmann E., et al. Altered expression of two light-dependent genes in a microcystin-lacking mutant of Microcystis aeruginosa PCC 7806. Microbiol. 147:2001;3113-3119.
65. Krehenbrink M., et al. Evaluation of non-cyanobacterial genome sequences for occurrence of genes encoding proteins homologous to cyanophycin synthetase and cloning of an active cyanophycin synthetase from Acinetobacter sp. strain DSM 587. Arch. Microbiol. 177:2002;371-380.
66. Ogawa, T. et al. (2002) Genes essential to sodium-dependent bicarbonate transport in cyanobacteria: function and phylogenetic analysis. In 5th European Workshop on the Molecular Biology of Cyanobacteria, 9-12 June 2002, The Royal Swedish Academy of Sciences.
67. Liaimer, A. (2002) Molecular communication and responses in Nostoc: plant symbiosis. Doctorial Thesis, Department of Botany, Stockholm University, Sweden.
68. Choi J., et al. Proteome analysis of light-induced proteins in Synechocystis sp. PCC 6803: identification of proteins separated by 2D-PAGE using N-terminal sequencing and MALDI-TOF MS. Mol. Cells. 10:2000;705-711.
69. Huang, F. et al. (2002) Proteomics of Synechocystis 6803: identification of plasma membrane proteins. In 5th European Workshop on the Molecular Biology of Cyanobacteria, 9-12 June 2002, The Royal Swedish Academy of Sciences.
70. Kashino Y., et al. Proteomic analysis of a highly active photosystem II preparation from the cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel polypeptides. Biochemistry. 41:2002;8004-8012.