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Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains
BACKGROUND: S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-ty...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733707/ https://www.ncbi.nlm.nih.gov/pubmed/23902230 http://dx.doi.org/10.1186/1471-2164-14-523 |
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author | Li, Yuan-Yuan Chang, Xiao Yu, Wen-Bang Li, Hao Ye, Zhi-Qiang Yu, Hui Liu, Bao-Hong Zhang, Yan Zhang, Si-Liang Ye, Bang-Ce Li, Yi-Xue |
author_facet | Li, Yuan-Yuan Chang, Xiao Yu, Wen-Bang Li, Hao Ye, Zhi-Qiang Yu, Hui Liu, Bao-Hong Zhang, Yan Zhang, Si-Liang Ye, Bang-Ce Li, Yi-Xue |
author_sort | Li, Yuan-Yuan |
collection | PubMed |
description | BACKGROUND: S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. RESULTS: We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. CONCLUSION: This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future. |
format | Online Article Text |
id | pubmed-3733707 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-37337072013-08-06 Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains Li, Yuan-Yuan Chang, Xiao Yu, Wen-Bang Li, Hao Ye, Zhi-Qiang Yu, Hui Liu, Bao-Hong Zhang, Yan Zhang, Si-Liang Ye, Bang-Ce Li, Yi-Xue BMC Genomics Research Article BACKGROUND: S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. RESULTS: We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. CONCLUSION: This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future. BioMed Central 2013-07-31 /pmc/articles/PMC3733707/ /pubmed/23902230 http://dx.doi.org/10.1186/1471-2164-14-523 Text en Copyright © 2013 Li et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Li, Yuan-Yuan Chang, Xiao Yu, Wen-Bang Li, Hao Ye, Zhi-Qiang Yu, Hui Liu, Bao-Hong Zhang, Yan Zhang, Si-Liang Ye, Bang-Ce Li, Yi-Xue Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains |
title | Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains |
title_full | Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains |
title_fullStr | Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains |
title_full_unstemmed | Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains |
title_short | Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains |
title_sort | systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of s. erythraea e3 and nrrl23338 strains |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733707/ https://www.ncbi.nlm.nih.gov/pubmed/23902230 http://dx.doi.org/10.1186/1471-2164-14-523 |
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