Resurrection of an urbilaterian U1A/U2B″/SNF protein

Journal of Molecular Biology

Volumn 425, Issue 20, 2013, Pages 3846-3862

  Williams, Sandra G ^a   Harms, Michael J ^b   Hall, Kathleen B ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF OREGON   (United States)

Author keywords

ancestral reconstruction; protein phylogeny; RNA binding; RRM; U1A protein

Indexed keywords

SMALL NUCLEAR RNA; TRANSCRIPTION FACTOR SNF;

ARTICLE; BILATERIA; BINDING AFFINITY; DROSOPHILA; GENE DUPLICATION; GENE OVEREXPRESSION; GENETIC CONSERVATION; HUMAN; LAST COMMON ANCESTOR; LOPHOTROCHOZOA; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NEMATODE; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA BINDING; RNA SEQUENCE;

BILATERIA;

EID: 84885189866     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.05.031     Document Type: Article

References (53)

1. M. Polycarpou-Schwarz, S.I. Gunderson, S. Kandels-Lewis, B. Seraphin, and I.W. Mattaj Drosophila SNF/D25 combines the functions of the two snRNP proteins U1A and U2B' that are encoded separately in human, potato, and yeast RNA 2 1996 11 23
2. D. Scherly, W. Boelens, N.A. Dathan, W.J. van Venrooij, and I.W. Mattaj Major determinants of the specificity of interaction between small nuclear ribonucleoproteins U1A and U2B″ and their cognate RNAs Nature 345 1990 502 506
3. K.B. Hall, and W.T. Stump Interaction of N-terminal domain of U1A protein with an RNA stem/loop Nucleic Acids Res 20 1992 4283 4290
4. S.G. Williams, and K.B. Hall Human U2B″ protein binding to snRNA stemloops Biophys Chem 159 2011 82 89
5. S.G. Williams, and K.B. Hall Coevolution of Drosophila snf protein and its snRNA targets Biochemistry 49 2010 4571 4582
6. L. Pauling, and E. Zuckerkandl Chemical paleogenetics: molecular "Restoration Studies" of exctinct forms of life Acta Chem Scand 17 1963 S9 S16
7. Y. Shi, and S. Yokoyama Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates Proc Natl Acad Sci USA 100 2003 8308 8313
8. E.A. Gaucher, J.M. Thomson, M.F. Burgan, and S.A. Benner Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins Nature 425 2003 285 288
9. J.W. Thornton, E. Need, and D. Crews Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling Science 301 2003 1714 1717
10. J.A. Ugalde, B.S.W. Chang, and M.V. Matz Evolution of coral pigments recreated Science 305 2004 1433
11. M.J. Harms, and J.W. Thornton Analyzing protein structure and function using ancestral gene reconstruction Curr Opin Struct Biol 20 2010 360 366
12. S. Guindon, and O. Gascuel A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 2003 696 704
13. Z. Yang PAML 4: phylogenetic analysis by maximum likelihood Mol Biol Evol 24 2007 1586 1591
14. K.B. Hall Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain Biochemistry 33 1994 10076 10088
15. D.J. Williams, and K.B. Hall RNA hairpins with non-nucleotide spacers bind efficiently to the human U1A protein J Mol Biol 257 1996 265 275
16. Q. Zeng, and K.B. Hall Contribution of the C-terminal tail of U1A RBD1 to RNA recognition and protein stability RNA 3 1997 303 314
17. R.A. Goldstein The evolution and evolutionary consequences of marginal thermostability in proteins Proteins 79 2011 1396 1407
18. J. Hu, G. Cui, C. Li, C. Liu, E. Shang, and L. Lai Structure and novel functional mechanism of Drosophila SNF in sex-lethal splicing PLoS One 4 2009 e6890
19. D. Lee, C. Hilty, G. Wider, and K. Wuthrich Effective rotational correlation times of proteins from NMR relaxation interference J Magn Reson 178 2006 72 76
20. S.A. Showalter, and K.B. Hall Altering the RNA-binding mode of the U1A RBD1 protein J Mol Biol 335 2004 465 480
21. X. Gu Functional divergence in protein (family) sequence evolution Genetica 118 2003 133 141
22. J.K. Kranz, and K.B. Hall RNA recognition by the human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface J Mol Biol 285 1999 215 231
23. S.A. Showalter, and K.B. Hall Correlated motions in the U1 snRNA stem/loop 2: U1A RBD1 complex Biophys J 89 2005 2046 2058
24. S.A. Showalter, and K.B. Hall A functional role for correlated motion in the N-terminal RNA-binding domain of human U1A protein J Mol Biol 322 2002 533 542
