New insights into the genome of Rhodococcus ruber strain Chol-4
Abstract Background Rhodococcus ruber strain Chol-4, a strain isolated from a sewage sludge sample, is able to grow in minimal medium supplemented with several compounds, showing a broad catabolic capacity. We have previously determined its genome sequence but a more comprehensive study of their met...
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doaj-836510ba9aef4a83920542d56c9208082020-11-25T02:10:35ZengBMCBMC Genomics1471-21642019-05-0120111710.1186/s12864-019-5677-2New insights into the genome of Rhodococcus ruber strain Chol-4Govinda Guevara0Maria Castillo Lopez1Sergio Alonso2Julián Perera3Juana María Navarro-Llorens4Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de MadridDepartamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de MadridProgram of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP)Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de MadridDepartamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad Complutense de MadridAbstract Background Rhodococcus ruber strain Chol-4, a strain isolated from a sewage sludge sample, is able to grow in minimal medium supplemented with several compounds, showing a broad catabolic capacity. We have previously determined its genome sequence but a more comprehensive study of their metabolic capacities was necessary to fully unravel its potential for biotechnological applications. Results In this work, the genome of R. ruber strain Chol-4 has been re-sequenced, revised, annotated and compared to other bacterial genomes in order to investigate the metabolic capabilities of this microorganism. The analysis of the data suggests that R. ruber Chol-4 contains several putative metabolic clusters of biotechnological interest, particularly those involved on steroid and aromatic compounds catabolism. To demonstrate some of its putative metabolic abilities, R. ruber has been cultured in minimal media containing compounds belonging to several of the predicted metabolic pathways. Moreover, mutants were built to test the naphtalen and protocatechuate predicted catabolic gene clusters. Conclusions The genomic analysis and experimental data presented in this work confirm the metabolic potential of R. ruber strain Chol-4. This strain is an interesting model bacterium due to its biodegradation capabilities. The results obtained in this work will facilitate the application of this strain as a biotechnological tool.http://link.springer.com/article/10.1186/s12864-019-5677-2Rhodococcus ruberCatabolismBiodegradationGenome analysis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Govinda Guevara Maria Castillo Lopez Sergio Alonso Julián Perera Juana María Navarro-Llorens |
spellingShingle |
Govinda Guevara Maria Castillo Lopez Sergio Alonso Julián Perera Juana María Navarro-Llorens New insights into the genome of Rhodococcus ruber strain Chol-4 BMC Genomics Rhodococcus ruber Catabolism Biodegradation Genome analysis |
author_facet |
Govinda Guevara Maria Castillo Lopez Sergio Alonso Julián Perera Juana María Navarro-Llorens |
author_sort |
Govinda Guevara |
title |
New insights into the genome of Rhodococcus ruber strain Chol-4 |
title_short |
New insights into the genome of Rhodococcus ruber strain Chol-4 |
title_full |
New insights into the genome of Rhodococcus ruber strain Chol-4 |
title_fullStr |
New insights into the genome of Rhodococcus ruber strain Chol-4 |
title_full_unstemmed |
New insights into the genome of Rhodococcus ruber strain Chol-4 |
title_sort |
new insights into the genome of rhodococcus ruber strain chol-4 |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-05-01 |
description |
Abstract Background Rhodococcus ruber strain Chol-4, a strain isolated from a sewage sludge sample, is able to grow in minimal medium supplemented with several compounds, showing a broad catabolic capacity. We have previously determined its genome sequence but a more comprehensive study of their metabolic capacities was necessary to fully unravel its potential for biotechnological applications. Results In this work, the genome of R. ruber strain Chol-4 has been re-sequenced, revised, annotated and compared to other bacterial genomes in order to investigate the metabolic capabilities of this microorganism. The analysis of the data suggests that R. ruber Chol-4 contains several putative metabolic clusters of biotechnological interest, particularly those involved on steroid and aromatic compounds catabolism. To demonstrate some of its putative metabolic abilities, R. ruber has been cultured in minimal media containing compounds belonging to several of the predicted metabolic pathways. Moreover, mutants were built to test the naphtalen and protocatechuate predicted catabolic gene clusters. Conclusions The genomic analysis and experimental data presented in this work confirm the metabolic potential of R. ruber strain Chol-4. This strain is an interesting model bacterium due to its biodegradation capabilities. The results obtained in this work will facilitate the application of this strain as a biotechnological tool. |
topic |
Rhodococcus ruber Catabolism Biodegradation Genome analysis |
url |
http://link.springer.com/article/10.1186/s12864-019-5677-2 |
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