PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2014 | 83 | 4 |

Tytuł artykułu

Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer

Treść / Zawartość

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
This review focuses on plant-to-plant horizontal gene transfer (HGT) involving the three DNA-containing cellular compartments. It highlights the great incidence of HGT in the mitochondrial genome (mtDNA) of angiosperms, the increasing number of examples in plant nuclear genomes, and the lack of any convincing evidence for HGT in the well-studied plastid genome of land plants. Most of the foreign mitochondrial genes are non-functional, generally found as pseudogenes in the recipient plant mtDNA that maintains its functional native genes. The few exceptions involve chimeric HGT, in which foreign and native copies recombine leading to a functional and single copy of the gene. Maintenance of foreign genes in plant mitochondria is probably the result of genetic drift, but a possible evolutionary advantage may be conferred through the generation of genetic diversity by gene conversion between native and foreign copies. Conversely, a few cases of nuclear HGT in plants involve functional transfers of novel genes that resulted in adaptive evolution. Direct cell-to-cell contact between plants (e.g. host-parasite relationships or natural grafting) facilitate the exchange of genetic material, in which HGT has been reported for both nuclear and mitochondrial genomes, and in the form of genomic DNA, instead of RNA. A thorough review of the literature indicates that HGT in mitochondrial and nuclear genomes of angiosperms is much more frequent than previously expected and that the evolutionary impact and mechanisms underlying plant-to-plant HGT remain to be uncovered.

Wydawca

-

Rocznik

Tom

83

Numer

4

Opis fizyczny

p.317-323,fig.,ref.

Twórcy

  • IBAM-CONICET and FCA, FCEN, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza 5505, Argentina

