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2014 | 83 | 4 |

Tytuł artykułu

The old and new RNA world

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Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
Among the numerous hypotheses offering a scenario for the origin of life on Earth, the one called “The RNA World” has gained the most attention. According to this hypothesis RNA acted as a genetic information storage material, as a catalyst of all metabolic reactions, and as a regulator of all processes in the primordial world. Various experiments show that RNA molecules could have been synthesized abiotically, with the potential to mediate a whole repertoire of metabolic reactions. Ribozymes carrying out aminoacyl-tRNA reactions have been found in SELEX (systematic evolution of ligands by exponential enrichment) approaches and the development of a ribosome from a RNA-built protoribosome is easy to imagine. Transfer RNA aminoacylation, protoribosome origin, and the availability of amino acids on early Earth allowed the genetic code to evolve. Encoded proteins most likely stabilized RNA molecules and were able to create channels across membranes. In the modern cell, DNA replaced RNA as the main depositor of genetic information and proteins carry out almost all metabolic reactions. However, RNA is still playing versatile, crucial roles in the cell. Apart from its classical functions in the cell, a huge small RNA world is controlling gene expression, chromatin condensation, response to environmental cues, and protecting the cell against the invasion of various nucleic acids forms. Long non-coding RNAs act as crucial gene expression regulators. Riboswitches act at the level of transcription, splicing or translation and mediate feedback regulation on biosynthesis and transport of the ligand they sense. Alternative splicing generates genetic variability and increases the protein repertoire in response to developmental or environmental changes. All these regulatory functions are essential in shaping cell plasticity in the changing milieu. Recent discoveries of new, unexpected and important functions of RNA molecules support the hypothesis that we live in a New RNA World.

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-

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Tom

83

Numer

4

Opis fizyczny

p.441-448,fig.,ref.

