Mechanisms of StpA-mediated RNA remodeling

References

• Akins RA, Lambowitz AM. A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof. Cell 1987; 50:331 - 345
   PubMed Web of Science ®Google Scholar
• Dujardin G, Jacq C, Slonimski PP. Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene. Nature 1982; 298:628 - 632
   PubMed Web of Science ®Google Scholar
• Labouesse M, Netter P, Schroeder R. Molecular basis of the ‘box effect’, A maturase deficiency leading to the absence of splicing of two introns located in two split genes of yeast mitochondrial DNA. European journal of biochemistry/FEBS 1984; 144:85 - 93
   PubMedGoogle Scholar
• Lazowska J, Jacq C, Slonimski PP. Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron. Cell 1980; 22:333 - 348
   PubMed Web of Science ®Google Scholar
• Seraphin B, Simon M, Faye G. MSS18, a yeast nuclear gene involved in the splicing of intron aI5 beta of the mitochondrial cox1 transcript. EMBO J 1988; 7:1455 - 1464
   PubMed Web of Science ®Google Scholar
• De la Salle H, Jacq C, Slonimski PP. Critical sequences within mitochontrial introns: pleiotropic mRNA maturase and cis-dominant signals of the box intron controlling reductase and oxidase. Cell 1982; 721 - 732
   PubMed Web of Science ®Google Scholar
• Zhang A, Derbyshire V, Salvo JL, Belfort M. Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro. RNA 1995; 1:783 - 793
   PubMed Web of Science ®Google Scholar
• Dorman CJ, Hinton JC, Free A. Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol 1999; 7:124 - 128
   PubMed Web of Science ®Google Scholar
• Zhang A, Belfort M. Nucleotide sequence of a newly-identified Escherichia coli gene, stpA, encoding an H-NS-like protein. Nucleic Acids Res 1992; 20:6735
   PubMed Web of Science ®Google Scholar
• Zhang A, Rimsky S, Reaban ME, Buc H, Belfort M. Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics. EMBO J 1996; 15:1340 - 1349
   PubMed Web of Science ®Google Scholar
• Muller CM, Schneider G, Dobrindt U, Emody L, Hacker J, Uhlin BE. Differential effects and interactions of endogenous and horizontally acquired H-NS-like proteins in pathogenic Escherichia coli. Mol Microbiol 75:280 - 293
   PubMed Web of Science ®Google Scholar
• Free A, Dorman CJ. The Escherichia coli stpA gene is transiently expressed during growth in rich medium and is induced in minimal medium and by stress conditions. Journal of bacteriology 1997; 179:909 - 918
   PubMed Web of Science ®Google Scholar
• Waldsich C, Grossberger R, Schroeder R. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes and Dev 2002; 16:2300 - 2312
   PubMed Web of Science ®Google Scholar
• Herschlag D, Khosla M, Tsuchihashi Z, Karpel RL. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J 1994; 13:2913 - 2924
   PubMed Web of Science ®Google Scholar
• Coetzee T, Herschlag D, Belfort M. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev 1994; 8:1575 - 1588
   PubMed Web of Science ®Google Scholar
• Mayer O, Rajkowitsch L, Lorenz C, Konrat R, Schroeder R. RNA chaperone activity and RNA-binding properties of the E. coli protein StpA. Nucleic Acids Res 2007; 35:1257 - 1269
   PubMed Web of Science ®Google Scholar
• Negroni M, Buc H. Copy-choice recombination by reverse transcriptases: reshuffling of genetic markers mediated by RNA chaperones. Proc Natl Acad Sci USA 2000; 97:6385 - 6390
   PubMed Web of Science ®Google Scholar
• Jiang W, Hou Y, Inouye M. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J Biol Chem 1997; 272:196 - 202
   PubMed Web of Science ®Google Scholar
• Llopis PM, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, et al. Spatial organization of the flow of genetic information in bacteria. Nature 2010; 466:77 - 81
   PubMed Web of Science ®Google Scholar
• Cusick ME, Belfort M. Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA. Mol Microbiol 1998; 28:847 - 857
   PubMed Web of Science ®Google Scholar
• Leonard PG, Ono S, Gor J, Perkins SJ, Ladbury JE. Investigation of the self-association and hetero-association interactions of H-NS and StpA from Enterobacteria. Mol Microbiol 2009; 73:165 - 179
