Transcriptome analysis of wild-type and afsS deletion mutant strains identifies synergistic transcriptional regulator of afsS for a high antibiotic-producing strain of Streptomyces coelicolor A3(2)

Kim, Min Woo; Lee, Bo-Rahm; You, SungYong; Kim, Eun-Jung; Kim, Ji-Nu; Song, Eunjung; Yang, Yung-Hun; Hwang, Daehee; Kim, Byung-Gee

doi:10.1007/s00253-018-8838-3

Applied genetics and molecular biotechnology
Published: 17 February 2018

Transcriptome analysis of wild-type and afsS deletion mutant strains identifies synergistic transcriptional regulator of afsS for a high antibiotic-producing strain of Streptomyces coelicolor A3(2)

Min Woo Kim¹^na1,
Bo-Rahm Lee²^na1,
SungYong You³,
Eun-Jung Kim²,
Ji-Nu Kim²,
Eunjung Song²,
Yung-Hun Yang⁴,
Daehee Hwang⁵ &
…
Byung-Gee Kim ORCID: orcid.org/0000-0002-3776-1001^1,2

Applied Microbiology and Biotechnology volume 102, pages 3243–3253 (2018)Cite this article

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Abstract

Most secondary metabolism in Actinobacteria is controlled by multi-layered, gene-regulatory networks. These regulatory mechanisms are not easily identified due to their complexity. As a result, when a strong transcriptional regulator (TR) governs activation of biosynthetic pathways of target antibiotics such as actinorhodin (ACT), additional enhancement of the biosynthesis is difficult in combination with other TRs. To find out any “synergistic transcriptional regulators (sTRs)” that show an additive effect on the major, often strong, transcriptional regulator (mTR), here, we performed a clustering analysis using the transcriptome datasets of an mTR deletion mutant and wild-type strain. In the case of ACT biosynthesis in Streptomyces coelicolor, PhoU (SCO4228) and RsfA (SCO4677) were selected through the clustering analysis, using AfsS (SCO4425) as a model mTR, and experimentally validated their roles as sTRs. Furthermore, through analysis of synergistic effects, we were able to suggest a novel regulation mechanism and formulate a strategy to maximize the synergistic effect. In the case of the double TR mutant strain (ΔrsfA pIBR25::afsS), it was confirmed that the increase of cell mass was the major cause of the synergistic effect. Therefore, the strategy to increase the cell mass of double mutant was further attempted by optimizing the expression of efflux pump, which resulted in 2-fold increase in the cell mass and 24-fold increase in the production of ACT. This result is the highest ACT yield from S. coelicolor ever reported.

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Acknowledgments

This research was supported by the National Research Foundation of Korea(NRF) funded by the Ministry of Science, ICT and Future Planning (2016953757), and by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through Agri-Bio industry Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA)(116139-03-1-SB010), and by the Institute for Basic Science (IBS-R13-G1).

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Min Woo Kim and Bo-Rahm Lee contributed equally to this work.

Authors and Affiliations

Interdisciplinary Program for Biochemical Engineering, Seoul National University, Seoul, South Korea
Min Woo Kim & Byung-Gee Kim
School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, South Korea
Bo-Rahm Lee, Eun-Jung Kim, Ji-Nu Kim, Eunjung Song & Byung-Gee Kim
Division of Cancer Biology and Therapeutics, Departments of Surgery & Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
SungYong You
Department of Microbial Engineering, College of Engineering, Konkuk University, Seoul, South Korea
Yung-Hun Yang
Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu, Republic of Korea
Daehee Hwang

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Min Woo Kim
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Bo-Rahm Lee
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SungYong You
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Kim, M.W., Lee, BR., You, S. et al. Transcriptome analysis of wild-type and afsS deletion mutant strains identifies synergistic transcriptional regulator of afsS for a high antibiotic-producing strain of Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol 102, 3243–3253 (2018). https://doi.org/10.1007/s00253-018-8838-3

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Received: 01 November 2017
Revised: 01 February 2018
Accepted: 04 February 2018
Published: 17 February 2018
Issue Date: April 2018
DOI: https://doi.org/10.1007/s00253-018-8838-3

Transcriptome analysis of wild-type and afsS deletion mutant strains identifies synergistic transcriptional regulator of afsS for a high antibiotic-producing strain of Streptomyces coelicolor A3(2)

Abstract