Twórcy

  • Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland

Bibliografia

  • 1. Orgel LE. Evolution of the genetic apparatus. J Mol Biol. 1968;38(3):381–393.
  • 2. Crick FH. The origin of the genetic code. J Mol Biol. 1968;38(3):367–379.
  • 3. Woese CR. The genetic code: the molecular basis for genetic expression. New York, NY: Harper & Row; 1967.
  • 4. Eigen M, Schuster P. A principle of natural self-organization. Naturwissenschaften. 1977;64(11):541–565. http://dx.doi.org/10.1007/BF00450633
  • 5. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. Self-splicing RNA: autoexcision and autocyclization of the ribosomalRNA intervening sequence of Tetrahymena. Cell. 1982;31(1):147–157.
  • 6. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell.1983;35(3 pt 2):849–857.
  • 7. Leslie E. O. Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol. 2004;39(2):99–123. http://dx.doi.org/10.1080/10409230490460765
  • 8. Powner MW, Gerland B, Sutherland JD. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature.2009;459(7244):239–242. http://dx.doi.org/10.1038/nature08013
  • 9. Bowler FR, Chan CKW, Duffy CD, Gerland B, Islam S, Powner MW, et al. Prebiotically plausible oligoribonucleotide ligation facilitatedby chemoselective acetylation. Nat Chem. 2013;5(5):383–389. http://dx.doi.org/10.1038/nchem.1626
  • 10. Adamala K, Szostak JW. Nonenzymatic template-directed RNA synthesis inside model protocells. Science. 2013;342(6162):1098–1100. http://dx.doi.org/10.1126/science.1241888
  • 11. Talini G, Gallori E, Maurel MC. Natural and unnatural ribozymes: back to the primordial RNA world. Res Microbiol. 2009;160(7):457–465. http://dx.doi.org/10.1016/j.resmic.2009.05.005
  • 12. Gold L, Janjic N, Jarvis T, Schneider D, Walker JJ, Wilcox SK, et al. Aptamers and the RNA world, past and present. Cold SpringHarb Perspect Biol. 2012;4(3):a003582. http://dx.doi.org/10.1101/cshperspect.a003582
  • 13. Bartel DP, Szostak JW. Isolation of new ribozymes from a large pool of random sequences. Science. 1993;261(5127):1411–1418. http://dx.doi.org/10.1126/science.7690155
  • 14. Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP. RNAcatalyzed RNA polymerization: accurate and general RNA-templatedprimer extension. Science. 2001;292(5520):1319–1325. http://dx.doi.org/10.1126/science.1060786
  • 15. Lee N, Bessho Y, Wei K, Szostak JW, Suga H. Ribozyme-catalyzed tRNA aminoacylation. Nat Struct Mol Biol. 2000;7(1):28–33. http:// dx.doi.org/10.1038/71225
  • 16. Tsukiji S, Pattnaik SB, Suga H. An alcohol dehydrogenase ribozyme. Nat Struct Mol Biol. 2003;10(9):713–717. http://dx.doi.org/10.1038/ nsb964
  • 17. Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E, Höbartner C, et al. Structural basis for Diels–Alder ribozyme-catalyzed carboncarbon bond formation. Nat Struct Mol Biol. 2005;12(3):218–224. http://dx.doi.org/10.1038/nsmb906
  • 18. Jadhav VR, Yarus M. Acyl-CoAs from coenzyme ribozymes. Biochemistry (Mosc). 2002;41(3):723–729. http://dx.doi.org/10.1021/bi011803h
  • 19. Parker ET, Cleaves HJ, Dworkin JP, Glavin DP, Callahan M, Aubrey A, et al. Primordial synthesis of amines and amino acids in a 1958Miller H2S-rich spark discharge experiment. Proc Natl Acad Sci USA. 2011;108(14):5526–5531. http://dx.doi.org/10.1073/pnas.1019191108
  • 20. Joyce GF. The antiquity of RNA-based evolution. Nature. 2002;418(6894):214–221. http://dx.doi.org/10.1038/418214a
  • 21. Illangasekare M, Yarus M. A tiny RNA that catalyzes both aninoacyltRNA and peptidyl-RNA synthesis. RNA. 1999;5:1482–1489.
  • 22. Steitz TA, Moore PB. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci. 2003;28(8):411–418.http://dx.doi.org/10.1016/S0968-0004(03)00169-5
  • 23. Lear JD, Wasserman ZR, DeGrado WF. Synthetic amphiphilic peptide models for protein ion channels. Science. 1988;240(4856):1177–1181.http://dx.doi.org/10.1126/science.2453923
  • 24. Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 1999;286(5441):950–952. http://dx.doi.org/10.1126/science.286.5441.950
  • 25. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNAin Caenorhabditis elegans. Nature. 1998;391(6669):806–811. http://dx.doi.org/10.1038/35888
  • 26. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. Expression of Arabidopsis MIRNA genes. Plant Physiol. 2005;138(4):2145–2154. http://dx.doi.org/10.1104/pp.105.062943
  • 27. Szweykowska-Kulińska Z, Jarmolowski A, Vazquez F. The crosstalk between plant microRNA biogenesis factors and the spliceosome. PlantSignal Behav. 2013;8(11):e26955. http://dx.doi.org/10.4161/psb.26955
  • 28. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, et al. Widespread translational inhibitionby plant miRNAs and siRNAs. Science. 2008;320(5880):1185–1190.http://dx.doi.org/10.1126/science.1159151
  • 29. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell. 2004;16(1):69–79. http://dx.doi. org/10.1016/j.molcel.2004.09.028
  • 30. Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell.2005;121(2):207–221. http://dx.doi.org/10.1016/j.cell.2005.04.004
  • 31. Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, et al. Regulation of AUXIN RESPONSE FACTOR3 byTAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis.Curr Biol. 2006;16(9):939–944. http://dx.doi.org/10.1016/j.cub.2006.03.065
  • 32. Zhou C, Han L, Fu C, Wen J, Cheng X, Nakashima J, et al. The transacting short interfering RNA3 pathway and NO APICAL MERISTEMantagonistically regulate leaf margin development and lateral organseparation, as revealed by analysis of an argonaute7/lobed leaflet1mutant in Medicago truncatula. Plant Cell. 2013;4845–4862. http://dx.doi.org/10.1105/tpc.113.117788
