Genomes and Genes
Experts and Doctors on rna binding proteins in Boulder, Colorado, United States
Locale: Boulder, Colorado, United States
Topic: rna binding proteins
- Tsu C, Uhlenbeck O. Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry. 1998;37:16989-96 pubmed..Taken together with the tight, site-specific binding to naked, unmodified 23S rRNA, this suggests a role for DbpA in ribosome biogenesis rather than translation. ..
- Shtatland T, Gill S, Javornik B, Johansson H, Singer B, Uhlenbeck O, et al. Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res. 2000;28:E93 pubmed..Such methods may be useful tools for both randomized sequence SELEX and genomic SELEX...
- Parma D, Bennett P, Boswell R. Mago Nashi and Tsunagi/Y14, respectively, regulate Drosophila germline stem cell differentiation and oocyte specification. Dev Biol. 2007;308:507-19 pubmed..On the other hand, Tsunagi/Y14 is essential for restricting oocyte fate to a single cell and may function with mago nashi in this process. ..
- Roberts E, Hammond K, Traish A, Resing K, Ahn N. Identification of G2/M targets for the MAP kinase pathway by functional proteomics. Proteomics. 2006;6:4541-53 pubmed
- Gawande B, Robida M, Rahn A, Singh R. Drosophila Sex-lethal protein mediates polyadenylation switching in the female germline. EMBO J. 2006;25:1263-72 pubmed..The sex-specific poly(A) switching of e(r) provides a means for translational regulation in germ cells. We present a model for the SXL-dependent poly(A) site choice in the female germline. ..
- Hamady M, Peden E, Knight R, Singh R. Fast-Find: a novel computational approach to analyzing combinatorial motifs. BMC Bioinformatics. 2006;7:1 pubmed..We have used it to generate hypotheses about interactions between specific polyadenylation factors, which we will test experimentally. ..
- Kossen K, Uhlenbeck O. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Res. 1999;27:3811-20 pubmed..We propose that the C-terminus identifies a protein sub-family whose members bind 23S rRNA and that proteins of this family are likely to function in rRNA maturation/ribosome biogenesis or an unappreciated aspect of translation. ..
- Tsu C, Kossen K, Uhlenbeck O. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA. 2001;7:702-9 pubmed..A model relating the RNA binding and ATPase activities of DbpA is presented. ..
- Diges C, Uhlenbeck O. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 2001;20:5503-12 pubmed..This work indicates that certain RNA helicases require particular RNA structures in order for optimal unwinding activity to be observed. ..
- Luca F, Winey M. MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. Mol Biol Cell. 1998;9:29-46 pubmed..Perhaps in addition to, or as part of, its essential function in late mitosis, MOB1 is required for a cell cycle reset function necessary for the initiation of the spindle pole body duplication. ..
- Fillman C, Lykke Andersen J. RNA decapping inside and outside of processing bodies. Curr Opin Cell Biol. 2005;17:326-31 pubmed..Recent evidence suggests that the processing bodies may constitute specialized cellular compartments of mRNA turnover, which suggests that mRNA and protein localization may be integral to mRNA decay...
- Cui M, Allen M, Larsen A, MacMorris M, Han M, Blumenthal T. Genes involved in pre-mRNA 3'-end formation and transcription termination revealed by a lin-15 operon Muv suppressor screen. Proc Natl Acad Sci U S A. 2008;105:16665-70 pubmed publisher..Furthermore, our results implicate a serine/arginine-rich (SR) protein, SRp20, in events following 3'-end cleavage, leading to termination of transcription. ..
- Singh G, Jakob S, Kleedehn M, Lykke Andersen J. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. Mol Cell. 2007;27:780-92 pubmed..Furthermore, retention of the NMD factor hUpf1 in the nucleus strongly impairs NMD. These observations suggest that the hUpf complex communicates with the EJC and triggers NMD in the cytoplasm...
- Pleshe E, Truesdell J, Batey R. Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:722-8 pubmed..The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the alpha/beta-knot superfamily, with alpha-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding. ..
- Kossen K, Karginov F, Uhlenbeck O. The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. J Mol Biol. 2002;324:625-36 pubmed..These data support a model in which the carboxy-terminal domain binds hairpin 92 to target the protein to 23S rRNA. ..
- Lykke Andersen J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol. 2002;22:8114-21 pubmed..These data suggest that a human decapping complex may be recruited to mRNAs containing premature termination codons by the hUpf proteins...
- Polach K, Uhlenbeck O. Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA. Biochemistry. 2002;41:3693-702 pubmed..This cooperativity is lost upon removal of helix 89 from R153, suggesting this helix is either the preferred target for DbpA's helicase activity or is a necessary structural element for organization of the target site within R153. ..
- Livengood A, Zaug A, Cech T. Essential regions of Saccharomyces cerevisiae telomerase RNA: separate elements for Est1p and Est2p interaction. Mol Cell Biol. 2002;22:2366-74 pubmed..More generally, our results support a role for the telomerase RNA serving as a scaffold for binding key protein subunits. ..
- Mohr S, Dillon S, Boswell R. The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis. Genes Dev. 2001;15:2886-99 pubmed
- Banerjee H, Rahn A, Gawande B, Guth S, Valcarcel J, Singh R. The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro. RNA. 2004;10:240-53 pubmed..We propose that RRM3 has an unrecognized function that is possibly relevant for the splicing of only a subset of cellular introns. We discuss the implications of these observations on previous models of U2AF function. ..