A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Rogers, Matthew B ^a   Watkins, Russell F ^b,d   Harper, James T ^a   Durnford, Dion G ^c   Gray, Michael W ^b   Keeling, Patrick J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b DALHOUSIE UNIVERSITY   (Canada)

^c UNIVERSITY OF NEW BRUNSWICK   (Canada)

^d Centre for Molecular Medicine and Therapeutics   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; ENZYME; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; RIBULOSEPHOSPHATE 3 EPIMERASE; TRANSKETOLASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; DNA; EPIMERASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE (NADP); GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE (NADP)(PHOSPHORYLATING); RIBULOSEPHOSPHATE 3-EPIMERASE;

ARTICLE; BACTERIAL GENE; BACTERIUM; CELLULAR DISTRIBUTION; CONTROLLED STUDY; ENZYME ANALYSIS; EUKARYOTE; EUKARYOTIC CELL; GENE TRANSFER; GENETIC ANALYSIS; GENETIC LINE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PHYLOGENETIC TREE; PHYLOGENY; ANIMAL; COMPARATIVE STUDY; ENZYMOLOGY; EXPRESSED SEQUENCE TAG; GENE; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); EUKARYOTA;

ANIMALS; BACTERIA; BACTERIAL PROTEINS; CARBOHYDRATE EPIMERASES; CONSERVED SEQUENCE; DNA; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE TRANSFER, HORIZONTAL; GENES; GENES, BACTERIAL; GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (NADP+); GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)(PHOSPHORYLATING); MOLECULAR SEQUENCE DATA; SPECIES SPECIFICITY; TRANSKETOLASE;

EID: 34447509748     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-89     Document Type: Article

References (51)