   PubMed Web of Science ®Google Scholar
• Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005; 6:197 - 208
   PubMed Web of Science ®Google Scholar
• Garner E, Romero P, Dunker AK, Brown C, Obradovic Z. Predicting Binding Regions within Disordered Proteins. Genome informatics 1999; 10:41 - 50
   PubMedGoogle Scholar
• Tompa P, Csermely P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004; 18:1169 - 1175
   PubMed Web of Science ®Google Scholar
• Konrat R. The protein meta-structure: a novel concept for chemical and molecular biology. Cell Mol Life Sci 2009; 66:3625 - 3639
   PubMed Web of Science ®Google Scholar
• Bloch V, Yang Y, Margeat E, Chavanieu A, Auge MT, Robert B, et al. The H-NS dimerization domain defines a new fold contributing to DNA recognition. Nat Struct Biol 2003; 10:212 - 218
   PubMedGoogle Scholar
• Shindo H, Iwaki T, Ieda R, Kurumizaka H, Ueguchi C, Mizuno T, et al. Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. FEBS letters 1995; 360:125 - 131
   PubMed Web of Science ®Google Scholar
• Sette M, Spurio R, Trotta E, Brandizi C, Brandi A, Pon CL, et al. Sequence-specific recognition of DNA by the C-terminal domain of nucleoid-associated protein H-NS. J Biol Chem 2009; 284:30453 - 30462
   PubMed Web of Science ®Google Scholar
• Cristofari G, Darlix JL. The ubiquitous nature of RNA chaperone proteins. Prog Nucleic Acid Res Mol Biol 2002; 72:223 - 268
   PubMed Web of Science ®Google Scholar
• Rajkowitsch L, Schroeder R. Dissecting RNA chaperone activity. RNA 2007; 13:2053 - 2060
   PubMed Web of Science ®Google Scholar
• Mayer O, Waldsich C, Grossberger R, Schroeder R. Folding of the td pre-RNA with the help of the RNA chaperone StpA. Biochem Soc Trans 2002; 30:1175 - 1180
   PubMed Web of Science ®Google Scholar
• Salvo JL, Coetzee T, Belfort M. Deletion-tolerance and trans-splicing of the bacteriophage T4 td intron. Analysis of the P6-L6a region. J Mol Biol 1990; 211:537 - 549
   PubMed Web of Science ®Google Scholar
• Clodi E, Semrad K, Schroeder R. Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J 1999; 18:3776 - 3782
   PubMed Web of Science ®Google Scholar
• Webb AE, Weeks KM. A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nat Struct Biol 2001; 8:135 - 140
   PubMedGoogle Scholar
• Furtig B, Buck J, Manoharan V, Bermel W, Jaschke A, Wenter P, et al. Time-resolved NMR studies of RNA folding. Biopolymers 2007; 86:360 - 383
   Google Scholar
• Woodson SA. RNA folding and ribosome assembly. Current opinion in chemical biology 2008; 12:667 - 673
   PubMed Web of Science ®Google Scholar
• Williamson JR. Biophysical studies of bacterial ribosome assembly. Current opinion in structural biology 2008; 18:299 - 304
   PubMed Web of Science ®Google Scholar
• Zarrinkar PP, Williamson JR. Kinetic intermediates in RNA folding. Science 1994; 265:918 - 924
   PubMed Web of Science ®Google Scholar
• Treiber DK, Rook MS, Zarrinkar PP, Williamson JR. Kinetic intermediates trapped by native interactions in RNA folding. Science 1998; 279:1943 - 1946
   PubMed Web of Science ®Google Scholar
• Mayer O, Windbichler N, Wank H, Schroeder R. Silvermann SK. Protein-induced RNA Switches in Nature. Nucleic Acid Switches and Sensors: Landes Bioscience 2005;
   Google Scholar
• Schwalbe H, Buck J, Furtig B, Noeske J, Wohnert J. Structures of RNA switches: insight into molecular recognition and tertiary structure. Angewandte Chemie (International ed) 2007; 46:1212 - 1219
   PubMed Web of Science ®Google Scholar
• Wong CH, Hendrix M, Priestley ES, Greenberg WA. Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA. Chem Biol 1998; 5:397 - 406
   PubMed Web of Science ®Google Scholar
• Semrad K, Schroeder R. A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo. Genes Dev 1998; 12:1327 - 1337
   PubMed Web of Science ®Google Scholar
• Duncan CD, Weeks KM. Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry 49:5418 - 5425
