Literature DB >> 537920

Secondary structure of MS2 phage RNA and bias in code word usage.

M Hasegawa, T Yasunaga, T Miyata.   

Abstract

Based on the secondary structural model of MS2 RNA, it is shown that, in base-pairing regions of the RNA, there is a bias in the use of synonymous codons which favours C and/or G over U and/or A in the third codon positions, and that in non-pairing regions, there is an opposite bias which favours U and/or A over C and/or G. This nature is interpreted as a result of selective constraint which stabilises the secondary structure of the single-stranded RNA genome of the MS2 phage.

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Year:  1979        PMID： 537920      PMCID： PMC342367          DOI： 10.1093/nar/7.7.2073

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  20 in total

1.  Viral, prokaryote and eukaryote genes contrasted by mRNA sequence indexes.

Authors:  R Grantham
Journal:  FEBS Lett       Date:  1978-11-01       Impact factor: 4.124

2.  The genome of simian virus 40.

Authors:  V B Reddy; B Thimmappaya; R Dhar; K N Subramanian; B S Zain; J Pan; P K Ghosh; M L Celma; S M Weissman
Journal:  Science       Date:  1978-05-05       Impact factor: 47.728

3.  Complete nucleotide sequence of SV40 DNA.

Authors:  W Fiers; R Contreras; G Haegemann; R Rogiers; A Van de Voorde; H Van Heuverswyn; J Van Herreweghe; G Volckaert; M Ysebaert
Journal:  Nature       Date:  1978-05-11       Impact factor: 49.962

4.  Bacteriophage MS2 RNA: a correlation between the stability of the codon: anticodon interaction and the choice of code words.

Authors:  H Grosjean; D Sankoff; W M Jou; W Fiers; R J Cedergren
Journal:  J Mol Evol       Date:  1978-12-29       Impact factor: 2.395

5.  On codon usage.

Authors:  W Fiers; H Grosjean
Journal:  Nature       Date:  1979-01-25       Impact factor: 49.962

6.  Pattern and chance in the use of the genetic code.

Authors:  E M Berger
Journal:  J Mol Evol       Date:  1978-02-21       Impact factor: 2.395

7.  The primary sequence of rabbit alpha-globin mRNA.

Authors:  H C Heindell; A Liu; G V Paddock; G M Studnicka; W A Salser
Journal:  Cell       Date:  1978-09       Impact factor: 41.582

8.  The regulatory region of MS2 phage RNA replicase cistron. Functional activity of individual MS2 RNA fragments.

Authors:  V Berzin; G P Borisova; I Cielens; V A Gribanov; I Jansone; G Rosenthal; E J Gren
Journal:  J Mol Biol       Date:  1978-02-15       Impact factor: 5.469

9.  Nucleotide sequence of bacteriophage fd DNA.

Authors:  E Beck; R Sommer; E A Auerswald; C Kurz; B Zink; G Osterburg; H Schaller; K Sugimoto; H Sugisaki; T Okamoto; M Takanami
Journal:  Nucleic Acids Res       Date:  1978-12       Impact factor: 16.971

10.  Codons and nearest-neighbor nucleotide pairs in mammalian messenger RNA.

Authors:  T H Jukes
Journal:  J Mol Evol       Date:  1978-06-20       Impact factor: 2.395
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  26 in total

1.  Synonymous rates at the RpII215 gene of Drosophila: variation among species and across the coding region.

Authors:  A Llopart; M Aguadé
Journal:  Genetics       Date:  1999-05       Impact factor: 4.562

2.  Codon usage between genomes is constrained by genome-wide mutational processes.

Authors:  Swaine L Chen; William Lee; Alison K Hottes; Lucy Shapiro; Harley H McAdams
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-27       Impact factor: 11.205

3.  Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure.

Authors:  M A Huynen; D A Konings; P Hogeweg
Journal:  J Mol Evol       Date:  1992-04       Impact factor: 2.395

4.  Essential factors determining codon usage in ubiquitin genes.

Authors:  K Mita; S Ichimura; M Nenoi
Journal:  J Mol Evol       Date:  1991-09       Impact factor: 2.395

5.  The simian herpesvirus SA8 homologue of the herpes simplex virus gB gene: mapping, sequencing, and comparison to the HSV gB.

Authors:  R Eberle; D Black
Journal:  Arch Virol       Date:  1991       Impact factor: 2.574

6.  The selection-mutation-drift theory of synonymous codon usage.

Authors:  M Bulmer
Journal:  Genetics       Date:  1991-11       Impact factor: 4.562

7.  Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

Authors:  Brejnev Muhizi Muhire; Michael Golden; Ben Murrell; Pierre Lefeuvre; Jean-Michel Lett; Alistair Gray; Art Y F Poon; Nobubelo Kwanele Ngandu; Yves Semegni; Emil Pavlov Tanov; Adérito Luis Monjane; Gordon William Harkins; Arvind Varsani; Dionne Natalie Shepherd; Darren Patrick Martin
Journal:  J Virol       Date:  2013-11-27       Impact factor: 5.103

8.  Variation in G + C-content and codon choice: differences among synonymous codon groups in vertebrate genes.

Authors:  A Marín; J Bertranpetit; J L Oliver; J R Medina
Journal:  Nucleic Acids Res       Date:  1989-08-11       Impact factor: 16.971

9.  Compositional constraints and genome evolution.

Authors:  G Bernardi; G Bernardi
Journal:  J Mol Evol       Date:  1986       Impact factor: 2.395

10.  Codon usage and secondary structure of MS2 phage RNA.

Authors:  M Bulmer
Journal:  Nucleic Acids Res       Date:  1989-03-11       Impact factor: 16.971
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