1. Lateral genomics. WF Doolittle, Trends Cell Biol 1999 9 M5 8 10.1016/S0962-8924(99)01664-5 10611671
2. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. JA Eisen, Curr Opin Genet Dev 2000 10 606 611 10.1016/S0959-437X(00)00143-X 11088009
3. Genomic islands and the ecology and evolution of Prochlorococcus. ML Coleman MB Sullivan AC Martiny C Steglich K Barry EF Delong SW Chisholm, Science 2006 311 1768 70 10.1126/science.1122050 16556843
4. Horizontal gene transfer in prokaryotes: quantification and classification. EV Koonin KS Makarova L Aravind, Annu Rev Microbiol 2001 55 709 742 10.1146/annurev.micro.55.1.709 11544372
5. Lateral gene transfer and the nature of bacterial innovation. H Ochman JG Lawrence EA Groisman, Nature 2000 405 299 304 10.1038/35012500 10830951
6. Highways of gene sharing in prokaryotes. RG Beiko TJ Harlow MA Ragan, Proc Natl Acad Sci USA 2005 102 14332 14337 16176988 10.1073/pnas.0504068102
7. Do different surrogate methods detect lateral genetic transfer events of different relative ages? MA Ragan TJ Harlow RG Beiko, Trends Microbiol 2006 14 4 8 10.1016/j.tim.2005.11.004 16356716
8. Lateral gene transfer: when will adolescence end? JG Lawrence H Hendrickson, Mol Microbiol 2003 50 739 749 10.1046/j.1365-2958.2003.03778.x 14617137
9. What tangled web: barriers to rampant horizontal gene transfer. CG Kurland, Bioessays 2005 27 741 747 10.1002/bies.20258 15954096
10. The fate of laterally transferred genes: life in the fast lane to adaptation or death. W Hao GB Golding, Genome Res 2006 16 636 643 16651664 10.1101/gr.4746406
11. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. MJ Stanhope A Lupas MJ Italia KK Koretke C Volker JR Brown, Nature 2001 411 940 944 10.1038/35082058 11418856
12. Microbial genes in the human genome: lateral transfer or gene loss? SL Salzberg O White J Peterson JA Eisen, Science 2001 292 1903 1906 10.1126/science.1061036 11358996
13. The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Y Boucher WF Doolittle, Mol Microbiol 2000 37 703 16 10.1046/j.1365-2958.2000.02004.x 10972794
14. Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica. JE Nixon A Wang J Field HG Morrison AG McArthur ML Sogin BJ Loftus J Samuelson, Eukaryot Cell 2002 1 181 90 12455953 10.1128/EC.1.2.181-190.2002
15. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. JM Archibald MB Rogers M Toop K Ishida PJ Keeling, Proc Natl Acad Sci USA 2003 100 7678 7683 12777624 10.1073/pnas.1230951100
16. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. JO Andersson AM Sjogren LA Davis TM Embley AJ Roger, Curr Biol 2003 13 94 104 10.1016/S0960-9822(03)00003-4 12546782
17. Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein. RF Waller CH Slamovits PJ Keeling, Mol Biol Evol 2006 23 1437 1443 10.1093/molbev/msl008 16675503
18. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. PJ Keeling JD Palmer, Proc Natl Acad Sci USA 2001 98 10745 10750 11526220 10.1073/pnas.191337098
19. Lateral gene transfer in eukaryotes. JO Andersson, Cell Mol Life Sci 2005 62 1182 97 10.1007/s00018-005-4539-z 15761667
20. Widespread horizontal transfer of mitochondrial genes in flowering plants. U Bergthorsson KL Adams B Thomason JD Palmer, Nature 2003 424 197 201 10.1038/nature01743 12853958
21. An enigmatic GAPDH gene in the symbiotic dinoflagellate genus Symbiodinium and its related species (the order Suessiales): possible lateral gene transfer between two eukaryotic algae, dinoflagellate and euglenophyte. K Takishita K Ishida T Maruyama, Protist 2003 154 443 54 10.1078/ 143446103322454176 14658500
22. On surrogate methods for detecting lateral gene transfer. MA Ragan, FEMS Microbiol Lett 2001 201 187 91 10.1111/j.1574-6968.2001.tb10755.x 11470360
23. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. AJ Roger LA Hug, Philos Trans R Soc Lond B Biol Sci 2006 361 1039 54 10.1098/rstb.2006.1845 16754613
24. A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha. PJ Keeling Y Inagaki, Proc Natl Acad Sci USA 2004 101 15380 15385 15492217 10.1073/pnas.0404505101
25. Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. JO Andersson RP Hirt PG Foster AJ Roger, BMC Evol Biol 2006 6 27 16551352 10.1186/1471-2148-6-27
26. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. SL Baldauf JD Palmer, Proc Natl Acad Sci USA 1993 90 11558 11562 8265589 10.1073/pnas.90.24.11558
27. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. JM Archibald D Longet J Pawlowski PJ Keeling, Mol Biol Evol 2002 20 62 66 10.1093/molbev/msg006
28. Rooting the eukaryote tree by using a derived gene fusion. A Stechmann T Cavalier-Smith, Science 2002 297 89 91 10.1126/science.1071196 12098695
29. Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids. JO Andersson SW Sarchfield AJ Roger, Mol Biol Evol 2005 22 85 90 10.1093/molbev/msh254 15356278
30. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. J Huang Y Xu JP Gogarten, Mol Biol Evol 2005 22 2142 2146 10.1093/molbev/msi221 16049196
31. A glyceraldehyde-3-phosphate dehydrogenase with eubacterial features in the amitochondriate eukaryote, Trichomonas vaginalis. A Markos A Miretsky M Muller, J Mol Evol 1993 37 631 43 8114116
32. Molecular analysis of glyceraldehyde-3-phosphate dehydrogenase in Trypanoplasma borelli: an evolutionary scenario of subcellular compartmentation in kinetoplastida. EA Wiemer V Hannaert PRLA van den Ijssel J Van Roy FR Opperdoes PA Michels, J Mol Evol 1995 40 443 54 10.1007/BF00164030 7769620
33. Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer. Q Qian PJ Keeling, Protist 2001 152 193 201 10.1078/1434-4610-00059 11693658
34. Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer. RM Figge M Schubert H Brinkmann R Cerff, Mol Biol Evol 1999 16 429 440 10331270
35. The tree of eukaryotes. PJ Keeling G Burger DG Durnford BF Lang RW Lee RE Pearlman AJ Roger MW Gray, Trends Ecol Evol 2005 20 670 676 10.1016/j.tree.2005.09.005 16701456
36. A transcriptional fusion of genes encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and enolase in dinoflagellates. K Takishita NJ Patron K Ishida T Maruyama PJ Keeling, J Eukaryot Microbiol 2005 52 343 8 10.1111/j.1550-7408.2005.00042x 16014012
37. Compartment-specific isoforms of TPI and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of the eukaryotic glycolytic pathway. MF Liaud C Lichtle K Apt W Martin R Cerff, Mol Biol Evol 2000 17 213 223 10677844
38. Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. W Martin H Brinkmann C Savonna R Cerff, Proc Natl Acad Sci USA 1993 90 8692 8696 8378350 10.1073/pnas.90.18.8692
39. A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. K Henze A Badr M Wettern R Cerff W Martin, Proc Natl Acad Sci USA 1995 92 9122 9126 7568085 10.1073/pnas.92.20.9122
40. Phylogenetic relationships of the glycolytic enzyme, glyceraldehyde-3- phosphate dehydrogenase, from parabasalid flagellates. E Viscogliosi M Muller, J Mol Evol 1998 47 190 199 10.1007/PL00006376 9694668
41. The transketolase gene family of the resurrection plant Craterostigma plantagineum: differential expression during the rehydration phase. G Bernacchia G Schwall F Lottspeich F Salamini D Bartels, Embo J 1995 14 610 8 7859749
42. Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. I Ruiz-Trillo CE Lane JM Archibald AJ Roger, J Eukaryot Microbiol 2006 53 379 384 10.1111/j.1550-7408.2006.00118.x 16968456
43. EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates. GH Gile NJ Patron PJ Keeling, Protist 2006 157 435 444 10.1016/j.protis.2006.06.002 16904374
44. http://amoebidia.bcm.umontreal.ca/pepdb/
45. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. EV Armbrust JA Berges C Bowler BR Green D Martinez NH Putnam S Zhou AE Allen KE Apt M Bechner, Science 2004 306 79 86 10.1126/science.1101156 15459382
46. http://genome.jgi-psf.org/Phatr1/Phatr1.home.html
47. Improved prediction of signal peptides: SignalP 3.0. JD Bendtsen H Nielsen G von Heijne S Brunak, J Mol Biol 2004 340 783 795 10.1016/j.jmb.2004. 05.028 15223320
48. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
49. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 4 10.1093/bioinformatics/btg180 12912839
50. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. HA Schmidt K Strimmer M Vingron A von Haeseler, Bioinformatics 2002 18 502 504 10.1093/bioinformatics/18.3.502 11934758
51. http://www.tree-puzzle.de