Binary function of mRNA

Biochimie

Volumn 93, Issue 11, 2011, Pages 1955-1961

  Kloc, Malgorzata ^a,b   Foreman, Victor ^b   Reddy, Sriyutha A ^b  

^a HOUSTON METHODIST HOSPITAL   (United States)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Cytoskeleton; mRNA; Multifunctional RNA; Nuclear bodies; RNA World Hypothesis; Structural RNA; VegT mRNA

Indexed keywords

CYTOKERATIN; MESSENGER RNA; MESSENGER RNA PRECURSOR; RECOMBINANT PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG; VEGT MESSENGER RNA; VIRUS RNA;

BIOGENESIS; CELL NUCLEUS INCLUSION BODY; CYTOPLASM; CYTOSKELETON; DROSOPHILA; ESCHERICHIA COLI; EUKARYOTE; HUMAN; MITOSIS; NONHUMAN; OOCYTE; POLYMERIZATION; PROKARYOTE; REVIEW; RNA STRUCTURE; STAPHYLOCOCCUS AUREUS; VIRUS ASSEMBLY; XENOPUS;

ANIMALS; BACTERIA; CYTOPLASM; DROSOPHILA; KERATINS; PROTEIN BIOSYNTHESIS; RIBOSWITCH; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; T-BOX DOMAIN PROTEINS; VIRUS ASSEMBLY; VIRUSES; XENOPUS LAEVIS; XENOPUS PROTEINS;

EUKARYOTA; PROKARYOTA;

EID: 80053565517     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2011.07.008     Document Type: Review

References (79)

