Articles producció científica> Bioquímica i Biotecnologia

Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes

  • Identification data

    Identifier: imarina:5122197
    Authors:
    Pallejà A, García-Vallvé S, Romeu A.
    Abstract:
    In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may influence the stop codon usage or the spacing lengths between co-directional genes.The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large number of genes with the SD sequence concentrate this regulatory motif from 4 to 11 bps before the start codon. However, not all genes seem to have the SD sequence. Genes separated from 1 to 4 bps from a co-directional upstream gene show a high SD presence, though this regulatory signal is located towards the 3' end of the coding sequence of the upstream gene. Genes separated from 9 to 15 bps show the highest SD presence as they accommodate the SD sequence within an intergenic region. However, genes separated from around 5 to 8 bps have a lower percentage of SD presence and when the SD is present, the stop codon usage of the upstream gene changes to accommodate the overlap between the SD sequence and the stop codon.The SD presence makes the intergenic lengths from 5 to 8 bps less frequent and causes an adaptation of the stop codon usage. Our results introduce new elements to the discussion of which factors affect the intergenic lengths, which cannot be totally explained by the pressure to compact the prokaryote genomes.
  • Others:

    Author, as appears in the article.: Pallejà A, García-Vallvé S, Romeu A.
    Department: Bioquímica i Biotecnologia
    e-ISSN: 1471-2164
    URV's Author/s: Garcia Vallve, Santiago / ROMEU FIGUEROLA, ANTONIO RAMÓN
    Abstract: In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may influence the stop codon usage or the spacing lengths between co-directional genes.The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large number of genes with the SD sequence concentrate this regulatory motif from 4 to 11 bps before the start codon. However, not all genes seem to have the SD sequence. Genes separated from 1 to 4 bps from a co-directional upstream gene show a high SD presence, though this regulatory signal is located towards the 3' end of the coding sequence of the upstream gene. Genes separated from 9 to 15 bps show the highest SD presence as they accommodate the SD sequence within an intergenic region. However, genes separated from around 5 to 8 bps have a lower percentage of SD presence and when the SD is present, the stop codon usage of the upstream gene changes to accommodate the overlap between the SD sequence and the stop codon.The SD presence makes the intergenic lengths from 5 to 8 bps less frequent and causes an adaptation of the stop codon usage. Our results introduce new elements to the discussion of which factors affect the intergenic lengths, which cannot be totally explained by the pressure to compact the prokaryote genomes.
    Thematic Areas: Zootecnia / recursos pesqueiros Saúde coletiva Química Odontología Medicina veterinaria Medicina iii Medicina ii Medicina i Matemática / probabilidade e estatística Interdisciplinar Genetics & heredity Genetics Farmacia Engenharias iv Engenharias iii Engenharias ii Educação física Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência de alimentos Ciência da computação Biotecnología Biotechnology & applied microbiology Biotechnology Biodiversidade Astronomia / física
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: santi.garcia-vallve@urv.cat
    Author identifier: 0000-0002-0348-7497
    Record's date: 2023-02-18
    Journal volume: 10
    Papper version: info:eu-repo/semantics/publishedVersion
    Link to the original source: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-10-537
    Papper original source: Bmc Genomics. 10
    APA: Pallejà A, García-Vallvé S, Romeu A. (2009). Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes. Bmc Genomics, 10(), -. DOI: 10.1186/1471-2164-10-537
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Article's DOI: 10.1186/1471-2164-10-537
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2009
    Publication Type: Journal Publications
  • Keywords:

    Biotechnology,Biotechnology & Applied Microbiology,Genetics,Genetics & Heredity
    Zootecnia / recursos pesqueiros
    Saúde coletiva
    Química
    Odontología
    Medicina veterinaria
    Medicina iii
    Medicina ii
    Medicina i
    Matemática / probabilidade e estatística
    Interdisciplinar
    Genetics & heredity
    Genetics
    Farmacia
    Engenharias iv
    Engenharias iii
    Engenharias ii
    Educação física
    Ciências biológicas iii
    Ciências biológicas ii
    Ciências biológicas i
    Ciências ambientais
    Ciências agrárias i
    Ciência de alimentos
    Ciência da computação
    Biotecnología
    Biotechnology & applied microbiology
    Biotechnology
    Biodiversidade
    Astronomia / física
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