The tryptophan pathway genes of the Sargasso Sea metagenome: New operon structures and the prevalence of non-operon organization

Genome Biology

Volumn 9, Issue 1, 2008, Pages

  Kagan, Juliana ^a   Sharon, Itai ^a   Beja, Oded ^a   Kuhn, Jonathan C ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRANILIC ACID; CHORISMIC ACID; CONTIG; DNA; INDOLE; TRYPTOPHAN; BACTERIAL DNA;

AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GENETICS; BACTEROIDES FRAGILIS; BIOSYNTHESIS; CLOSTRIDIUM KLUYVERI; CORYNEBACTERIUM; GENE CLUSTER; GENE ORDER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC DATABASE; LEPTOSPIRA; MARINE BACTERIUM; MICROBIAL GENETICS; NEISSERIA MENINGITIDIS; NONHUMAN; NOSTOC; NUCLEOTIDE SEQUENCE; OPERON; SULFOLOBUS SOLFATARICUS; THERMOANAEROBACTER; THERMOPLASMA ACIDOPHILUM; UNINDEXED SEQUENCE; BACTERIAL GENE; BACTERIAL GENOME; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MICROBIOLOGY; SEA;

DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; MARINE BIOLOGY; METABOLIC NETWORKS AND PATHWAYS; OCEANS AND SEAS; OPERON; TRYPTOPHAN; WATER MICROBIOLOGY;

EID: 46249098896     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-1-r20     Document Type: Article

References (35)