25. E. Katoh, J.M. Louis, T. Yamazaki, A.M. Gronenborn, D.A. Torchia, and R. Ishima A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex Protein Sci 12 2003 1376 1385
26. E. Papaleo, L. Riccardi, C. Villa, P. Fantucci, and L. De Gioia Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family Biochim Biophys Acta 1764 2006 1397 1406
27. J.A. Butterwick, and A.G.R. Palmer An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H Protein Sci 15 2006 2697 2707
28. K.A. Henzler-Wildman, M. Lei, V. Thai, S.J. Kerns, M. Karplus, and D. Kern A hierarchy of timescales in protein dynamics is linked to enzyme catalysis Nature 450 2007 913 916
29. M.S. Marlow, J. Dogan, K.K. Frederick, K.G. Valentine, and A.J. Wand The role of conformational entropy in molecular recognition by calmodulin Nat Chem Biol 6 2010 352 358
30. P.J. Sapienza, R.V. Mauldin, and A.L. Lee Multi-timescale dynamics study of FKBP12 along the rapamycin-mTOR binding coordinate J Mol Biol 405 2011 378 394
31. G. Bhabha, J. Lee, D.C. Ekiert, J. Gam, I.A. Wilson, and H.J. Dyson A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis Science 332 2011 234 238
32. I. Rivalta, M.M. Sultan, N.S. Lee, G.A. Manley, J.P. Loria, and V.S. Batista Allosteric pathways in imidazole glycerol phosphate synthase Proc Natl Acad Sci USA 109 2012 E1428 E1436
33. T. Saldi, C. Wilusz, M. MacMorris, and T. Blumenthal Functional redundancy of worm spliceosomal proteins U1A and U2B″ Proc Natl Acad Sci USA 104 2007 9753 9757
34. S.M. Stitzinger, T.R. Conrad, A.M. Zachlin, and H.K. Salz Functional analysis of SNF, the Drosophila U1A/U2B″ homolog: identification of dispensable and indispensable motifs for both snRNP assembly and function in vivo RNA 5 1999 1440 1450
35. L. Collins, and D. Penny Complex spliceosomal organization ancestral to extant eukaryotes Mol Biol Evol 22 2005 1053 1066
36. P. Tommaso, S. Moretti, I. Xenarios, M. Orobitg, A. Montanyola, and J.M. Chang T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension Nucleic Acids Res 39 2011 W13 W17
37. J. Castresana Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol Biol Evol 17 2000 540 552
38. G. Talavera, and J. Castresana Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments Syst Biol 56 2007 564 577
39. D. Darriba, G.L. Taboada, R. Doallo, and D. Posada ProtTest 3: fast selection of best-fit models of protein evolution Bioinformatics 27 2011 1164 1165
40. M. Anisimova, and O. Gascuel Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative Syst Biol 55 2006 539 552
41. Felsenstein J (2005). PHYLIP (Phylogeny Inference Package) version 3.6. [Distributed by the author].
42. Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 13 1997 555 556
43. M.M. Santoro, and D.W. Bolen Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants Biochemistry 27 1988 8063 8068
44. J.M. Avis, F.H. Allain, P.W. Howe, G. Varani, K. Nagai, and D. Neuhaus Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding J Mol Biol 257 1996 398 411
45. J.P. Loria, M. Rance, and A.G.R. Palmer A TROSY CPMG sequence for characterizing chemical exchange in large proteins J Biomol NMR 15 1999 151 155
46. X. Gu Statistical methods for testing functional divergence after gene duplication Mol Biol Evol 16 1999 1664 1674
47. X. Gu Maximum-likelihood approach for gene family evolution under functional divergence Mol Biol Evol 18 2001 453 464
48. X. Gu A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences Mol Biol Evol 23 2006 1937 1945
49. T.D. Schneider, and R.M. Stephens Sequence logos: a new way to display consensus sequences Nucleic Acids Res 18 1990 6097 6100
50. G.E. Crooks, G. Hon, J.M. Chandonia, and S.E. Brenner WebLogo: a sequence logo generator Genome Res 14 2004 1188 1190
51. K. Arnold, L. Bordoli, J. Kopp, and T. Schwede The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling Bioinformatics 22 2006 195 201
52. S.R. Price, P.R. Evans, and K. Nagai Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA Nature 394 1998 645 650
53. J. Lu, and K.B. Hall Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy Biochemistry 36 1997 10393 10405