Climbing the vertebrate branch of U1A/U2B″ protein evolution

RNA

Volumn 20, Issue 7, 2014, Pages 1035-1045

  Delaney, Kimberly J ^a   Williams, Sandra G ^a   Lawler, Mariah ^a   Hall, Kathleen B ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Ancestral reconstruction; RRM; RRM:RNA binding; snRNP; U1A

Indexed keywords

PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RNA; TRANSCRIPTION FACTOR SNF; U1A PROTEIN; U2B PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; GENE DUPLICATION; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; RNA BINDING; VERTEBRATE;

ANCESTRAL RECONSTRUCTION; RRM; RRM:RNA BINDING; SNRNP; U1A;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC SPECIATION; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RIBONUCLEOPROTEIN, U2 SMALL NUCLEAR; SEQUENCE HOMOLOGY, AMINO ACID; SNRNP CORE PROTEINS; VERTEBRATES;

EID: 84902582259     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.044255.114     Document Type: Article

References (32)

1. Baker CR, Hanson-Smith V, Johnson AD. 2013. Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science 342: 104-108.
2. Benitex Y, Baranger AM. 2007. Recognition of essential purines by the U1A protein. BMC Biochem 8: 22.
3. Collins L, Penny D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 22: 1053-1066.
4. Hall KB. 1994. Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain. Biochemistry 33: 10076-10088.
5. Hall KB, Stump WT. 1992. Interaction of N-terminal domain of U1A protein with an RNA stem/loop. Nucleic Acids Res 20: 4283-4290.
6. Harms MJ, Thornton JW. 2013. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet 14: 559-571.
7. Humphrey W, Dalke A, Schulten K. 1996. VMD: visual molecular dynamics. J Mol Graph 14: 33-38.
8. 3 loop in the interaction of U1A with U1 hairpin II RNA. J Biol Chem 277: 33267-33274.
9. Kranz JK, Hall KB. 1998. RNA binding mediates the local cooperativity between the β-sheet and the C-terminal tail of the human U1A RBD1 protein. J Mol Biol 275: 465-481.
10. Kranz JK, Lu J, Hall KB. 1996. Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain. Protein Sci 5: 1567-1583.
11. Laird-Offringa IA, Belasco JG. 1995. Analysis of RNA-binding proteins by in vitro genetic selection: identification of an amino acid residue important for locking U1A onto its RNA target. Proc Natl Acad Sci 92: 11859-11863.
12. Law MJ, Linde ME, Chambers EJ, Oubridge C, Katsamba PS, Nilsson L, Haworth IS, Laird-Offringa IA. 2006a. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res 34: 275 -285.
13. Law MJ, Rice AJ, Lin P, Laird-Offringa IA. 2006b. The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA. RNA 12: 1168-1178.
14. McConnell TS, Lokken RP, Steitz JA. 2003. Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA. RNA 9: 193-201.
15. Oubridge C, Ito N, Evans PR, Teo CH, Nagai K. 1994. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372: 432-438.
16. Polycarpou-Schwarz M, Gunderson SI, Kandels-Lewis S, Seraphin B, Mattaj IW. 1996. 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: 11-23.
17. Price SR, Evans PR, Nagai K. 1998. Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394: 645-650.
18. Record MT, Lohman TM, de Haseth P. 1976. Ion effects on ligand-nucleic acid interactions. J Mol Biol 107: 145-158.
19. Rimmele ME, Belasco JG. 1998. Target discrimination by RNA-binding proteins: role of the ancillary protein U2A′ and a critical leucine residue in differentiating the RNA-binding specificity of spliceosomal proteins U1A and U2B″. RNA 4: 1386-1396.
20. Saldi T, Wilusz C, MacMorris M, Blumenthal T. 2007. Functional redundancy of worm spliceosomal proteins U1A and U2B″. Proc Natl Acad Sci 104: 9753-9757.
21. Scherly D, BoelensW, Dathan NA, van Venrooij WJ, Mattaj IW. 1990a. Major determinants of the specificity of interaction between small nuclear ribonucleoproteins U1A and U2B″ and their cognate RNAs. Nature 345: 502-506.
22. Scherly D, Dathan NA, BoelensW, van Venrooij WJ, Mattaj IW. 1990b. The U2B″ RNP motif as a site of protein-protein interaction. EMBO J 9: 3675-3681.
23. Scherly D, Kambach C, Boelens W, van Venrooij WJ, Mattaj IW. 1991. Conserved amino acid residues within and outside of the N-terminal ribonucleoprotein motif of U1A small nuclear ribonucleoprotein involved in U1 RNA binding. J Mol Biol 219: 577-584.
24. Schimmel P. 1989. Parameters for the molecular recognition of transfer RNAs. Biochemistry 28: 2747-2759.
25. Stump WT, Hall KB. 1995. Crosslinking of an iodo-uridine-RNA hairpin to a single site on the human U1A N-terminal RNA binding domain. RNA 1: 55-63.
26. Williams DJ, Hall KB. 1996. RNA hairpins with non-nucleotide spacers bind efficiently to the human U1A protein. J Mol Biol 257: 265-275.
27. Williams SG, Hall KB. 2010. Coevolution of Drosophila snf protein and its snRNA targets. Biochemistry 49: 4571-4582.
28. Williams SG, Hall KB. 2011. Human U2B″ protein binding to snRNA stemloops. Biophys Chem 159: 82-89.
29. Williams SG, Harms MJ, Hall KB. 2013. Resurrection of an Urbilaterian U1A/U2B″/SNF protein. J Mol Biol 425: 3846-3862.
30. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
31. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
32. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.