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Literature DB >> 7038623

Key for protein coding sequences identification: computer analysis of codon strategy.

F Rodier, J Gabarro-Arpa, R Ehrlich, C Reiss.

Abstract

The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA.

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Year: 1982 PMID： 7038623 PMCID： PMC326141 DOI： 10.1093/nar/10.1.391

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

7 in total

1. Correlation of local stability of DNA during melting with environmental conditions.

Authors: J Gabbarro-Arpa; P Tougard; C Reiss
Journal: Nature Date: 1979-08-09 Impact factor: 49.962

2. Sequence and symmetry in ribosome binding sites of bacteriophage f1 RNA.

Authors: G Pieczenik; P Model; H D Robertson
Journal: J Mol Biol Date: 1974-12-05 Impact factor: 5.469

Review 3. Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs.

Authors: J Ninio
Journal: Biochimie Date: 1979 Impact factor: 4.079

4. The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments.

Authors: G F Scherer; M D Walkinshaw; S Arnott; D J Morré
Journal: Nucleic Acids Res Date: 1980-09-11 Impact factor: 16.971

5. The nucleotide sequence of bacteriophage phiX174.

Authors: F Sanger; A R Coulson; T Friedmann; G M Air; B G Barrell; N L Brown; J C Fiddes; C A Hutchison; P M Slocombe; M Smith
Journal: J Mol Biol Date: 1978-10-25 Impact factor: 5.469

6. 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

7. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.

Authors: J Shine; L Dalgarno
Journal: Proc Natl Acad Sci U S A Date: 1974-04 Impact factor: 11.205

7 in total

1. DNA sequences specifying the transcription of the streptococcal kanamycin resistance gene in Escherichia coli and Bacillus subtilis.

Authors: P Trieu-Cuot; A Klier; P Courvalin
Journal: Mol Gen Genet Date: 1985

Key for protein coding sequences identification: computer analysis of codon strategy.

1. Correlation of local stability of DNA during melting with environmental conditions.

2. Sequence and symmetry in ribosome binding sites of bacteriophage f1 RNA.

Review 3. Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs.

4. The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments.

5. The nucleotide sequence of bacteriophage phiX174.

6. Nucleotide sequence of bacteriophage fd DNA.

7. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.

1. DNA sequences specifying the transcription of the streptococcal kanamycin resistance gene in Escherichia coli and Bacillus subtilis.

2. Strong doublet preferences in nucleotide sequences and DNA geometry.

3. Physical characteristics in eucaryotic promoters.

4. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.

5. Recognition of protein coding regions in DNA sequences.

6. Analysis of the nucleotide sequence of the ereB gene encoding the erythromycin esterase type II.

7. Divergence in codon usage of Lactobacillus species.