1. L. Astrachan, and E. Volkin The absence of ribonucleic acid in bacteriophage T2r+ Virology 2 1956 594 598
2. E. Volkin, and L. Atrachan Phosphorus incorporation Escherichia coli ribo-nucleic acid after infection bacteriophage T2 Virology 2 1956 149 161
3. F. Jacob, and J. Monod Genetic regulatory mechanisms in the synthesis of proteins J. Mol. Biol. 3 1961 318 356
4. S. Brenner, F. Jacob, and M. Meselson An unstable intermediate carrying information from genes to ribosomes for protein synthesis Nature 190 1961 576 581
5. M. Kloc Emerging novel functions of RNAs, and binary phenotype? Dev. Biol. 317 2008 401 404
6. M. Kloc Teachings egg: new unexpected functions RNAs Mol. Rep. Dev. 76 2009 922 932
7. S.A. Benner, A.D. Ellington, and A. Tauer Modern metabolism as a palimpsest of the RNA world Proc. Natl. Acad. Sci. USA 86 1989 7054 7058 (Pubitemid 19240865)
8. C.B. Burge, T. Tuschl, and T.P.A. Sharp R.F. Gesteland, T.R. Cech, J.F. Atkins, The RNA World second ed. 1999 Cold Spring Harbor Laboratory Press New York 525 560
9. S.R. Eddy Non-coding RNA genes and the modern RNA world Nat. Rev. Genet. 2 2001 919 929 (Pubitemid 33691089)
10. W. Gilbert The RNA world Nature 319 1986 618
11. D.C. Jeffares, A.M. Poole, and D. Penny Relics from the RNA world J. Mol. Evol. 46 1998 18 36 (Pubitemid 28047236)
12. A.M. Poole, D.C. Jeffares, and D. Penny The path from the RNA world J. Mol. Evol. 46 1998 1 17 (Pubitemid 28047235)
13. Y.T. Yu, E.C. Scharl, C.M. Smith, and J.A. Steitz R.F. Gesteland, T.R. Cech, J.F. Atkins, The RNA World second ed. 1999 Cold Spring Harbor Laboratory Press New York 487 524
14. M.G. Caprara, and T.W. Nilsen RNA: versatility in form and function Nat. Struct. Biol. 7 2000 831 833
15. F.H.C. Crick The origin of the genetic code J. Mol. Biol. 38 1968 367 379
16. L.E. Orgel Evolution of the genetic apparatus J. Mol. Biol. 38 1968 381 393
17. J.P. Ferris The prebiotic Leslie Orgel: some of his contributions to our understanding of the origins of life Orig. Life Evol. Biosph. 27 1997 431 435
18. A. Schneemann The structural and functional role of RNA in icosahedral virus assembly Annu. Rev. Microbiol. 60 2006 51 67 (Pubitemid 44627940)
19. M.A. Krol, N.H. Olson, J. Tate, J.E. Johnson, T.S. Baker, and P. Ahlquist RNA-controlled polymorphism in the in vivo assembly of 180-subunit and 120-subunit virions from a single capsid protein PNAS 96 1999 13650 13655
20. Y.G. Choi, and A.L. Rao Packaging of tobacco mosaic virus subgenomic RNAs by brome mosaic virus coat protein exhibits RNA controlled polymorphism Virology 275 2000 249 257
21. S.B. Larson, and A. McPherson Satellite tobacco mosaic virus RNA: structure and implications for assembly Curr. Opin. Struct. Biol. 11 2001 59 65 (Pubitemid 32155553)
22. C.S. Wadler, and C.K. Vanderpool A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide PNAS 104 2007 20454 20459
23. S. Boisset, T. Geissmann, E. Huntzinger, P. Fechter, N. Bendridi, M. Possedko, C. Chevalier, A.C. Helfer, Y. Benito, and A. Jacquier Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator rot by an antisense mechanism Genes Dev. 21 2007 1353 1366 (Pubitemid 46871039)
24. F. Huntzinger, S. Boisset, C. Saveanu, Y. Benito, T. Geissmann, A. Namane, G. Lina, J. Etienne, B. Ehresmann, and C. Ehresmann Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression EMBO J. 24 2005 824 835 (Pubitemid 40396111)
25. G. Biamonti, and C. Vourc'h Nuclear stress bodies Cold Spring Harb. Perspect. Biol. 2 2010 a000695
26. L. Bongiorno-Borbone, A. De Cola, P. Vernole, L. Finos, D. Barcaroli, R.A. Knight, G. Melino, and V. De Laurenzi FLASH and NPAT positive but not coilin positive cajal bodies correlate with cell ploidy Cell Cycle 7 2008 2357 2367
27. K.E. Handwerger, and J.G. Gall Subnuclear organelles: new insights into form and function Trends Cell. Biol. 16 2006 19 26 (Pubitemid 43077091)
28. A.G. Matera, M. Izaguire-Sierra, K. Praveen, and T.K. Rajendra Nuclear bodies: random aggregates of sticky proteins or crucibles of macromolecular assembly? Dev. Cell 17 2009 639 647