Bibliografia

  • 1. Andersson JO. Lateral gene transfer in eukaryotes. Cell Mol Life Sci. 2005;62(11):1182–1197. http://dx.doi.org/10.1007/s00018-005-4539-z
  • 2. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405(6784):299–304.http://dx.doi.org/10.1038/35012500
  • 3. Koonin EV, Makarova KS, Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol.2001;55(1):709–742. http://dx.doi.org/10.1146/annurev.micro.55.1.709
  • 4. Ford Doolittle W. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes.Trends Genet. 1998;14(8):307–311. http://dx.doi.org/10.1016/S0168-9525(98)01494-2
  • 5. Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet. 2008;9(8):605–618. http://dx.doi.org/10.1038/ nrg2386
  • 6. Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ. Phylogenomic analysis demonstrates a pattern of rare andancient horizontal gene transfer between plants and fungi. Plant Cell.2009;21(7):1897–1911. http://dx.doi.org/10.1105/tpc.109.065805
  • 7. Huang J. Horizontal gene transfer in eukaryotes: the weak-link model. Bioessays. 2013;35(10):868–875. http://dx.doi.org/10.1002/ bies.201300007
  • 8. Schönknecht G, Weber APM, Lercher MJ. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays.2014;36(1):9–20. http://dx.doi.org/10.1002/bies.201300095
  • 9. Bock R. The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci. 2010;15(1):11–22. http://dx.doi.org/10.1016/j.tplants.2009.10.001
  • 10. Bergthorsson U, Adams KL, Thomason B, Palmer JD. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature.2003;424(6945):197–201. http://dx.doi.org/10.1038/nature01743
  • 11. Davis CC, Wurdack KJ. Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales. Science.2004;305(5684):676–678. http://dx.doi.org/10.1126/science.1100671
  • 12. Mower JP, Stefanović S, Young GJ, Palmer JD. Plant genetics: gene transfer from parasitic to host plants. Nature. 2004;432(7014):165–166.http://dx.doi.org/10.1038/432165b
  • 13. Park JM, Manen JF, Schneeweiss GM. Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobancheand Phelipanche (Orobanchaceae). Mol Phylogenet Evol. 2007;43(3):974–985. http://dx.doi.org/10.1016/j.ympev.2006.10.011
  • 14. Baidouri ME, Carpentier MC, Cooke R, Gao D, Lasserre E, Llauro C, et al. Widespread and frequent horizontal transfers of transposableelements in plants. Genome Res. 2014;24:831–838. http://dx.doi.org/10.1101/gr.164400.113
  • 15. Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, et al. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science. 2013;342(6165):1468–1473. http://dx.doi.org/10.1126/science.1246275
  • 16. Sanchez-Puerta MV, Cho Y, Mower JP, Alverson AJ, Palmer JD. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Mol Biol Evol. 2008;25(8):1762–1777. http://dx.doi.org/10.1093/molbev/msn129
  • 17. Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD. Massive horizontal transfer of mitochondrial genes from diverseland plant donors to the basal angiosperm Amborella. Proc Natl AcadSci USA. 2004;101(51):17747–17752. http://dx.doi.org/10.1073/pnas.0408336102
  • 18. Barkman TJ, McNeal JR, Lim SH, Coat G, Croom HB, Young ND, et al. Mitochondrial DNA suggests at least 11 origins of parasitism inangiosperms and reveals genomic chimerism in parasitic plants. BMCEvol Biol. 2007;7(1):248. http://dx.doi.org/10.1186/1471-2148-7-248
  • 19. Cho Y, Qiu YL, Kuhlman P, Palmer JD. Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci USA. 1998;95(24):14244–14249. http://dx.doi.org/10.1073/pnas.95.24.14244
  • 20. Mower JP, Stefanović S, Hao W, Gummow JS, Jain K, Ahmed D, et al. Horizontal acquisition of multiple mitochondrial genes from a parasiticplant followed by gene conversion with host mitochondrial genes.BMC Biol. 2010;8(1):150. http://dx.doi.org/10.1186/1741-7007-8-150
  • 21. Davis CC, Anderson WR, Wurdack KJ. Gene transfer from a parasitic flowering plant to a fern. Proc Biol Sci. 2005;272(1578):2237–2242. http://dx.doi.org/10.1098/rspb.2005.3226
  • 22. Xi Z, Bradley RK, Wurdack KJ, Wong K, Sugumaran M, Bomblies K, et al. Horizontal transfer of expressed genes in a parasiticflowering plant. BMC Genomics. 2012;13:227. http://dx.doi.org/10.1186/1471-2164-13-227
