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

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:
 [1] ;  [2] ;  [3] ;  [2] ;  [2] ;  [2] ;  [4] ;  [5]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center for Interdisciplinary Research and Graduate Education; Univ. of Illinois, Urbana, IL (United States). Integrated Bioprocessing Research Lab.
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). The Graduate School of Genome Science and Technology
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). The Graduate School of Genome Science and Technology; LanzaTech Inc., Skokie, IL (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center for Interdisciplinary Research and Graduate Education
Publication Date:
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
Type:
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
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)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; consolidated bioprocessing; C1 metabolism; stress response; robustness; lignocellulosic ethanol
OSTI Identifier:
1468680
Alternate Identifier(s):
OSTI ID: 1474657

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. United States: N. p., 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. United States. 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.. 2018. "Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains". United States. 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},
number = ,
volume = ,
place = {United States},
year = {2018},
month = {9}
}

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