Multiple horizontal gene transfer events and domain fusions have created novel regulatory and metabolic networks in the oomycete genome

PLoS ONE

Volumn 4, Issue 7, 2009, Pages

  Morris, Paul Francis ^a   Schlosser, Laura Rose ^a   Onasch, Katherine Diane ^a   Wittenschlaeger, Tom ^a   Austin, Ryan ^b   Provart, Nicholas ^b  

^a BOWLING GREEN STATE UNIVERSITY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

3 OXOACID COENZYME A TRANSFERASE; 6 PHOSPHOFRUCTO 2 KINASE; ACETYL COENZYME A CARBOXYLASE; ADENOSINE TRIPHOSPHATE CITRATE LYASE; ADENOSINE TRIPHOSPHATE PHOSPHORIBOSYLTRANSFERASE; ANTHRANILATE SYNTHASE; ASPARTATE KINASE; CARBAMOYL PHOSPHATE SYNTHASE; DNA DIRECTED RNA POLYMERASE III; DNA TOPOISOMERASE; GLUTAMINASE; GUANOSINE TRIPHOSPHATE CYCLOHYDROLASE II; HOMOSERINE DEHYDROGENASE; METHYLMALONYL COENZYME A MUTASE; MOLYBDOPTERIN; OROTIDINE 5' PHOSPHATE DECARBOXYLASE; PEROXIREDOXIN; PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE; PROTEOME; PYRROLINE 5 CARBOXYLATE REDUCTASE; PYRUVATE CARBOXYLASE; RNA POLYMERASE II;

ARABIDOPSIS; ARTICLE; BACTERIAL GENOME; CONTROLLED STUDY; DIATOM; ENDOSYMBIONT; ENZYME ACTIVITY; EUKARYOTE; FUNGAL GENETICS; GENETIC ANALYSIS; GENETIC CONSERVATION; HORIZONTAL GENE TRANSFER; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; OOMYCETES; ORTHOLOGY; PHYLOGENY; PHYTOPHTHORA; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; FUNGAL GENOME; GENE FUSION; GENETICS; METABOLISM; SPECIES DIFFERENCE;

ANIMALIA; BACILLARIOPHYTA; BACTERIA (MICROORGANISMS); EUKARYOTA; OOMYCETES; PHYTOPHTHORA SOJAE; STRAMENOPILES;

GENE FUSION; GENE TRANSFER, HORIZONTAL; GENOME, FUNGAL; OOMYCETES; SPECIES SPECIFICITY;

EID: 67650511674     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006133     Document Type: Article

References (43)

