Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylellaspecies and in heterocystous cyanobacteria

Genome Biology

Volumn 4, Issue 2, 2003, Pages

  Xie, Gary ^a,b   Bonner, Carol A ^a   Brettin, Tom ^b   Gottardo, Raphael ^b   Keyhani, Nemat O ^a   Jensen, Roy A ^a,b,c  

^a UNIVERSITY OF FLORIDA   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c CITY COLLEGE OF NEW YORK   (United States)

Author keywords

Anthranilate; Codon Usage; Coxiella Burnetii; Gene Block; Lateral Gene Transfer

Indexed keywords

BACTERIAL PROTEIN; REPRESSOR PROTEIN; TRYPTOPHAN; TRYPTOPHAN REPRESSOR PROTEIN;

AMINO ACID SEQUENCE; ANABAENA; ARTICLE; BIOSYNTHESIS; CODON; CYANOBACTERIUM; GAMMAPROTEOBACTERIA; GENETICS; HORIZONTAL GENE TRANSFER; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANABAENA; BACTERIAL PROTEINS; BASE SEQUENCE; CODON; CYANOBACTERIA; GAMMAPROTEOBACTERIA; GENE TRANSFER, HORIZONTAL; MOLECULAR SEQUENCE DATA; OPERON; PHYLOGENY; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRYPTOPHAN;

EID: 0037264679     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2003-4-2-r14     Document Type: Article

References (58)

