Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli
The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with b...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2018-05-01
|
Series: | Frontiers in Microbiology |
Subjects: | |
Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.01059/full |
id |
doaj-9e1460efaec54fe593cecf22390d01fd |
---|---|
record_format |
Article |
spelling |
doaj-9e1460efaec54fe593cecf22390d01fd2020-11-25T02:24:48ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-05-01910.3389/fmicb.2018.01059366220Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coliEnrique Martínez-Carranza0Hugo Barajas1Luis-David Alcaraz2Luis-David Alcaraz3Luis Servín-González4Gabriel-Yaxal Ponce-Soto5Gloria Soberón-Chávez6Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, MexicoDepartamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, MexicoDepartamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, MexicoLaboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, MexicoDepartamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, MexicoDepartamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, MexicoDepartamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, MexicoThe definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as “non-orthologous gene displacement” that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species.https://www.frontiersin.org/article/10.3389/fmicb.2018.01059/fullessential-genescore-genomenon-orthologous gene displacementEscherichia coliwhole genome sequence databases |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Enrique Martínez-Carranza Hugo Barajas Luis-David Alcaraz Luis-David Alcaraz Luis Servín-González Gabriel-Yaxal Ponce-Soto Gloria Soberón-Chávez |
spellingShingle |
Enrique Martínez-Carranza Hugo Barajas Luis-David Alcaraz Luis-David Alcaraz Luis Servín-González Gabriel-Yaxal Ponce-Soto Gloria Soberón-Chávez Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli Frontiers in Microbiology essential-genes core-genome non-orthologous gene displacement Escherichia coli whole genome sequence databases |
author_facet |
Enrique Martínez-Carranza Hugo Barajas Luis-David Alcaraz Luis-David Alcaraz Luis Servín-González Gabriel-Yaxal Ponce-Soto Gloria Soberón-Chávez |
author_sort |
Enrique Martínez-Carranza |
title |
Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli |
title_short |
Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli |
title_full |
Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli |
title_fullStr |
Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli |
title_full_unstemmed |
Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli |
title_sort |
variability of bacterial essential genes among closely related bacteria: the case of escherichia coli |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2018-05-01 |
description |
The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as “non-orthologous gene displacement” that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species. |
topic |
essential-genes core-genome non-orthologous gene displacement Escherichia coli whole genome sequence databases |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2018.01059/full |
work_keys_str_mv |
AT enriquemartinezcarranza variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli AT hugobarajas variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli AT luisdavidalcaraz variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli AT luisdavidalcaraz variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli AT luisservingonzalez variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli AT gabrielyaxalponcesoto variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli AT gloriasoberonchavez variabilityofbacterialessentialgenesamongcloselyrelatedbacteriathecaseofescherichiacoli |
_version_ |
1724853466149421056 |