1. Dorrance AE, McClure SA, DeSilva A (2003) Pathogenic Diversity of Phytophthora sojae in Ohio Soybean Fields. Plant Dis 87: 139-146.
2. Judelson H (2007) Genomics of the plant pathogenic oomycete Phytophthora: insights into biology and evolution. Adv Genet 57: 97-141.
3. Simpson AGB, Roger AJ (2004) The real kingdoms of eukaryotes. Curr Biol 14.
4. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, et al. (2006) Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis. Science 313: 1261-1266.
5. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239-244.
6. Reyes-Prieto A, Moustafa A, Bhattacharya D (2008) Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol 18: 956-962.
7. Bordenstein SR (2008) Evolutionary genomics: Transdomain gene transfers. Curr Biol 17: R935-R936.
8. Peixoto L, Roos D (2007) Genomic scale analysis of lateral gene transfer in Apicomplexan parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development. BMC Bioinformatics 8(Suppl 8): S5.
9. Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ (2006) Evolution of Filamentous Plant Pathogens: Gene Exchange across Eukaryotic Kingdoms. Curr Biol 16: 1857-1864.
10. Andersson JO (2006) Convergent Evolution: Gene Sharing by Eukaryotic Plant Pathogens. Curr Biol 16: R804-R806.
11. Anantharamana V, Iyer ML, Aravind L (2007) Comparative genomics of protists:new insights into the evolution of eukaryotic signal transduction and gene regulation. Annu Rev Microbiol 61.
12. Nosenko T, Bhattacharya D (2007) Horizontal gene transfer in chromalveolates. BMC Evol Biol 7.
13. Martens C, Vandepoele K, Van de Peer Y (2008) Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc Natl Acad Sci USA 105: 3427-3432.
14. Durrens P, Nikolski M, Sherman D (2008) Fusion and fission of genes define a metric between fungal genomes. PLoS Comput Biol.
15. Kamburov A, Goldovsky L, Freilich S, Kapazoglou A, Kunin V, et al. (2007) Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics 8: 460.
16. Enright A, Iliopoulos I, Kyrpides N, Ouzounis C (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
17. Marcotte CJV, Marcotte EM (2002) Predicting functional linkages from gene fusions with confidence. Applied Bioinformatics 2: 1-8.
18. Tsoka S, Ouzounis CA (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genetics 26: 141-142.
19. Basu MK, Carmel L, Rogozin IB, VKE (2008) Evolution of protein domain promiscuity in eukaryotes. Genome Res 18: 449-461.
20. Bornberg-Bauer E, Beaussart F, Kummerfeld SK, Teichmann SA, Weiner JI (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci 62: 443-445.
21. Wolf YI, Kondrashov AS, Koonin EV (2000) Interkingdom gene fusions. Genome Biol 1: RESEARCH0013.
22. Wall DP, Fraser HB, Hirsh AE (2003) Detecting putative orthologs. Bioinformatics 19: 1710-1711.
23. Zdobnov EM, Apweiler R (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
24. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365-370.
25. Caspi R, Foerster H, Fulcher C, Kaipa P, Krummenacker M, et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 36 Database issue: D633-D631.
26. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment using the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
27. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
28. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, et al. (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8: 460.
29. Miller C (2000) An overview of the potassium channel family. Genome Biol 1: reviews0004.0001-reviews0004.0005.
30. Cheng JB, Russell DW (2004) Mammalian Wax Biosynthesis I. I. Identification of two fatty acyl-coenzyme a reductases with different substrate specificities and tissue distributions. J Biol Chem 279: 37789-37797.
31. Aarts MG, Hodge R, Kalantidis K, D.F, Wilson ZA, et al. (1997) The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes. Plant J 12: 615-623.
32. Moore BD (2004) Bifunctional and moonlighting enzymes:lighting the way to regulatory control. Trends in Plant Sci 9: 221-228.
33. Yiting Y, Chaturvedi I, Meow LK, Kangueane P, Sakharkar MK (2004) Can ends justify the means? digging deep for human fusion genes of prokaryotic origin. Frontiers in Bioscience 9: 2964-2971.
34. Makiuchi T, Nara T, Annoura T, Hashimoto T, Aoki T (2007) Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups. Gene 394: 78-86.
35. Machida M, Takechi K, Sato H, Chung SJ, Kuroiwa H, et al. (2006) Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss. PNAS 103: 6753-6758.
36. Srere P (2000) macromolecular interactions:tracing the roots. Trends Biochem Sci 25: 150-153.
37. Winkel B, SJ (2004) Metabolic channeling in plants. Annu Rev Plant Biol 55: 85-107.
38. Tang G, Xiaohong Z, Gakiere B, Levanony B, Kahana A, et al. (2002) The Bifunctional LKR/SDH Locus of Plants Also Encodes a Highly Active Monofunctional Lysine-Ketoglutarate Reductase Using a Polyadenylation Signal Located within an Intron. Plant Physiol 130: 147-152.
39. Patron NJ, Durnford DG, Kopriva S (2008) Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfe. BMC Evol Biol 8: 39.
40. Koonin E, Makarova K, L. A (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55: 709-742.
41. Yanai I, Wolf YI, EV. K (2002) Evolution of gene fusions: horizontal transfer versus independent events. Genome Biology 3: research0024.
42. Wolf YI, Kondrashov AS, EV. K (2000) Interkingdom gene fusions. Genome Biology 1: RESEARCH0013.
43. Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9: 605-618.