Gene duplications in the E. coli genome : common themes among pathotypes
Bernabeu, Manuel (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Sánchez Herrero, José Francisco (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Huedo Moreno, Pol (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Prieto, Alejandro (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Hüttener, Mario (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Rozas, Julio (Institut de Recerca de la Biodiversitat)
Juárez, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)

Fecha:	2019
Resumen:	Background: gGene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorganism is needed. - Results: the genomes of the E. coli enteroaggregative strain 042 and other pathogenic strains contain duplications of the gene that codes for the global regulator Hha. To determine whether the presence of additional copies of the hha gene correlates with the presence of other genes, we performed a comparative genomic analysis between E. coli strains with and without hha duplications. The results showed that strains harboring additional copies of the hha gene also encode the yeeR irmA (aec69) gene cluster, which, in turn, is also duplicated in strain 042 and several other strains. The identification of these duplications prompted us to obtain a global map of gene duplications, first in strain 042 and later in other E. coli genomes. Duplications in the genomes of the enteroaggregative strain 042, the uropathogenic strain CFT073 and the enterohemorrhagic strain O145:H28 have been identified by a BLASTp protein similarity search. This algorithm was also used to evaluate the distribution of the identified duplicates among the genomes of a set of 28 representative E. coli strains. Despite the high genomic diversity of E. coli strains, we identified several duplicates in the genomes of almost all studied pathogenic strains. Most duplicated genes have no known function. Transcriptomic analysis also showed that most of these duplications are regulated by the H-NS/Hha proteins. - Conclusions: several duplicated genes are widely distributed among pathogenic E. coli strains. In addition, some duplicated genes are present only in specific pathotypes, and others are strain specific. This gene duplication analysis shows novel relationships between E. coli pathotypes and suggests that newly identified genes that are duplicated in a high percentage of pathogenic E. coli isolates may play a role in virulence. Our study also shows a relationship between the duplication of genes encoding regulators and genes encoding their targets.
Ayudas:	Ministerio de Economía y Competitividad CGL2016-75255 Ministerio de Economía y Competitividad BIO2016-76412-C2-1-R
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Pathotypes ; Gene duplication ; Escherichia coli 042 ; H-NS ; Hha
Publicado en:	BMC genomics, Vol. 20 (2019) , art. 313, ISSN 1471-2164

DOI: 10.1186/s12864-019-5683-4
PMID: 31014240

11 p, 2.4 MB

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