Literature DB >> 18255277

Towards deciphering the principles underlying an mRNA recognition code.

Alexander Serganov1, Dinshaw J Patel.   

Abstract

Messenger RNAs interact with a number of different molecules that determine the fate of each transcript and contribute to the overall pattern of gene expression. These interactions are governed by specific mRNA signals, which in principle could represent a special mRNA recognition 'code'. Both, small molecules and proteins demonstrate a diversity of mRNA binding modes often dependent on the structural context of the regions surrounding specific target sequences. In this review, we have highlighted recent structural studies that illustrate the diversity of recognition principles used by mRNA binders for timely and specific targeting and processing of the message.

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Year:  2008        PMID: 18255277      PMCID: PMC3744885          DOI: 10.1016/j.sbi.2007.12.006

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  60 in total

1.  Interaction of the Bacillus stearothermophilus ribosomal protein S15 with its 5'-translational operator mRNA.

Authors:  L G Scott; J R Williamson
Journal:  J Mol Biol       Date:  2001-11-30       Impact factor: 5.469

2.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs.

Authors:  Alexander Serganov; Yu-Ren Yuan; Olga Pikovskaya; Anna Polonskaia; Lucy Malinina; Anh Tuân Phan; Claudia Hobartner; Ronald Micura; Ronald R Breaker; Dinshaw J Patel
Journal:  Chem Biol       Date:  2004-12

3.  Structural basis for mRNA recognition by elongation factor SelB.

Authors:  Satoko Yoshizawa; Linda Rasubala; Toyoyuki Ose; Daisuke Kohda; Dominique Fourmy; Katsumi Maenaka
Journal:  Nat Struct Mol Biol       Date:  2005-01-23       Impact factor: 15.369

4.  Molecular basis of RNA recognition by the human alternative splicing factor Fox-1.

Authors:  Sigrid D Auweter; Rudi Fasan; Luc Reymond; Jason G Underwood; Douglas L Black; Stefan Pitsch; Frédéric H-T Allain
Journal:  EMBO J       Date:  2005-12-15       Impact factor: 11.598

5.  Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.

Authors:  Stefano Marzi; Alexander G Myasnikov; Alexander Serganov; Chantal Ehresmann; Pascale Romby; Marat Yusupov; Bruno P Klaholz
Journal:  Cell       Date:  2007-09-21       Impact factor: 41.582

6.  New insights into the interaction of ribosomal protein L1 with RNA.

Authors:  Natalia Nevskaya; Svetlana Tishchenko; Sergey Volchkov; Vladislav Kljashtorny; Ekaterina Nikonova; Oleg Nikonov; Alexei Nikulin; Caroline Köhrer; Wolfgang Piendl; Robert Zimmermann; Peter Stockley; Maria Garber; Stanislav Nikonov
Journal:  J Mol Biol       Date:  2005-11-17       Impact factor: 5.469

7.  Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.

Authors:  Marianna Teplova; Yu-Ren Yuan; Anh Tuân Phan; Lucy Malinina; Serge Ilin; Alexei Teplov; Dinshaw J Patel
Journal:  Mol Cell       Date:  2006-01-06       Impact factor: 17.970

8.  Do mRNA and rRNA binding sites of E.coli ribosomal protein S15 share common structural determinants?

Authors:  Alexander Serganov; Eric Ennifar; Claude Portier; Bernard Ehresmann; Chantal Ehresmann
Journal:  J Mol Biol       Date:  2002-07-26       Impact factor: 5.469

9.  Structure of the L1 protuberance in the ribosome.

Authors:  Alexei Nikulin; Irina Eliseikina; Svetlana Tishchenko; Natalia Nevskaya; Natalia Davydova; Olga Platonova; Wolfgang Piendl; Maria Selmer; Anders Liljas; Denis Drygin; Robert Zimmermann; Maria Garber; Stanislav Nikonov
Journal:  Nat Struct Biol       Date:  2003-02

10.  Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA.

Authors:  Natalia Nevskaya; Svetlana Tishchenko; Azat Gabdoulkhakov; Ekaterina Nikonova; Oleg Nikonov; Alexei Nikulin; Olga Platonova; Maria Garber; Stanislav Nikonov; Wolfgang Piendl
Journal:  Nucleic Acids Res       Date:  2005-01-19       Impact factor: 16.971

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  16 in total

1.  Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex.

Authors:  Ursula Schulze-Gahmen; James H Hurley
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-04       Impact factor: 11.205

2.  Known and novel post-transcriptional regulatory sequences are conserved across plant families.

Authors:  Justin N Vaughn; Sally R Ellingson; Flavio Mignone; Albrecht von Arnim
Journal:  RNA       Date:  2012-01-11       Impact factor: 4.942

Review 3.  Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.

Authors:  Qi Zhang; Hashim M Al-Hashimi
Journal:  RNA       Date:  2009-09-23       Impact factor: 4.942

Review 4.  An overview of RNAs with regulatory functions in gram-positive bacteria.

Authors:  Pascale Romby; Emmanuelle Charpentier
Journal:  Cell Mol Life Sci       Date:  2009-10-27       Impact factor: 9.261

Review 5.  Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers.

Authors:  Charles A Abbas; Andriy A Sibirny
Journal:  Microbiol Mol Biol Rev       Date:  2011-06       Impact factor: 11.056

Review 6.  RNA Structures as Mediators of Neurological Diseases and as Drug Targets.

Authors:  Viachaslau Bernat; Matthew D Disney
Journal:  Neuron       Date:  2015-07-01       Impact factor: 17.173

Review 7.  Themes and variations in riboswitch structure and function.

Authors:  Alla Peselis; Alexander Serganov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

Review 8.  Amino acid recognition and gene regulation by riboswitches.

Authors:  Alexander Serganov; Dinshaw J Patel
Journal:  Biochim Biophys Acta       Date:  2009-07-18

9.  Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs.

Authors:  Jaime Prilusky; Eitan Bibi
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-06       Impact factor: 11.205

10.  Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface.

Authors:  Marc Parisien; Xiaoyun Wang; George Perdrizet; Corissa Lamphear; Carol A Fierke; Ketan C Maheshwari; Michael J Wilde; Tobin R Sosnick; Tao Pan
Journal:  Cell Rep       Date:  2013-05-09       Impact factor: 9.423

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