Horizontal acquisition of prokaryotic genes for Eukaryote functioning and Niche adaptation

Evolutionary Biology: Exobiology and Evolutionary Mechanisms

Volumn , Issue , 2013, Pages 165-179

  Bruto, Maxime ^a,b,c   Prigent Combaret, Claire ^a,b,c   Luis, Patricia ^a,b,c   Hoff, Grégory ^a,b,c   Moënne Loccoz, Yvan ^a,b,c   Muller, Daniel ^a,b,c  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ LYON 1   (France)

^c University of Lyon   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84903737164     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-38212-3_11     Document Type: Chapter

References (101)

1. Abby SS, Tannier E, Gouy M, Daubin V (2012) Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci USA 109:4962-4967
2. Acuña R, Padilla BE, Flórez-Ramos CP, Rubio JD, Herrera JC, Benavides P, Lee S-J, Yeats TH, Egan AN, Doyle JJ et al (2012) Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proc Natl Acad Sci USA 109:4197-4202
3. Akagi Y, Akamatsu H, Otani H, Kodama M (2009) Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus. Eukaryot Cell 8:1732-1738
4. Anderson MT, Seifert HS (2011) Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen. MBio 2:e00005-e00011
5. Andersson JO (2009) Gene transfer and diversification of microbial eukaryotes. Annu Rev Microbiol 63:177-193
6. Aoki S, Syōno K (1999) Horizontal gene transfer and mutation: Ngrol genes in the genome of Nicotiana glauca. Proc Natl Acad Sci USA 96:13229-13234
7. Archibald J, Rogers M, Toop M, Ishida K, Keeling P (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci USA 100:7678-7683
8. Arsène-Ploetze F, Koechler S, Marchal M, Coppée J-Y, Chandler M et al (2010) Structure, function, and evolution of the Thiomonas spp. genome. PLoS Genet 6:e1000859
9. Belbahri L, Calmin G, Mauch F, Andersson JO (2008) Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor. Gene 408:1-8
10. Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197-201
11. Bergthorsson U, Richardson A, Young G, Goertzen L, Palmer J (2004) Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA 101:17747-17752
12. Bock R (2010) The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci 15:11-22
13. Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, Barraclough TG, Micklem G, Tunnacliffe A (2012) Biochemical diversification through foreign gene expression in bdelloid rotifers. PLoS Genet 8:e1003035
14. Boto L (2010) Horizontal gene transfer in evolution: facts and challenges. Proc R Soc B 277:819-827
15. Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D et al (2010) The dynamic genome of Hydra. Nature 464:592-596
16. Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S et al (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5:e1000618
17. Cook RJ, Thomashow LS, Weller DM, Fujimoto D, Mazzola M, Bangera G, Kim D (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci USA 92:4197-4201
18. Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105:10039-10044
19. Danchin EG (2010) Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci USA 107:17651-17656
20. Danchin EG (2011) What nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals. Mob Genet Elem 1: 269-292
21. Daniels SB, Peterson KR, Strausbaugh LD, Kidwell MG, Chovnick A (1990) Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124:339-355
22. de la Cruz F, Davies J (2000) Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol 8:128-133
23. Doolittle W (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14:307-311
24. Dubey GP, Ben-Yehuda S (2011) Intercellular nanotubes mediate bacterial communication. Cell 144:590-600
25. Dunning Hotopp JC (2011) Horizontal gene transfer between bacteria and animals. Trends Genet 27:157-163
26. Dunning Hotopp JC, Clark ME, Oliveira DCSG, Foster JM, Fischer P, Muñoz Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S et al (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753-1756
27. Felsenstein J (1974) The evolutionary advantage of recombination. Genetics 78:737-756
28. Fenn K, Conlon C, Jones M, Quail MA, Holroyd NE, Parkhill J, Blaxter M (2006) Phylogenetic relationships of the Wolbachia of nematodes and arthropods. PLoS Pathog 2:e94
29. Filée J, Siguier P, Chandler M (2007) I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet 23:10-15
30. Frapolli M, Pothier JF, Défago G, Moënne-Loccoz Y (2012) Evolutionary history of synthesis pathway genes for phloroglucinol and cyanide antimicrobials in plant-associated fluorescent pseudomonads. Mol Phylogenet Evol 63:877-890
31. Garcia-Vallvé S, Romeu A, Palau J (2000) Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17:352-361
32. Gladyshev EA, Meselson M, Arkhipova IR (2008) Massive horizontal gene transfer in bdelloid rotifers. Science 320:1210-1213
33. Graham LA, Lougheed SC, Ewart KV, Davies PL (2008) Lateral transfer of a lectin-like antifreeze protein gene in fishes. PLoS ONE 3:e2616
34. Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P, Grbić V, Osborne EJ, Dermauw W, Thi Ngoc PC, Ortego F et al (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479:487-492
35. Haegeman A, Jones JT, Danchin EGJ (2011) Horizontal gene transfer in nematodes: a catalyst for plant parasitism? Mol Plant-Microbe Interact 24:879-887
36. Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4:1102-1115
37. Hughes AL, Friedman R (2005) Poxvirus genome evolution by gene gain and loss. Mol Phylogenet Evol 35:186-195
38. Hughes AL, Irausquin S, Friedman R (2010) The evolutionary biology of poxviruses. Infect Genet Evol 10:50-59
39. Jackson D, Macis L, Reitner J, Worheide G (2011) A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy. BMC Evol Biol 11:238
40. Keeling P, Palmer J (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9:605-618
41. Keeling PJ (2009) Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr Opin Genet Dev 19:613-619
42. Keeling PJ, Inagaki Y (2004) A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha. Proc Natl Acad Sci USA 101:15380-15385
43. Kidarsa TA, Goebel NC, Zabriskie TM, Loper JE (2011) Phloroglucinol mediates cross-talk between the pyoluteorin and 2,4-diacetylphloroglucinol biosynthetic pathways in Pseudomonas fluorescens Pf-5. Mol Microbiol 81:395-414
44. Klotz MG, Loewen PC (2003) The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota. Mol Biol Evol 20:1098-1112
45. Koonin E (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res 37:1011-1034
46. Koonin E, Makarova K, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709-742
47. Koonin E, Wolf Y (2009) Is evolution Darwinian or/and Lamarckian? Biol Direct 4:42
48. Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V (2001) Genetic transformation of HeLa cells by Agrobacterium. Proc Natl Acad Sci USA 98:1871-1876
49. Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13:1589-1594
50. Kuo C-H, Ochman H (2009) The fate of new bacterial genes. FEMS Microbiol Rev 33:38-43
51. Lander ES (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
52. Lang A, Beatty J (2007) Importance of widespread gene transfer agent genes in alphaproteobacteria. Trends Microbiol 15:54-62
53. Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger-Desfeux C et al (2011) Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol 3:762-781
54. Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383-397
55. Lerat E, Daubin V, Ochman H, Moran NA (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3:e130
56. Li Z-W, Shen Y-H, Xiang Z-H, Zhang Z (2011) Pathogen-origin horizontally transferred genes contribute to the evolution of Lepidopteran insects. BMC Evol Biol 11:356
57. Lurie-Weinberger MN, Gomez-Valero L, Merault N, Glöckner G, Buchrieser C, Gophna U (2010) The origins of eukaryotic-like proteins in Legionella pneumophila. Int J Med Microbiol 300:470-481
58. Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi M-J, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B et al (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367-373
59. Marcet-Houben M, Gabaldón T (2010) Acquisition of prokaryotic genes by fungal genomes. Trends Genet 26:5-8
60. Matveeva TV, Bogomaz DI, Pavlova OA, Nester EW, Lutova LA (2012) Horizontal gene transfer from genus Agrobacterium to the plant Linaria in Nature. Mol Plant-Microbe Interact 25:1542-1551
61. Moran Y, Fredman D, Szczesny P, Grynberg M, Technau U (2012) Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. Mol Biol Evol 29:2223-2230
62. Muller D, Médigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsène-Ploetze F, Carapito C et al (2007) A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 3:e53
63. Muller HJ (1964) The relation of recombination to mutational advance. Mutat Res 106:2-9
64. Nelson KE (1999) Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329
65. Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF (2012) Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci USA 109:20537-20542
66. Nikoh N, Hosokawa T, Oshima K, Hattori M, Fukatsu T (2011) Reductive evolution of bacterial genome in insect gut environment. Genome Biol Evol 3:702-714
67. Nikoh N, McCutcheon JP, Kudo T, Miyagishima SY, Moran NA, Nakabachi A (2010) Bacterial genes in the Aphid genome: absence of functional gene transfer from Buchnera to its host. PLoS Genet 6:e1000827
68. Nikoh N, Tanaka K, Shibata F, Kondo N, Hizume M, Shimada M, Fukatsu T (2008) Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes. Genome Res 18:272-280
69. Ochman H, Lawrence J, Groisman E (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304
70. Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1099
71. Patrick S, Blakely GW (2012) Crossing the eukaryote-prokaryote divide: a ubiquitin homolog in the human commensal bacterium Bacteroides fragilis. Mob Genet Elem 2:149-151
72. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599-609
73. Pothier JF, Prigent-Combaret C, Haurat J, Moënne-Loccoz Y, Wisniewski-Dyé F (2008) Duplication of plasmid-borne nitrite reductase gene nirK in the wheat-associated plant growth-promoting rhizobacterium Azospirillum brasilense Sp245. Mol Plant-Microbe Interact 21:831-842
74. Prigent-Combaret C, Blaha D, Pothier J, Vial L, Poirier M, Wisniewski-Dyé F, Moënne-Loccoz Y (2008) Physical organization and phylogenetic analysis of acdR as leucine-responsive regulator of the 1-aminocyclopropane-1-carboxylate deaminase gene acdS in phytobeneficial Azospirillum lipoferum 4B and other Proteobacteria. FEMS Microbiol Ecol 65:202-219
75. Puigbo P, Wolf Y, Koonin E (2009) Search for a tree of life in the thicket of the phylogenetic forest. J Biol 8:59
76. Ramette A, Moënne-Loccoz Y, Défago G (2001) Polymorphism of the polyketide synthase gene phlD in biocontrol fluorescent pseudomonads producing 2,4-diacetylphloroglucinol and comparison of PhlD with plant polyketide synthases. Mol Plant-Microbe Interact 14:639-652
77. Raz Y, Tannenbaum E (2010) The influence of horizontal gene transfer on the mean fitness of unicellular populations in static environments. Genetics 185:327-337
78. Redrejo-Rodríguez M, Muñoz-Espín D, Holguera I, Mencía M, Salas M (2012) Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages. Proc Natl Acad Sci USA 109:18482-18487
79. Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ (2009) Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. The Plant Cell Online 21: 1897-1911
80. Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G, Paszkiewicz K, Foster PG, Hall N, Talbot NJ (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci USA 108:15258-15263
81. Rogers MB (2007) A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol Biol 7:89
82. Sagane Y, Zech K, Bouquet J-M, Schmid M, Bal U, Thompson EM (2010) Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans. Development 137:1483-1492
83. Salzberg SL, White O, Peterson J, Eisen JA (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292:1903-1906
84. Sanders IR (2006) Rapid disease emergence through horizontal gene transfer between eukaryotes. Trends Ecol Evol 21:656-658
85. Scholl E, Thorne J, McCarter J, Bird DM (2003) Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol 4:R39
86. Schröder G, Schuelein R, Quebatte M, Dehio C (2011) Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae. Proc Natl Acad Sci USA 108:14643-14648
87. Slot JC, Rokas A (2011) Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between Fungi. Curr Biol 21:134-139
88. Sormacheva I, Smyshlyaev G, Mayorov V, Blinov A, Novikov A, Novikova O (2012) Vertical evolution and horizontal transfer of CR1 Non-LTR Retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species. Mol Biol Evol 29:3685-3702
89. Stegemann S, Bock R (2009) Exchange of genetic material between cells in plant tissue grafts. Science 324:649-651
90. Stegemann S, Hartmann S, Ruf S, Bock R (2003) High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci USA 100:8828-8833
91. Sun BF, Xiao JH, He SM, Liu L, Murphy RW, Huang DW (2013) Multiple ancient horizontal gene transfers and duplications in lepidopteran species. Insect Mol Biol 22:72-87
92. Syvanen M (2012) Evolutionary implications of horizontal gene transfer. Annu Rev Genet 46:341-358
93. Treangen TJ, Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7:e1001284
94. Vial L, Lavire C, Mavingui P, Blaha D, Haurat J, Moënne-Loccoz Y, Bally R, Wisniewski-Dyé F (2006) Phase variation and genomic architecture changes in Azospirillum. J Bacteriol 188:5364-5373
95. Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, The Nasonia Genome Working Group (2010). Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327:343-348
96. Werner S, Steiner U, Bechner R, Kortekamp A, Zyprian E, Deising HB (2002) Chitin synthesis during in planta growth and asexual propagation of the cellulosic oomycete and obligate biotrophic grapevine pathogen plasmopara viticola. FEMS Microbiol Letters 208: 169-173
97. Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V et al (2011) Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet 7:e1002430
98. Wybouw N, Balabanidou V, Ballhorn DJ, Dermauw W, Grbić M, Vontas J, Van Leeuwen T (2012) A horizontally transferred cyanase gene in the spider mite Tetranychus urticae is involved in cyanate metabolism and is differentially expressed upon host plant change. Insect Biochem Mol Biol 42:881-889
99. Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P et al (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5:e156
100. Yue J, Hu X, Sun H, Yang Y, Huang J (2012) Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun 3:1152
101. Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099-1108