  • 23. Hao W, Richardson AO, Zheng Y, Palmer JD. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion.Proc Natl Acad Sci USA. 2010;107(50):21576–21581. http://dx.doi.org/10.1073/pnas.1016295107
  • 24. Hepburn NJ, Schmidt DW, Mower JP. Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss. Mol Biol Evol. 2012;29(10):3111–3120. http://dx.doi.org/10.1093/ molbev/mss130
  • 25. Nickrent DL, Blarer A, Qiu YL, Vidal-Russell R, Anderson FE. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneityand horizontal gene transfer. BMC Evol Biol. 2004;4(1):40. http://dx.doi.org/10.1186/1471-2148-4-40
  • 26. Schönenberger J, Anderberg AA, Sytsma KJ. Molecular phylogenetics and patterns of floral evolution in the Ericales. Int J Plant Sci. 2005;166(2):265–288. http://dx.doi.org/10.1086/427198
  • 27. Cho Y, Adams KL, Qiu YL, Kuhlman P, Vaughn JC, Palmer JD. A highly invasive group I intron in the mitochondrial cox1 gene. In: Moller K,Gardestrom P, Glimelius K, Glaser E, editors. Plant mitochondria:from gene to function. Leiden: Backhuys Publishers; 1998. p. 19–23.
  • 28. Koulintchenko M, Konstantinov Y, Dietrich A. Plant mitochondria actively import DNA via the permeability transition pore complex.EMBO J. 2003;22(6):1245–1254. http://dx.doi.org/10.1093/emboj/cdg128
  • 29. Duchêne AM, Pujol C, Maréchal-Drouard L. Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet. 2009;55(1):1–18. http://dx.doi.org/10.1007/s00294-008-0223-9
  • 30. Arimura S, Yamamoto J, Aida GP, Nakazono M, Tsutsumi N. Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution.Proc Natl Acad Sci USA. 2004;101(20):7805–7808. http://dx.doi.org/10.1073/pnas.0401077101
  • 31. Sheahan MB, McCurdy DW, Rose RJ. Mitochondria as a connected population: ensuring continuity of the mitochondrial genome during plant cell dedifferentiation through massive mitochondrial fusion. Plant J. 2005;44(5):744–755. http://dx.doi.org/10.1111/j.1365-313X.2005.02561.x
  • 32. Manchekar M, Scissum-Gunn K, Song D, Khazi F, McLean SL, Nielsen BL. DNA recombination activity in soybean mitochondria. J Mol Biol.2006;356(2):288–299. http://dx.doi.org/10.1016/j.jmb.2005.11.070
  • 33. Shedge V, Arrieta-Montiel M, Christensen AC, Mackenzie SA. Plant mitochondrial recombination surveillance requires unusual RecAand MutS homologs. Plant Cell. 2007;19(4):1251–1264. http://dx.doi.org/10.1105/tpc.106.048355
  • 34. Backert S, Lynn Nielsen B, Börner T. The mystery of the rings: structure and replication of mitochondrial genomes from higher plants. Trends Plant Sci. 1997;2(12):477–483. http://dx.doi.org/10.1016/ S1360-1385(97)01148-5
  • 35. Maréchal A, Brisson N. Recombination and the maintenance of plant organelle genome stability. New Phytol. 2010;186(2):299–317. http:// dx.doi.org/10.1111/j.1469-8137.2010.03195.x
  • 36. Palmer JD, Shields CR. Tripartite structure of the Brassica campestris mitochondrial genome. Nature. 1984;307(5950):437–440. http://dx.doi. org/10.1038/307437a0
  • 37. Stern DB, Lonsdale DM. Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common. Nature.1982;299(5885):698–702. http://dx.doi.org/10.1038/299698a0
  • 38. Unseld M, Marienfeld JR, Brandt P, Brennicke A. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924nucleotides. Nat Genet. 1997;15(1):57–61. http://dx.doi.org/10.1038/ng0197-57
  • 39. Palmer JD, Herbon LA. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol. 1988;28(1–2):87–97.
  • 40. Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA. 1987;84(24):9054–9058.
  • 41. Mower JP, Sloan DB, Alverson AJ. Plant mitochondrial genome diversity: the genomics revolution. In: Wendel JF, Greilhuber J, Dolezel J, Leitch IJ, editors. Plant genome diversity. Vienna: Springer; 2012.p. 123–144. (vol 1). http://dx.doi.org/10.1007/978-3-7091-1130-7_9
  • 42. Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, et al. Rapid evolution of enormous, multichromosomal genomesin flowering plant mitochondria with exceptionally high mutationrates. PLoS Biol. 2012;10(1):e1001241. http://dx.doi.org/10.1371/journal.pbio.1001241
  • 43. Ward BL, Anderson RS, Bendich AJ. The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell.1981;25(3):793–803.