29. M. Cioce, and A.I. Lamond Cajal bodies: a long history of discovery Annu. Rev. Cell Dev. Biol. 21 2005 105 131 (Pubitemid 41740629)
30. D.L. Spector, and A.I. Lamond Nuclear speckles Cold Spring Harb. Perspect. Biol. 3 2011 a000646
31. G.E. Morris The cajal body Biochim. Biophys. Acta 1783 2008 2108 2115
32. S.P. Shevtsov, and M. Dundr Nucleation of nuclear bodies by RNA Nat. Cell Biol. 13 2011 167 173
33. M. Kloc, K. Wilk, D. Vargas, Y. Shirato, S. Bilinski, and L.D. Etkin Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes Development 132 2005 3445 3457 (Pubitemid 41246119)
34. M. Kloc, S. Bilinski, and M.T. Dougherty Organization of cytokeratin cytoskeleton and germ plasm in the vegetal cortex of Xenopus laevis oocytes depends on coding and non-coding RNAs: three dimensional and ultrastructural analysis Exp. Cell Res. 313 2007 1639 1651 (Pubitemid 46589440)
35. M.D. Blower, M. Nachury, R. Heald, and K. Weis A Rae1-containing ribonucleoprotein complex is required for mitotic spindle assembly Cell 121 2005 223 345
36. M.D. Blower, E. Feric, K. Weis, and R. Heald Genome-wide analysis demonstrates conserved localization of messenger RNAs to mitotic microtubules J. Cell Biol. 179 2007 1365 1373
37. E. Lécuyer, H. Yoshida, and N. Parsatharathy Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function Cell 131 2007 174 187 (Pubitemid 47498530)
38. J.D. Lambert, and L.M. Nagy Asymmetric inheritance of centrosomally-localized mRNAs during embryonic cleavages Nature 420 2002 682 686 (Pubitemid 36764501)
39. E.P. Kingsley, X.Y. Chan, Y. Duan, and J.D. Lambert Widespread RNA segregation in a spiralian embryo Evol. Dev. 9 2007 527 539 (Pubitemid 350045751)
40. M.C. Alliegro, M.A. Alliegro, and R.E. Palazzo Centrosome associated RNA surf clam oocytes PNAS USA 103 2006 9034 9038 (Pubitemid 43902528)
41. M.A. Alliegro, J. Henry, and M.C. Alliegro Rediscovery of the nucleolinus, a dynamic RNA-rich organelle associated with the nucleolus, spindle, and centrosomes PNAS USA 107 2010 13718 13723
42. M.C. Alliegro, and M.A. Alliegro Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes PNAS USA 105 2008 6993 6997 (Pubitemid 351754518)
43. M.C. Alliegro The centrosome and spindle as a ribonucleoprotein complex Chromosome Res. 2011 Feb 2. [Epub ahead of print]
44. A. Jenny, O. Hachet, P. Zavorszky, A. Cyrklaff, M.D. Weston, D.S. Johnston, M. Erdelyi, and A. Ephrussi A translation-independent role of oskar RNA in early Drosophila oogenesis Development 133 2006 2827 2833 (Pubitemid 44314260)
45. W. O'Gorman, and A. Akoulitchev What is so special about oskarwild? Sci. STKE 365 2006 pe51
46. S.L. Bullock, I. Ringel, D. Ish-Horowicz, and P.J. Lukavsky A'-form RNA helices are required for cytoplasmic mRNA transport Drosophila Nat. Str. Mol. Biol. 17 2010 703 710
47. M. Kloc, N.R. Zearfoss, and L.D. Etkin Mechanisms of subcellular mRNA localization Cell 108 2002 533 544 (Pubitemid 34260878)
48. V. Van De Bor, E. Hartswood, C. Jones, D. Finnegan, and I. Davis Gurken and the I factor retrotransposon RNAs share common localization signals and machinery Dev. Cell 9 2005 51 62 (Pubitemid 40903659)
49. M.J. Snee, E.A. Arn, S.L. Bullock, and P.M. Macdonald Recognition of the bcd mRNA localization signal in Drosophila embryos and ovaries Mol. Cell. Biol. 25 2005 1501 1510 (Pubitemid 40204925)
50. S.L. Bullock, D. Zicha, and D. Ish-Horowicz The Drosophila hairy RNA localization signal modulates the kinetics of cytoplasmic mRNA transport EMBO J. 22 2003 2484 2494 (Pubitemid 36604987)
51. P.M. Macdonald, and K. Kerr Mutational analysis of an RNA recognition element that mediates localization of bicoid mRNA Mol. Cell. Biol. 18 1998 3788 3795 (Pubitemid 28287901)
52. G. dos Santos, A.J. Simmonds, and H.M. Krause A stem-loop structure in the wingless transcript defines a consensus motif for apical RNA transport Development 135 2008 133 143 (Pubitemid 351201487)
53. T.L. Serano, and R.S. Cohen A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA Development 121 1995 3809 3818 (Pubitemid 3000455)
54. R.S. Cohen, S. Zhang, and G.L. Dollar The positional, structural, and sequence requirements of the Drosophila TLS RNA localization element RNA 11 2005 1017 1029 (Pubitemid 40994183)