   PubMed Web of Science ®Google Scholar
• Gething MJ, Sambrook J. Protein folding in the cell. Nature 1992; 355:33 - 45
   PubMed Web of Science ®Google Scholar
• Ghisolfi L, Joseph G, Amalric F, Erard M. The glycine-rich domain of nucleolin has an unusual supersecondary structure responsible for its RNA-helix-destabilizing properties. J Biol Chem 1992; 267:2955 - 2959
   PubMed Web of Science ®Google Scholar
• Sapp M, Knippers R, Richter A. DNA binding properties of a 110 kDa nucleolar protein. Nucleic Acids Res 1986; 14:6803 - 6820
   PubMed Web of Science ®Google Scholar
• Portman DS, Dreyfuss G. RNA annealing activities in HeLa nuclei. EMBO J 1994; 13:213 - 221
   PubMed Web of Science ®Google Scholar
• Munroe SH, Dong XF. Heterogeneous nuclear ribonucleoprotein A1 catalyzes RNA.RNA annealing. Proc Natl Acad Sci USA 1992; 89:895 - 899
   PubMed Web of Science ®Google Scholar
• Cobianchi F, Calvio C, Stoppini M, Buvoli M, Riva S. Phosphorylation of human hnRNP protein A1 abrogates in vitro strand annealing activity. Nucleic Acids Res 1993; 21:949 - 955
   PubMed Web of Science ®Google Scholar
• Ammerman ML, Fisk JC, Read LK. gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16. RNA 2008; 14:1069 - 1080
   PubMed Web of Science ®Google Scholar
• Schreiber G, Haran G, Zhou HX. Fundamental aspects of protein-protein association kinetics. Chem Rev 2009; 109:839 - 860
   PubMed Web of Science ®Google Scholar
• Nedbal W, Frey M, Willemann B, Zentgraf H, Sczakiel G. Mechanistic insights into p53-promoted RNA-RNA annealing. J Mol Biol 1997; 266:677 - 687
   PubMed Web of Science ®Google Scholar
• Nedbal W, Homann M, Sczakiel G. The association of complementary ribonucleic acids can be strongly increased without lowering Arrhenius activation energies or significantly altering structures. Biochemistry 1997; 36:13552 - 13557
   PubMed Web of Science ®Google Scholar
• Muller UF, Goringer HU. Mechanism of the gBP21-mediated RNA/RNA annealing reaction: matchmaking and charge reduction. Nucleic Acids Res 2002; 30:447 - 455
   PubMed Web of Science ®Google Scholar
• Hitti E, Neunteufel A, Jantsch MF. The double-stranded RNA-binding protein X1rbpa promotes RNA strand annealing. Nucleic Acids Res 1998; 26:4382 - 4388
   PubMed Web of Science ®Google Scholar
• Lee CG, Zamore PD, Green MR, Hurwitz J. RNA annealing activity is intrinsically associated with U2AF. J Biol Chem 1993; 268:13472 - 13478
   PubMed Web of Science ®Google Scholar
• Muller UF, Lambert L, Goringer HU. Annealing of RNA editing substrates facilitated by guide RNA-binding protein gBP21. EMBO J 2001; 20:1394 - 1404
   PubMed Web of Science ®Google Scholar
• Schumacher MA, Karamooz E, Zikova A, Trantirek L, Lukes J. Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. Cell 2006; 126:701 - 711
   PubMed Web of Science ®Google Scholar
• Furtig B, Wenter P, Reymond L, Richter C, Pitsch S, Schwalbe H. Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy. Journal of the American Chemical Society 2007; 129:16222 - 16229
   PubMed Web of Science ®Google Scholar
• Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, et al. RNA chaperones, RNA annealers and RNA helicases. RNA Biol 2007; 4:118 - 130
   PubMed Web of Science ®Google Scholar
• Grossberger R, Mayer O, Waldsich C, Semrad K, Schroeder R. Influence of RNA structural stability on the RNA chaperone activity of the E. coli portein StpA. Nuc Acids Res 2005; 33:2280 - 2289
   PubMed Web of Science ®Google Scholar
• Mohan S, Hsiao C, VanDeusen H, Gallagher R, Krohn E, Kalahar B, et al. Mechanism of RNA double helix-propagation at atomic resolution. The journal of physical chemistry 2009; 113:2614 - 2623
   Web of Science ®Google Scholar
• Porschke D. A direct measurement of the unzippering rate of a nucleic acid double helix. Biophysical chemistry 1974; 2:97 - 101
   PubMed Web of Science ®Google Scholar
• Porschke D. Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction. Biophysical chemistry 1974; 2:83 - 96
   PubMed Web of Science ®Google Scholar