1. Yanofsky C Using studies of tryptophan metabolism to answer basic biology questions. J Biol Chem 2003, 278:10859-10878. 10.1074/ jbc.X200012200 12556463
2. Li Y Wexler M Richardson DJ Bond PL Johnston AWB Screening a wide host-range, waste-water metagenomic library in tryptophan auxotrophs of Rhizobium leguminosarum and of Escherichia coli reveals different classes of cloned trp genes. Environ Microbiol 2005, 7:1927-1936. 10.1111/j.1462-2920.2005.00853.x 16309391
3. Schwarz T Uthoff K Klinger C Meyer HE Bartholmes P Kaufmann M Multifunctional tryptophan-synthesizing enzyme the molecular weight of the Euglena Gracilis protein is unexpectedly low. Journal of Biological Chemistry 1997, 272:10616-10623. 10.1074/jbc.272.16.10616 9099709
4. Xie G Keyhani NO Bonner CA Jensen RA Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol Mol Biol Rev, 2003 67:303-342. 193870 12966138 10.1128/MMBR.67.3.303-342.2003
5. Xie G Bonner CA Song J Keyhani NO Jensen RA Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy. BMC Biology 2004, 2:15. 471576 15214963 10.1186/ 1741-7007-2-15
6. Venter JC Remington K Heidelberg JF Halpern AL Rusch D Eisen JA Wu D Paulsen I Nelson KE Nelson W Fouts DE Levy S Knap AH Lomas MW Nealson K White O Peterson J Hoffman J Parsons R Baden-Tillson H Pfannkoch C Rogers YH Smith HO Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74. 10.1126/science.1093857 15001713
7. Rodríguez-Valera F Environmental genomics, the big picture? FEMS Microbiol Lett 2004, 231:153-158. 10.1016/S0378-1097(04)00006-0 15027428
8. Crawford IP Milkman R Orthologous and paralogous divergence, reticulate evolution, and lateral gene transfer in bacterial trp genes. Evolution at the molecular level Sunderland, MA: Sinauer and Assoc Inc Selander RK, Clark AG, Whittam TS 1991:77-95.
9. Falkowski PG De Vargas C Genomics and evolution. Shotgun sequencing in the sea: A blast from the past? Science 2004, 304:58-60. 10.1126/ science.1097146 15066774
10. DeLong EF Microbial community genomics in the ocean. Nat Rev Microbiol 2005, 3:459-469. 10.1038/nrmicro1158 15886695
11. Tatusov RL Fedorova ND Jackson JD Jacobs AR Kiryutin B Koonin EV Krylov DM Mazumder R Mekhedov SL Nikolskaya AN Rao BS Smirnov S Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA The COG database: An updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41. 222959 12969510 10.1186/1471-2105-4-41
12. Xie G Frost C Bonner CA Jensen RA Significance of two distinct types of tryptophan synthase beta chain in bacteria, archaea and higher plants. Genome Biol 2001, 3;0004.0001-0004.0013. 10.1186/gb-2001-3-1-research0004
13. Merkl R Modelling the evolution of the archeal tryptophan synthase. BMC Evolutionary Biology 2007, 7:59. 1854888 17425797 10.1186/1471-2148-7-59
14. Leopoldseder S Hettwer S Sterner R Evolution of multi-enzyme complexes: the case of tryptophan synthase. Biochemistry 2006, 45:14111-14119. 10.1021/bi061684b 17115706
15. Hettwer S Sterner R A novel tryptophan synthase b-subunit from the hyperthermophile Thermotoga maritima. Quarternary structure, steady-state kinetics, and putative physiological role. J Biol Chem 2002, 277:8194-8201. 10.1074/jbc.M111541200 11756459
16. Hyde CC Ahmed SA Padlan EA Miles EW Davies DR Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium. J Biol Chem 1988, 263:17857-17871. 3053720
17. Oppenheim DS Yanofsky C Translational coupling during expression of the tryptophan operon of Escherichia coli. Genetics 1980, 95;785-795. 1214269 6162715
18. Weber-Ban E Hur O Bagwell C Banik U Yang LH Miles EW Dunn MF Investigation of allosteric linkages in the regulation of tryptophan synthase: The roles of salt bridges and monovalent cations probed by site-directed mutation, optical spectroscopy, and kinetics. Biochemistry 2001, 40:3497-3511. 10.1021/bi002690p 11297416
19. Giovannoni SJ Tripp HJ Givan S Podar M Vergin KL Baptista D Bibbs L Eads J Richardson TH Noordewier M Rappe MS Short JM Carrington JC Mathur EJ Genome streamlining in a cosmopolitan oceanic bacterium. Science 2005, 309:1242-1245. 10.1126/science.1114057 16109880
20. Hendrix RW Lawrence JG Hatfull GF Casjens S The origins and ongoing evolution of viruses. Trends Microbiol 2000, 8:504-508. 11121760 10.1016/ S0966-842X(00)01863-1
21. Glansdorff N On the origin of operons and their possible role in evolution toward thermophily. J Mol Evol 1999, 49:432-438. 10.1007/ PL00006566 10486001
22. Pabst MJ Kuhn JC Somerville RL Feedback regulation in the anthranilate aggregate from wild type and mutant strains of Escherichia coli. J Biol Chem 1973, 248:901-914. 4567790
23. Balbinder E Intergeneric complementation between A and B components of bacterial tryptophan synthetases. Biochem and Biophys Res Commun 1964, 17:770-774. 10.1016/0006-291X(64)90429-2
24. Dicamelli RF Balbinder E The association of tryptophan synthetase subunits from Escherichia coli and Salmonella typhimurium in homologous and heterologous combinations. Genet Res 1976, 27:323-333. 776745
25. Dicamelli RF Balbinder E Lebowits J Pressure effects on the association of the 2 subunits of tryptophan synthetase from Escherichia coli and Salmonella typhimurium. Arch Biochem and Biophys 1973, 155:315-324. 10.1016/0003-9861(73)90120-3
26. Barona-Gómez F Hodgson DA Occurrence of a putative ancient-like isomerase involved in histidine and tryptophan biosynthesis. EMBO reports 2003, 4:296-300. 1315899 12634849 10.1038/sj.embor.embor771
27. Crawford IP Milkman R Orthologous and paralogous divergence, reticulate evolution, and lateral gene transfer in bacterial trp genes. Evolution at the molecular level Sunderland, MA: Sinauer and Assoc Inc Selander RK, Clark AG, Whittam TS 1991:77-95.
28. Kane JF Holmes WM Jensen RA Metabolic interlock. The dual function of a folate pathway gene as an extra-operonic gene of tryptophan biosynthesis. J Biol Chem 1972, 247:1587-1596. 4622231
29. BLAST x: NCBI database http://www.ncbi.nlm.nih.gov/blast/
30. Losick R Sonenshein AL Molecular biology. Turning gene regulation on its head. Science 2001, 293:2018-2019. 10.1126/science.1064982 11557871
31. Yanofsky C Advancing our knowledge in biochemistry, genetics, and microbiology through studies on tryptophan metabolism. Annu Rev Biochem 2001, 70:1-37. 10.1146/annurev.biochem.70.1.1 11395401
32. Tam le T Eymann C Antelmann H Albrecht D Hecker M Global gene expression profiling of Bacillus subtilis in response to ammonium and tryptophan starvation as revealed by transcriptome and proteome analysis. J Mol Microbiol Biotechnol 2007, 12:121-130. 10.1159/000096467 17183219
33. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 1994, 22:4673-4680. 308517 7984417 10.1093/nar/22.22.4673
34. Swofford DL PAUP*. Phylogenetic analysis using parsimony (*and other methods) Sunderland, Massachusetts, USA Sinauer Associates Incorporated 4.0; 2002. 12504223
35. Page RDM TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996, 12:357-358. 8902363