  • 44. Vaughn JC, Mason MT, Sperwhitis GL, Kuhlman P, Palmer JD. Fungal origin by horizontal transfer of a plant mitochondrial group I intronin the chimeric cox1 gene of Peperomia. J Mol Evol. 1995;41:563–572.
  • 45. Sanchez-Puerta MV, Abbona CC, Zhuo S, Tepe EJ, Bohs L, Olmstead RG, et al. Multiple recent horizontal transfers of the cox1 intron inSolanaceae and extended co-conversion of flanking exons. BMC EvolBiol. 2011;11(1):277. http://dx.doi.org/10.1186/1471-2148-11-277
  • 46. Cho Y, Palmer JD. Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial cox1 gene during evolution of theAraceae family. Mol Biol Evol. 1999;16(9):1155–1165.
  • 47. Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, et al. Massive mitochondrial gene transfer in a parasitic flowering plantclade. PLoS Genet. 2013;9(2):e1003265. http://dx.doi.org/10.1371/journal.pgen.1003265
  • 48. Christin PA, Edwards EJ, Besnard G, Boxall SF, Gregory R, Kellogg EA, et al. Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Curr Biol. 2012;22(5):445–449. http://dx.doi. org/10.1016/j.cub.2012.01.054
  • 49. Vallenback P, Jaarola M, Ghatnekar L, Bengtsson BO. Origin and timing of the horizontal transfer of a PgiC gene from Poa to Festucaovina. Mol Phylogenet Evol. 2008;46(3):890–896. http://dx.doi.org/10.1016/j.ympev.2007.11.031
  • 50. Yoshida S, Maruyama S, Nozaki H, Shirasu K. Horizontal gene transfer by the parasitic plant Striga hermonthica. Science.2010;328(5982):1128–1128. http://dx.doi.org/10.1126/science.1187145
  • 51. Zhang D, Qi J, Yue J, Huang J, Sun T, Li S, et al. Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australisobtained Brassicaceae-specific strictosidine synthase-like genes byhorizontal gene transfer. BMC Plant Biol. 2014;14(1):19. http://dx.doi.org/10.1186/1471-2229-14-19
  • 52. Zhang Y, Fernandez-Aparicio M, Wafula EK, Das M, Jiao Y, Wickett NJ, et al. Evolution of a horizontally acquired legume gene, albumin 1,in the parasitic plant Phelipanche aegyptiaca and related species. BMCEvol Biol. 2013;13(1):48. http://dx.doi.org/10.1186/1471-2148-13-48
  • 53. Diao X, Freeling M, Lisch D. Horizontal transfer of a plant transposon. PLoS Biol. 2006;4(1):e5. http://dx.doi.org/10.1371/journal.pbio.0040005
  • 54. Roulin A, Piegu B, Wing RA, Panaud O. Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J. 2008;53(6):950–959. http://dx.doi. org/10.1111/j.1365-313X.2007.03388.x
  • 55. Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, et al. Horizontal transfer of an adaptive chimeric photoreceptor frombryophytes to ferns. Proc Natl Acad Sci USA. 2014;111(18):6672–6677.http://dx.doi.org/10.1073/pnas.1319929111
  • 56. Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 2007;41:331–368. http://dx.doi. org/10.1146/annurev.genet.40.110405.090448
  • 57. Schaack S, Gilbert C, Feschotte C. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryoticevolution. Trends Ecol Evol. 2010;25(9):537–546. http://dx.doi.org/10.1016/j.tree.2010.06.001
  • 58. Huang J, Yue J. Horizontal gene transfer in the evolution of photosynthetic eukaryotes. J Syst Evol. 2013;51(1):13–29. http://dx.doi. org/10.1111/j.1759-6831.2012.00237.x
  • 59. Delwiche CF, Palmer JD. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol Biol Evol. 1996;13(6):873–882.
  • 60. Khan H, Parks N, Kozera C, Curtis BA, Parsons BJ, Bowman S, et al. Plastid genome sequence of the cryptophyte alga Rhodomonassalina CCMP1319: lateral transfer of putative DNA replicationmachinery and a test of chromist plastid phylogeny. Mol Biol Evol.2007;24(8):1832–1842. http://dx.doi.org/10.1093/molbev/msm101
  • 61. Rice DW, Palmer JD. An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidencethat haptophyte and cryptophyte plastids are sisters. BMC Biol.2006;4(1):31. http://dx.doi.org/10.1186/1741-7007-4-31
  • 62. Moszczynski K, Mackiewicz P, Bodyl A. Evidence for horizontal gene transfer from bacteroidetes bacteria to dinoflagellate minicircles. Mol Biol Evol. 2012;29(3):887–892. http://dx.doi.org/10.1093/molbev/ msr276
  • 63. Goremykin VV, Salamini F, Velasco R, Viola R. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer.Mol Biol Evol. 2009;26(1):99–110. http://dx.doi.org/10.1093/molbev/msn226
