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

Licence document URL: http://repositori.urv.cat/ca/proteccio-de-dades/

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

Article's DOI: 10.1186/1471-2164-10-537

Entity: Universitat Rovira i Virgili

Journal publication year: 2009

Publication Type: Journal Publications