55. R.T. Batey, R.P. Rambo, L. Lucast, B. Rha, and J.A. Doudna Crystal structure of the ribonucleoprotein core of the signal recognition particle Science 287 2000 1232 1239 (Pubitemid 30112139)
56. S. Altuvia, and E.G. Wagner Switching on and off with RNA PNAS USA 97 2000.9824 9826
57. J.D. Helmann Measuring metals with RNA Mol. Cell. 27 2007 859 860 (Pubitemid 47488192)
58. P. Romby, and E.G. Wagner Exploring the complex world of RNA regulation Biol. Cell 100 2008 e1 3
59. L.S. Waters, and G. Storz Regulatory RNAs in bacteria Cell 136 2009 615 628
60. R.C. Wilson, A.M. Smith, R.T. Fuchs, I.R. Kleckner, T.M. Henkin, and M.P. Foster Tuning riboswitch regulation through conformational selection J. Mol. Biol. 405 2011 926 938
61. F. Rastinejad, and H.M. Blau Genetic complementation reveals a novel regulatory role for 3′ untranslated regions growth and differentiation Cell 72 1993 903 917 (Pubitemid 23110232)
62. F. Rastinejad, M.J. Conboy, T.A. Rando, and H.M. Blau Tumor suppression by RNA from the 3′ untranslated region of alpha-tropomyosin Cell 75 1993 1107 1117 (Pubitemid 24006107)
63. H. Fan, C. Villegas, A. Huang, and J.A. Wright Suppression of malignancy by the 3′ untranslated regions of ribonucleotide reductase R1 and R2 messenger RNAs Cancer Res. 56 1996 4366 4369 (Pubitemid 26330440)
64. E.R. Jupe, X.T. Liu, J.L. Kiehlbauch, J.K. McClung, and R.T. Dell'Orco The 3′ untranslated region of prohibition and cellular immortalization Exp Cell Res. 224 1996 128 135
65. E.R. Jupe, X.T. Liu, J.L. Kiehlbauch, J.K. McClung, and R.T. Dell'Orco Prohibition in breast cancer cell lines: loss of antiproliferative activity is linked to 3′ untranslated region mutations Cell Growth Differ. 7 1996 871 878 (Pubitemid 26360726)
66. J.D. Amack, A.P. Paguio, and M.S. Mahadeva Cis and trans effects of the myotonic dystrophy (DM) mutation in a cell culture model Hum. Mol. Genet. 11 1999 1975 1984 (Pubitemid 29458723)
67. T.R. Mercer, D. Wilhelm, M.E. Dinger, G. Sold, and D.J. Korbie Expression of distinct RNAs from 3′ untranslated regions Nucleic Acids Res. 39 2011 2393 2403
68. T. Bollenbach, K. Vetsigian, and R. Kishony Evolution and multilevel optimization of the genetic code Genome Res. 17 2007 401 404 (Pubitemid 46556443)
69. S. Itzkovitz, and U. Alon The genetic code is nearly optimal for allowing additional information within protein-coding sequences Genome Res. 17 2007 405 412 (Pubitemid 46556444)
70. Y. Xing, and C. Lee Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes Nat. Rev. Genet. 7 2006 499 509 (Pubitemid 43943568)
71. P. Schattner, and M. Diekhans Regions of extreme synonymous codon selection in mammalian genes Nuc. Acids Res. 34 2006 1700 1710
72. I. Hellmann, S. Zollner, W. Enard, I. Ebersberger, B. Nickel, and S. Paabo Selection on human genes as revealed by comparisons to chimpanzee cDNA Genome Res. 13 2003 831 837 (Pubitemid 36621743)
73. J.V. Chamary, J.L. Parmley, and L.D. Hurst Hearing silence: non-neutral evolution at synonymous sites in mammals Nat. Rev. Genet. 7 2006 98 108 (Pubitemid 43128905)
74. C. Kimchi-Sarfaty, J.M. Oh, I.W. Kim, Z.E. Sauna, A.M. Calcagno, S.V. Ambudkar, and M.M. Gottesman A "silent" polymorphism in the MDR1 gene changes substrate specificity Science 315 2007 525 528 (Pubitemid 46175758)
75. A.A. Komar Genetics. SNPs, silent but not invisible Science 315 2007 466 467 (Pubitemid 46178389)
76. X. Luo, S. nerlick, W. An, and M.L. King Xenopus germ; ine nanos1 is translationally repressed by a novel structure-based mechanism Development 138 2011 589 598
77. H.L. Ashe, J. Monks, M. Wijgerde, P. Fraser, and N.J. Proudfoot Intergenic transcription and transinduction of the human beta-globin locus Genes Dev. 11 1997 2494 2509 (Pubitemid 27438831)
78. M.E. Dinger, K.C. Pang, T.R. Mercer, and J.S. Mattick Differentiating protein-coding noncoding RNA: challenges ambiguities PLoS Comput. Biol. 4 2008 e1000176
79. S. Mili, K. Moissoglu, and I.G. Macara Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions Nature 453 2008 115 119 (Pubitemid 351630332)