1. Margulis L: Symbiosis in Cell Evolution. 1981, San Francisco: WH Freeman
2. Gray MW: Evolution of organellar genomes. Curr Opin Genet Dev. 1999, 9: 678-687. 10.1016/S0959-437X(99)00030-1. DOI: 10.1016/S0959-437X(99)00030-1
3. Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV: Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 1998, 14: 442-444. 10.1016/S0168-9525(98)01553-4. DOI: 10.1016/S0168-9525(98)01553-4
4. Lawrence JG, Ochman H: Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA. 1998, 95: 9413-9417. 10.1073/pnas.95.16.9413. DOI: 10.1073/pnas.95.16.9413
5. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, et al: Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 1999, 399: 323-329. 10.1038/20601. DOI: 10.1038/20601
6. Ochman H, Lawrence JG, Groisman EA: Lateral gene transfer and the nature of bacterial innovation. Nature. 2000, 405: 299-304. 10.1038/35012500. DOI: 10.1038/35012500
7. Doolittle WF: Phylogenetic classification and the universal tree. Science. 1999, 284: 2124-2129. 10.1126/science.284.5423.2124. DOI: 10.1126/science.284.5423.2124
8. Martin W: Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. BioEssays. 1999, 21: 99-104. 10.1002/(SICI)1521-1878(199902)21:2<99::AID-BIES3>3.3.CO;2-2. DOI: 10.1002/(SICI)1521-1878(199902)21:2<99::AID-BIES3>3.0.CO;2-B
9. Syvanen M: On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes. J Mol Evol. 2002, 54: 258-266. 10.1007/s0023901-0007-z. DOI: 10.1007/s0023901-0007-z
10. Kyrpides NC, Olsen GJ: Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry?. Trends Genet. 1999, 15: 298-299. 10.1016/S0168-9525(99)01811-9. DOI: 10.1016/S0168-9525(99)01811-9
11. Stiller JW, Hall BD: Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Science. 1999, 286: 1443-10.1126/science.286.5444.1443a. DOI: 10.1126/science.286.5444.1443a
12. Kurland CG: Something for everyone: Horizontal gene transfer in evolution. EMBO Rep. 2000, 1: 92-95. 10.1093/embo-reports/kvd042. DOI: 10.1093/embo-reports/kvd042
13. Salzberg SL, White O, Peterson J, Eisen JA: Microbial genes in the human genome: lateral transfer or gene loss?. Science. 2001, 292: 1903-1906. 10.1126/science.1061036. DOI: 10.1126/science.1061036
14. Stanhope MJ, Lupas A, Italia MJ, Koretke KK, Volker C, Brown JR: Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature. 2001, 411: 940-944. 10.1038/35082058. DOI: 10.1038/35082058
15. Glansdorff N: About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Mol Microbiol. 2000, 38: 177-185. 10.1046/j.1365-2958.2000.02126.x. DOI: 10.1046/j.1365-2958.2000.02126.x
16. Woese CR: Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA. 2000, 97: 8392-8396. 10.1073/pnas.97.15.8392. DOI: 10.1073/pnas.97.15.8392
17. Lawrence JG, Ochman H: Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA. 1998, 95: 9413-9417. 10.1073/pnas.95.16.9413. DOI: 10.1073/pnas.95.16.9413
18. Wang B: Limitations of compositional approach to identifying horizontally transferred genes. J Mol Evol. 2001, 53: 244-250. 10.1007/s002390010214. DOI: 10.1007/s002390010214
19. Koski LB, Morton RA, Golding GB: Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol. 2001, 18: 404-412. DOI: 10.1093/oxfordjournals.molbev.a003816
20. Ragan MA: On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett. 2001, 201: 187-191. 10.1016/S0378-1097(01)00262-2. DOI: 10.1111/j.1574-6968.2001.tb10755.x
21. Lawrence JG, Ochman H: Reconciling the many facets of lateral gene transfer. Trends Microbiol. 2002, 10: 1-4. 10.1016/S0966-842X(01)02282-X. DOI: 10.1016/S0966-842X(01)02282-X
22. Ragan M: Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev. 2001, 11: 620-626. 10.1016/S0959-437X(00)00244-6. DOI: 10.1016/S0959-437X(00)00244-6
23. Xie G, Bonner CA, Jensen RA: Dynamic diversity of the tryptophan pathway in the chlamydiae: reductive evolution and a novel operon for tryptophan recapture. Genome Biol. 2002, 3: research0005.1-0005.13. 10.1186/gb-2002-3-9-research0051. DOI: 10.1186/gb-2002-3-9-research0051
24. Henner D, Yanofsky C: Biosynthesis of aromatic amino acids. In Bacillus subtilis and other Gram-positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. Edited by: Sonenshein AL, Hoch J, Losick R. 1993, Washington, DC: ASM Press, 269-280. DOI: 10.1128/9781555818388.ch19
25. Subramaniam PS, Xie G, Xia T, Jensen RA: Substrate ambiguity of 3-deoxy-D-manno-octulosonate 8-phosphate synthase from Neisseria gonorrhoeae in the context of its membership in a protein family containing a subset of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases. J Bacteriol. 1998, 180: 119-127.
26. Jensen RA, Xie G, Bonner CA: The correct phylogenetic relationship of KdsA (3-deoxy-D-manno-octulosonate 8-phosphate synthase) with one of two independently evolved classes of AroA (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase. J Mol Evol. 2002, 54: 416-423. DOI: 10.1007/s00239-001-0031-z)
27. Gosset G, Bonner CA, Jensen RA: Microbial origin of plant-type 2-keto-3-deoxy-D-arabino-heptulosonate 7-phosphate synthases, exemplified by the chorismate-and tryptophan-regulated enzyme from Xanthomonas campestris. J Bacteriol. 2001, 183: 4061-4070. 10.1128/JB.183.13.4061-4070.2001. DOI: 10.1128/JB.183.13.4061-4070.2001
28. Xie G, Bonner CA, Jensen RA: Cyclohexadienyl dehydrogenase from Pseudomonas stutzeri exemplifies a widespread type of tyrosine-pathway dehydrogenase in the TyrA protein family. Comp Biochem Physiol C Toxicol Pharmacol. 2000, 125: 65-83. 10.1016/S0742-8413(99)00090-0.
