Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry.

Chromosomes, Bacterial Codon Usage Computational Biology DNA, Ribosomal / genetics Evolution, Molecular Genes, Bacterial Genome, Bacterial Plasmids / genetics Replicon Sinorhizobium meliloti / genetics
codon usage genome evolution host-microbe interaction mobile genetic elements plasmidome

Journal

mBio
ISSN: 2150-7511
Titre abrégé: mBio
Pays: United States
ID NLM: 101519231

Informations de publication

Date de publication:
28 05 2019
Historique:
entrez: 30 5 2019
pubmed: 30 5 2019
medline: 11 2 2020
Statut: epublish

Résumé

Prokaryotes represent an ancestral lineage in the tree of life and constitute optimal resources for investigating the evolution of genomes in unicellular organisms. Many bacterial species possess multipartite genomes offering opportunities to study functional variations among replicons, how and where new genes integrate into a genome, and how genetic information within a lineage becomes encoded and evolves. To analyze these issues, we focused on the model soil bacterium

Identifiants

DOI: 10.1128/mBio.00505-19 PMID: 31138741 PMC: PMC6538778
pubmed: 31138741
pii: mBio.00505-19
doi: 10.1128/mBio.00505-19
pmc: PMC6538778
pii:
doi:

Substances chimiques

DNA, Ribosomal 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

Copyright © 2019 López et al.

Références

Genome Biol. 2003;4(9):R57
pubmed: 12952536
J Proteome Res. 2009 Jun;8(6):2838-50
pubmed: 19290621
Anal Chem. 2003 Dec 15;75(24):6912-21
pubmed: 14670053
Genome Biol Evol. 2013;5(3):542-58
pubmed: 23431003
Science. 2001 Jul 27;293(5530):668-72
pubmed: 11474104
Gene. 2003 Nov 27;320:109-16
pubmed: 14597394
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9889-94
pubmed: 11481431
Nucleic Acids Res. 1986 Jul 11;14(13):5125-43
pubmed: 3526280
Bioinformatics. 1998;14(4):372-3
pubmed: 9632833
Cell. 2012 Mar 30;149(1):202-13
pubmed: 22464330
DNA Res. 2014 Oct;21(5):511-26
pubmed: 24906480
FEMS Microbiol Ecol. 2008 Sep;65(3):372-82
pubmed: 18537840
Nucleic Acids Res. 1980 Jan 11;8(1):r49-r62
pubmed: 6986610
PLoS One. 2012;7(10):e48494
pubmed: 23119037
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
pubmed: 3547335
Ann N Y Acad Sci. 1999 May 18;870:314-29
pubmed: 10415493
Nucleic Acids Res. 2012 Aug;40(15):7074-83
pubmed: 22581775
Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6595-9
pubmed: 15851673
Nucleic Acids Res. 1981 Jan 10;9(1):r43-74
pubmed: 7208352
Microb Genom. 2018 May;4(5):
pubmed: 29671722
BMC Genomics. 2015 Jan 22;16:6
pubmed: 25608745
J Mol Biol. 1982 Jul 15;158(4):573-97
pubmed: 6750137
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9883-8
pubmed: 11481432
FEMS Microbiol Rev. 2011 Sep;35(5):957-76
pubmed: 21711367
Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9413-7
pubmed: 9689094
Mol Gen Genet. 1981;182(2):189-95
pubmed: 6270502
BMC Bioinformatics. 2009 May 20;10:154
pubmed: 19457249
Nucleic Acids Res. 2004 Sep 24;32(17):5036-44
pubmed: 15448185
PLoS Genet. 2018 Apr 19;14(4):e1007357
pubmed: 29672509
Gene. 1999 Sep 30;238(1):143-55
pubmed: 10570992
Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1203-12
pubmed: 20308095
Bioinformatics. 2009 Dec 1;25(23):3128-34
pubmed: 19808875
Appl Environ Microbiol. 2006 May;72(5):3662-72
pubmed: 16672515
J Mol Biol. 1991 Dec 20;222(4):851-6
pubmed: 1762151
Bioinformatics. 2015 Nov 15;31(22):3718-20
pubmed: 26209431
J Mol Biol. 1981 Sep 25;151(3):389-409
pubmed: 6175758
J Bacteriol. 2017 Mar 28;199(8):
pubmed: 28167519
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20154-9
pubmed: 22128332
Mol Biol Evol. 2010 Apr;27(4):800-10
pubmed: 20018979
Nucleic Acids Res. 2003 Apr 15;31(8):2187-95
pubmed: 12682369
Nucleic Acids Res. 2005 Feb 23;33(4):1141-53
pubmed: 15728743
J Mol Evol. 2014 Oct;79(3-4):105-10
pubmed: 25239794
Mol Biol Evol. 2007 Feb;24(2):374-81
pubmed: 17101719
Mol Cell Proteomics. 2006 Jan;5(1):144-56
pubmed: 16219938
Nat Rev Genet. 2011 Jan;12(1):32-42
pubmed: 21102527
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
Microbiology. 2013 Mar;159(Pt 3):555-564
pubmed: 23288542
BMC Genomics. 2011 Sep 07;12:444
pubmed: 21899761
Trends Microbiol. 2010 Apr;18(4):141-8
pubmed: 20080407
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Plasmid. 2012 Nov;68(3):149-58
pubmed: 22813963
Curr Opin Genet Dev. 2005 Dec;15(6):589-94
pubmed: 16185861

Auteurs

J L López (JL)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.

M J Lozano (MJ)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.

A Lagares (A)

Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo, Universidad Nacional de Quilmes-CONICET, Bernal, Argentina.
LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.

M L Fabre (ML)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.

W O Draghi (WO)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.

M F Del Papa (MF)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.

M Pistorio (M)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.

A Becker (A)

LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.

D Wibberg (D)

CeBiTec-Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.

A Schlüter (A)

CeBiTec-Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.

A Pühler (A)

CeBiTec-Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.

J Blom (J)

Institute for Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Giessen, Germany.

A Goesmann (A)

Institute for Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Giessen, Germany.

A Lagares (A)

IBBM-Instituto de Biotecnología y Biología Molecular, CONICET, CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina lagares@biol.unlp.edu.ar.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › Chromosomes de bactérie › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Code génétique › Usage des codons › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › ADN ribosomique › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Gènes bactériens › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Plasmides › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Réplicon › Codon Usage Heterogeneity in the Multipartite...
questionsmedicales.fr › Bactéries › Proteobacteria › Alphaproteobacteria › Rhizobiaceae › Sinorhizobium › Sinorhizobium meliloti › Codon Usage Heterogeneity in the Multipartite...