  • 33. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. GenesDev. 2006;20(24):3407–3425. http://dx.doi.org/10.1101/gad.1476406
  • 34. Chen HM, Li YH, Wu SH. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascadein Arabidopsis. Proc Natl Acad Sci USA. 2007;104(9):3318–3323.http://dx.doi.org/10.1073/pnas.0611119104
  • 35. Vazquez F, Hohn T. Biogenesis and biological activity of secondary siRNAs in plants. Scientifica. 2013;2013:1–12. http://dx.doi. org/10.1155/2013/783253
  • 36. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell. 2005;123(7):1279–1291. http://dx.doi.org/10.1016/j.cell.2005.11.035
  • 37. Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H. A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev. 2007;21(23):3123–3134. http://dx.doi.org/10.1101/gad.1595107
  • 38. Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A, Zhu JK, et al. A pathogen-inducible endogenous siRNA in plant immunity.Proc Natl Acad Sci USA. 2006;103(47):18002–18007. http://dx.doi.org/10.1073/pnas.0608258103
  • 39. Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W. Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res. 2009;19(1):70–78. http:// dx.doi.org/10.1101/gr.084806.108
  • 40. Pikaard CS, Haag JR, Ream T, Wierzbicki AT. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci. 2008;13(7):390–397. http://dx.doi.org/10.1016/j.tplants.2008.04.008
  • 41. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ. RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol.2009;21(3):367–376. http://dx.doi.org/10.1016/j.ceb.2009.01.025
  • 42. Zheng B, Wang Z, Li S, Yu B, Liu JY, Chen X. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNAdirectedtranscriptional gene silencing in Arabidopsis. Genes Dev.2009;23(24):2850–2860. http://dx.doi.org/10.1101/gad.1868009
  • 43. Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, et al. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell.2007;19(5):1507–1521. http://dx.doi.org/10.1105/tpc.107.051540
  • 44. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet. 2009;41(5):630–634. http://dx.doi.org/10.1038/ng.365
  • 45. Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencingof overlapping and adjacent genes. Cell. 2008;135(4):635–648. http://dx.doi.org/10.1016/j.cell.2008.09.035
  • 46. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC. Small silencing RNAs in plants are mobile and direct epigeneticmodification in recipient cells. Science. 2010;328(5980):872–875.http://dx.doi.org/10.1126/science.1187959
  • 47. Vazquez F, Legrand S, Windels D. The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci. 2010;15(6):337– 345. http://dx.doi.org/10.1016/j.tplants.2010.04.001
  • 48. Bouche N, Lauressergues D, Gasciolli V, Vaucheret H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 2006;25(14):3347–3356. http://dx.doi.org/10.1038/sj.emboj.7601217
  • 49. Voinnet O. Non-cell autonomous RNA silencing. FEBS Lett. 2005;579(26):5858–5871. http://dx.doi.org/10.1016/j.febslet.2005.09.039
  • 50. Ding S-W, Voinnet O. Antiviral immunity directed by small RNAs. Cell. 2007;130(3):413–426. http://dx.doi.org/10.1016/j.cell.2007.07.039
  • 51. Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAsin Arabidopsis. Plant Cell. 2012;24(11):4333–4345. http://dx.doi.org/10.1105/tpc.112.102855
  • 52. Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, et al. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell.2014;55(3):383–396. http://dx.doi.org/10.1016/j.molcel.2014.06.011
  • 53. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, et al. Sensing small molecules by nascent RNA: a mechanism tocontrol transcription in bacteria. Cell. 2002;111(5):747–756. http://dx.doi.org/10.1016/S0092-8674(02)01134-0
  • 54. Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 2002;419(6910):952–956. http://dx.doi.org/10.1038/nature01145
  • 55. Reining A, Nozinovic S, Schlepckow K, Buhr F, Fürtig B, Schwalbe H. Three-state mechanism couples ligand and temperature sensingin riboswitches. Nature. 2013;499(7458):355–359. http://dx.doi.org/10.1038/nature12378
  • 56. Roth A, Breaker RR. The structural and functional diversity of metabolite- binding riboswitches. Annu Rev Biochem. 2009;78(1):305–334. http://dx.doi.org/10.1146/annurev.biochem.78.070507.135656
  • 57. Cheah MT, Wachter A, Sudarsan N, Breaker RR. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature. 2007;447(7143):497–500. http://dx.doi.org/10.1038/nature05769
  • 58. Wachter A. Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol. 2010;7(1):67–76. http://dx.doi.org/10.4161/rna.7.1.10489
  • 59. Simpson CG, Manthri S, Raczynska KD, Kalyna M, Lewandowska D, Kusenda B, et al. Regulation of plant gene expression by alternative splicing. Biochem Soc Trans. 2010;38(2):667. http://dx.doi.org/10.1042/BST0380667
  • 60. Reddy ASN, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. Plant Cell. 2013;25(10):3657–3683. http://dx.doi.org/10.1105/tpc.113.117523
  • 61. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat Genet. 2008;40(12):1413–1415. http://dx.doi.org/10.1038/ng.259
  • 62. Remy E, Cabrito TR, Baster P, Batista RA, Teixeira MC, Friml J, et al. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. PlantCell. 2013;25(3):901–926. http://dx.doi.org/10.1105/tpc.113.110353
  • 63. Remy E, Cabrito TR, Batista RA, Hussein MAM, Teixeira MC, Athanasiadis A, et al. Intron retention in the 5'UTR of the novel ZIF2transporter enhances translation to promote zinc tolerance in Arabidopsis.PLoS Genet. 2014;10(5):e1004375. http://dx.doi.org/10.1371/journal.pgen.1004375

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