29. Fitch WM: Homology: a personal view on some of the problems. Trends Genet. 2000, 16: 227-231. 10.1016/S0168-9525(00)02005-9. DOI: 10.1016/S0168-9525(00)02005-9
30. Van Vliet F, Boyen A, Glansdorff N: On interspecies gene transfer: the case of the argF gene of Escherichia coli. Ann Inst Pasteur Microbiol. 1988, 139: 493-496. 10.1016/0769-2609(88)90111-1. DOI: 10.1016/0769-2609(88)90111-1
31. Hooper SD, Berg OG: Detection of genes with atypical nucleotide sequence in microbial genomes. J Mol Evol. 2002, 54: 365-375. DOI: 10.1007/s00239-001-0051-8
32. Mohamed MES, Zaar A, Ebenau-Jehle C, Fuchs G: Reinvestigation of a new type of aerobic benzoate metabolism in the proteobacterium Azoarcus evansii. J Bacteriol. 2001, 183: 1899-1908. 10.1128/JB.183.6.1899-1908.2001. DOI: 10.1128/JB.183.6.1899-1908.2001
33. Schühle K, Jahn M, Ghisla S, Fuchs G: Two similar gene clusters coding for enzymes of a new type of aerobic 2-aminobenzoate (anthranilate) metabolism in the bacterium Azoarcus evansii. J Bacteriol. 2001, 183: 5268-5278. 10.1128/JB.183.18.5268-5278.2001. DOI: 10.1128/JB.183.18.5268-5278.2001
34. Calhoun DH, Bonner CA, Gu W, Xie G, Jensen RA: The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa. Genome Biol. 2001, 2: research0030.1-0030.16. 10.1186/gb-2001-2-8-research0030. DOI: 10.1186/gb-2001-2-8-research0030
35. Quadri LEN, Keating TA, Patel HM, Walsh CT: Assembly of the Pseudomonas aeruginosa nonribosomal peptide siderophore pyochelin: In vitro reconstitution of aryl-4,2-bisthiazoline synthetase activity from PchD, PchE, and PchF. Biochemistry. 1999, 38: 14941-14954. 10.1021/bi991787c. DOI: 10.1021/bi991787c
36. Patel HM, Walsh CT: In vitro reconstitution of the Pseudomonas aeruginosa nonribosomal peptide synthesis of pyochelin: characterization of backbone tailoring thiazoline reductase and N-methyltransferase activities. Biochemistry. 2001, 40: 9023-9031. 10.1021/bi010519n. DOI: 10.1021/bi010519n
37. Guindon S, Perrière S: Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Mol Biol Evol. 2001, 18: 1838-1840. DOI: 10.1093/oxfordjournals.molbev.a003972
38. Koski L, Golding GB: The closest BLAST hit is often not the nearest neighbor. J Mol Evol. 2001, 52: 540-542. DOI: 10.1007/s002390010184
39. Essar DW, Eberly L, Hadero A, Crawford IP: Identification and characterization of genes for a second anthranilate synthase in Pseudomonas aeruginosa: interchangeability of the two anthranilate synthases and evolutionary implications. J Bacteriol. 1990, 172: 884-900.
40. Mavrodi DV, Bonsall RF, Delaney SM, Soule MJ, Phillips G, Thomashow LS: Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PA01. J Bacteriol. 2001, 183: 6454-6465. 10.1128/JB.183.21.6454-6465.2001. DOI: 10.1128/JB.183.21.6454-6465.2001
41. Ryding JJ, Anderson TB, Champness WC: Regulation of the Streptomyces coelicolor calcium-dependent antibiotic by absA, encoding a cluster-linked two-component system. J Bacteriol. 2002, 184: 794-805. DOI: 10.1128/JB.184.3.794-805.2002
42. Jensen RA: Enzyme recruitment in the evolution of new function. Annu Rev Microbiol. 1976, 30: 409-425. 10.1146/annurev.mi.30.100176.002205. DOI: 10.1146/annurev.mi.30.100176.002205
43. Peden J: CodonW as a freeware release for codon usage analysis. [http://www.molbiol.ox.ac.uk/cu/culong.html#Codonw]
44. GenBank Database. [http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html]
45. Lehmann EL, D'Abrera HJM: Nonparametrics: Statistical Methods Based on Ranks, Rev Edn. 1998, Englewood Cliffs, NJ: Prentice-Hall, 292-323.
46. Pesole G, Attimonelli M, Liuni S: A backtranslation method based on codon usage strategy. Nucleic Acids Res. 1988, 16: 1715-1728. DOI: 10.1093/nar/16.5.1715
47. Nakamura Y, Gojobori T, Ikemura T: Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 2000, 28: 292-10.1093/nar/28.1.292. DOI: 10.1093/nar/28.1.292
48. Codon Usage Database. [http://www.kazusa.or.jp/codon]
49. Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM: The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 2001, 29: 173-174. 10.1093/nar/29.1.173. DOI: 10.1093/nar/29.1.173
50. Ribosomal Database Project II. [http://rdp.cme.msu.edu/html]
51. 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 Acids Res. 1994, 22: 4673-4680. DOI: 10.1093/nar/22.22.4673
52. Hall T: Biological Sequence Alignment Editor for Windows 95/98/NT, 5.0.9 Edn. Raleigh: North Carolina State University, [http://www.mbio.ncsu.edu/BioEdit/bioedit.html]
53. Felsenstein J: PHYLIP - Phylogeny inference package (version 3.2). Cladistics. 1989, 5: 164-166.
54. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH: CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acid Res. 2002, 30: 281-283. 10.1093/nar/30.1.281. DOI: 10.1093/nar/30.1.281
55. NCBI Conserved Domain Database.[http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml]
56. ERGO. [http://wit.integratedgenomics.com/ERGO]
57. Xie G, Forst C, Bonner C, Jensen RA: Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants. Genome Biol. 2002, 3: research0004.1-0004.13. 10.1186/gb-2001-3-1-research0004. DOI: 10.1186/gb-2002-3-9-research0051
58. Mackenzie C, Simmons AE, Kaplan S: Multiple chromosomes in bacteria: The yin and yang of trp gene localization in Rhodobacter sphaeroides 2.4.1. Genetics. 1999, 153: 525-538.