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Title: Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains

Abstract

Clostridium thermocellum is a potentially useful organism for the production of lignocellulosic biofuels because of its ability to directly deconstruct cellulose and convert it into ethanol. Previously engineered C. thermocellum strains have achieved higher yields and titers of ethanol. These strains often initially grow more poorly than the wild type. Adaptive laboratory evolution and medium supplementation have been used to improve growth, but the mechanism(s) by which growth improves remain(s) unclear. Here, we studied (1) wild-type C. thermocellum, (2) the slow-growing and high-ethanol-yielding mutant AG553, and (3) the faster-growing evolved mutant AG601, each grown with and without added formate. We used a combination of transcriptomics and proteomics to understand the physiological impact of the metabolic engineering, evolution, and medium supplementation. Medium supplementation with formate improved growth in both AG553 and AG601. Expression of C1 metabolism genes varied with formate addition, supporting the hypothesis that the primary benefit of added formate is the supply of C1 units for biosynthesis. Expression of stress response genes such as those involved in the sporulation cascade was dramatically over-represented in AG553, even after the addition of formate, suggesting that the source of the stress may be other issues such as redox imbalances. The sporulation responsemore » is absent in evolved strain AG601, suggesting that sporulation limits the growth of engineered strain AG553. A better understanding of the stress response and mechanisms of improved growth hold promise for informing rational improvement of C. thermocellum for lignocellulosic biofuel production.« less

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1468680
Alternate Identifier(s):
OSTI ID: 1474657
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Journal of Industrial Microbiology and Biotechnology
Additional Journal Information:
Journal Name: Journal of Industrial Microbiology and Biotechnology; Journal ID: ISSN 1367-5435
Publisher:
Springer
Country of Publication:
Germany
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; consolidated bioprocessing; C1 metabolism; stress response; robustness; lignocellulosic ethanol

Citation Formats

Papanek, Beth, O’Dell, Kaela B., Manga, Punita, Giannone, Richard J., Klingeman, Dawn M., Hettich, Robert L., Brown, Steven D., and Guss, Adam M. Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains. Germany: N. p., 2018. Web. doi:10.1007/s10295-018-2073-x.
Papanek, Beth, O’Dell, Kaela B., Manga, Punita, Giannone, Richard J., Klingeman, Dawn M., Hettich, Robert L., Brown, Steven D., & Guss, Adam M. Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains. Germany. doi:10.1007/s10295-018-2073-x.
Papanek, Beth, O’Dell, Kaela B., Manga, Punita, Giannone, Richard J., Klingeman, Dawn M., Hettich, Robert L., Brown, Steven D., and Guss, Adam M. Wed . "Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains". Germany. doi:10.1007/s10295-018-2073-x.
@article{osti_1468680,
title = {Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains},
author = {Papanek, Beth and O’Dell, Kaela B. and Manga, Punita and Giannone, Richard J. and Klingeman, Dawn M. and Hettich, Robert L. and Brown, Steven D. and Guss, Adam M.},
abstractNote = {Clostridium thermocellum is a potentially useful organism for the production of lignocellulosic biofuels because of its ability to directly deconstruct cellulose and convert it into ethanol. Previously engineered C. thermocellum strains have achieved higher yields and titers of ethanol. These strains often initially grow more poorly than the wild type. Adaptive laboratory evolution and medium supplementation have been used to improve growth, but the mechanism(s) by which growth improves remain(s) unclear. Here, we studied (1) wild-type C. thermocellum, (2) the slow-growing and high-ethanol-yielding mutant AG553, and (3) the faster-growing evolved mutant AG601, each grown with and without added formate. We used a combination of transcriptomics and proteomics to understand the physiological impact of the metabolic engineering, evolution, and medium supplementation. Medium supplementation with formate improved growth in both AG553 and AG601. Expression of C1 metabolism genes varied with formate addition, supporting the hypothesis that the primary benefit of added formate is the supply of C1 units for biosynthesis. Expression of stress response genes such as those involved in the sporulation cascade was dramatically over-represented in AG553, even after the addition of formate, suggesting that the source of the stress may be other issues such as redox imbalances. The sporulation response is absent in evolved strain AG601, suggesting that sporulation limits the growth of engineered strain AG553. A better understanding of the stress response and mechanisms of improved growth hold promise for informing rational improvement of C. thermocellum for lignocellulosic biofuel production.},
doi = {10.1007/s10295-018-2073-x},
journal = {Journal of Industrial Microbiology and Biotechnology},
issn = {1367-5435},
number = ,
volume = ,
place = {Germany},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1007/s10295-018-2073-x

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    Works referencing / citing this record:

    Engineering Geobacillus thermoglucosidasius for direct utilisation of holocellulose from wheat straw
    journal, August 2019