  • 64. Iorizzo M, Senalik D, Szklarczyk M, Grzebelus D, Spooner D, Simon P. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. BMC Plant Biol. 2012;12(1):61. http://dx.doi.org/10.1186/1471-2229-12-61
  • 65. Straub SCK, Cronn RC, Edwards C, Fishbein M, Liston A. Horizontal transfer of DNA from the mitochondrial to the plastid genome andits subsequent evolution in milkweeds (Apocynaceae). Genome BiolEvol. 2013;5(10):1872–1885. http://dx.doi.org/10.1093/gbe/evt140
  • 66. Maliga P. Plastid transformation in higher plants. Annu Rev Plant Biol. 2004;55:289–313. http://dx.doi.org/10.1146/annurev. arplant.55.031903.141633
  • 67. Wicke S, Müller KF, de Pamphilis CW, Quandt D, Wickett NJ, Zhang Y, et al. Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family. Plant Cell. 2013;25(10):3711–3725. http://dx.doi. org/10.1105/tpc.113.113373
  • 68. Woloszynska M, Bocer T, Mackiewicz P, Janska H. A fragment of chloroplast DNA was transferred horizontally, probably fromnon-eudicots, to mitochondrial genome of Phaseolus. Plant Mol Biol.2004;56(5):811–820. http://dx.doi.org/10.1007/s11103-004-5183-y
  • 69. Sanchez-Puerta MV, Zubko MK, Palmer JD. Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant. New Phytol. 2014 (in press). http://dx.doi.org/10.1111/nph.13188
  • 70. Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, et al. Possible loss of the chloroplast genome in the parasiticflowering plant Rafflesia lagascae (Rafflesiaceae). Mol Biol Evol.2014;31:793–803. http://dx.doi.org/10.1093/molbev/msu051
  • 71. Stegemann S, Bock R. Exchange of genetic material between cells in plant tissue grafts. Science. 2009;324(5927):649–651. http://dx.doi. org/10.1126/science.1170397
  • 72. Kim G, LeBlanc ML, Wafula EK, de Pamphilis CW, Westwood JH. Genomic-scale exchange of mRNA between a parasitic plant and itshosts. Science. 2014;345(6198):808–811. http://dx.doi.org/10.1126/science.1253122
  • 73. Roney JK, Khatibi PA, Westwood JH. Cross-species translocation of mRNA from host plants into the parasitic plant dodder. Plant Physiol.2007;143(2):1037–1043. http://dx.doi.org/10.1104/pp.106.088369
  • 74. Westwood JH, Roney JK, Khatibi PA, Stromberg VK. RNA translocation between parasitic plants and their hosts. Pest Manag Sci.2009;65(5):533–539. http://dx.doi.org/10.1002/ps.1727
  • 75. Hao J, Jia X, Yu J, Deng S. Direct visualization of horizontal gene transfer in cotton plants. J Hered. 2014;105(6):834–836. http://dx.doi.org/10.1093/jhered/esu052
  • 76. Fuentes I, Stegemann S, Golczyk H, Karcher D, Bock R. Horizontal genome transfer as an asexual path to the formation of new species. Nature.2014;511(7508):232–235. http://dx.doi.org/10.1038/nature13291
  • 77. Stegemann S, Keuthe M, Greiner S, Bock R. Horizontal transfer of chloroplast genomes between plant species. Proc Natl Acad Sci USA.2012;109(7):2434–2438. http://dx.doi.org/10.1073/pnas.1114076109
  • 78. Thyssen G, Svab Z, Maliga P. Cell-to-cell movement of plastids in plants. Proc Natl Acad Sci USA. 2012;109(7):2439–2443. http://dx.doi. org/10.1073/pnas.1114297109
  • 79. Earle ED. Mitochondrial DNA in somatic hybrids and cybrids. In: Levings C, Vasil IK, editors. The molecular biology of plant mitochondria.Dordrecht: Kluwer Academic Publishers; 1995. p. 557–584.
  • 80. Emiliani G, Fondi M, Fani R, Gribaldo S. A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol Direct. 2009;4:7. http://dx.doi.org/10.1186/1745-6150-4-7
  • 81. Yue J, Hu X, Sun H, Yang Y, Huang J. Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun. 2012;3:1152.http://dx.doi.org/10.1038/ncomms2148
  • 82. Zardoya R, Ding X, Kitagawa Y, Chrispeels MJ. Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment. Proc Natl Acad Sci USA. 2002;99(23):14893–14896. http://dx.doi.org/10.1073/pnas.192573799
  • 83. Knie N, Polsakiewicz M, Knoop V. Horizontal gene transfer of chlamydial- like tRNA genes into early vascular plant mitochondria. Mol Biol Evol. 2014 (in press). http://dx.doi.org/10.1093/molbev/msu324

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.agro-6386045f-a571-4dc2-810d-381f091f0026
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.