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System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus

Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements gove...

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Autores principales: Hwang, Soonkyu, Lee, Namil, Choe, Donghui, Lee, Yongjae, Kim, Woori, Kim, Ji Hun, Kim, Gahyeon, Kim, Hyeseong, Ahn, Neung-Ho, Lee, Byoung-Hee, Palsson, Bernhard O., Cho, Byung-Kwan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8914203/
https://www.ncbi.nlm.nih.gov/pubmed/35284422
http://dx.doi.org/10.3389/fbioe.2022.844200
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author Hwang, Soonkyu
Lee, Namil
Choe, Donghui
Lee, Yongjae
Kim, Woori
Kim, Ji Hun
Kim, Gahyeon
Kim, Hyeseong
Ahn, Neung-Ho
Lee, Byoung-Hee
Palsson, Bernhard O.
Cho, Byung-Kwan
author_facet Hwang, Soonkyu
Lee, Namil
Choe, Donghui
Lee, Yongjae
Kim, Woori
Kim, Ji Hun
Kim, Gahyeon
Kim, Hyeseong
Ahn, Neung-Ho
Lee, Byoung-Hee
Palsson, Bernhard O.
Cho, Byung-Kwan
author_sort Hwang, Soonkyu
collection PubMed
description Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in Streptomyces, system-level information remains limited. In this study, we integrated four multi-omics datasets from Streptomyces griseus NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3′-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5′-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in Streptomyces.
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spelling pubmed-89142032022-03-12 System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus Hwang, Soonkyu Lee, Namil Choe, Donghui Lee, Yongjae Kim, Woori Kim, Ji Hun Kim, Gahyeon Kim, Hyeseong Ahn, Neung-Ho Lee, Byoung-Hee Palsson, Bernhard O. Cho, Byung-Kwan Front Bioeng Biotechnol Bioengineering and Biotechnology Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in Streptomyces, system-level information remains limited. In this study, we integrated four multi-omics datasets from Streptomyces griseus NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3′-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5′-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in Streptomyces. Frontiers Media S.A. 2022-02-25 /pmc/articles/PMC8914203/ /pubmed/35284422 http://dx.doi.org/10.3389/fbioe.2022.844200 Text en Copyright © 2022 Hwang, Lee, Choe, Lee, Kim, Kim, Kim, Kim, Ahn, Lee, Palsson and Cho. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioengineering and Biotechnology
Hwang, Soonkyu
Lee, Namil
Choe, Donghui
Lee, Yongjae
Kim, Woori
Kim, Ji Hun
Kim, Gahyeon
Kim, Hyeseong
Ahn, Neung-Ho
Lee, Byoung-Hee
Palsson, Bernhard O.
Cho, Byung-Kwan
System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
title System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
title_full System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
title_fullStr System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
title_full_unstemmed System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
title_short System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus
title_sort system-level analysis of transcriptional and translational regulatory elements in streptomyces griseus
topic Bioengineering and Biotechnology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8914203/
https://www.ncbi.nlm.nih.gov/pubmed/35284422
http://dx.doi.org/10.3389/fbioe.2022.844200
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