Quantitative proteomic analysis of the influence of lignin on biofuel production by Clostridium acetobutylicum ATCC 824 View Full Text


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Article Info

DATE

2016-05-31

AUTHORS

Mahendra P. Raut, Narciso Couto, Trong K. Pham, Caroline Evans, Josselin Noirel, Phillip C. Wright

ABSTRACT

BackgroundClostridium acetobutylicum has been a focus of research because of its ability to produce high-value compounds that can be used as biofuels. Lignocellulose is a promising feedstock, but the lignin–cellulose–hemicellulose biomass complex requires chemical pre-treatment to yield fermentable saccharides, including cellulose-derived cellobiose, prior to bioproduction of acetone–butanol–ethanol (ABE) and hydrogen. Fermentation capability is limited by lignin and thus process optimization requires knowledge of lignin inhibition. The effects of lignin on cellular metabolism were evaluated for C. acetobutylicum grown on medium containing either cellobiose only or cellobiose plus lignin. Microscopy, gas chromatography and 8-plex iTRAQ-based quantitative proteomic technologies were applied to interrogate the effect of lignin on cellular morphology, fermentation and the proteome.ResultsOur results demonstrate that C. acetobutylicum has reduced performance for solvent production when lignin is present in the medium. Medium supplemented with 1 g L−1 of lignin led to delay and decreased solvents production (ethanol; 0.47 g L−1 for cellobiose and 0.27 g L−1 for cellobiose plus lignin and butanol; 0.13 g L−1 for cellobiose and 0.04 g L−1 for cellobiose plus lignin) at 20 and 48 h, respectively, resulting in the accumulation of acetic acid and butyric acid. Of 583 identified proteins (FDR < 1 %), 328 proteins were quantified with at least two unique peptides. Up- or down-regulation of protein expression was determined by comparison of exponential and stationary phases of cellobiose in the presence and absence of lignin. Of relevance, glycolysis and fermentative pathways were mostly down-regulated, during exponential and stationary growth phases in presence of lignin. Moreover, proteins involved in DNA repair, transcription/translation and GTP/ATP-dependent activities were also significantly affected and these changes were associated with altered cell morphology.ConclusionsThis is the first comprehensive analysis of the cellular responses of C. acetobutylicum to lignin at metabolic and physiological levels. These data will enable targeted metabolic engineering strategies to optimize biofuel production from biomass by overcoming limitations imposed by the presence of lignin. More... »

PAGES

113

References to SciGraph publications

  • 1982-07. Bioalteration of Kraft pine lignin byPhanerochaete chrysosporium in ARCHIVES OF MICROBIOLOGY
  • 2008-07-16. The transcriptional program underlying the physiology of clostridial sporulation in GENOME BIOLOGY
  • 2012-02-16. ppGpp: magic beyond RNA polymerase in NATURE REVIEWS MICROBIOLOGY
  • 2014-09-30. Microbial inhibitors: formation and effects on acetone-butanol-ethanol fermentation of lignocellulosic biomass in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2015-06-10. Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum in BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
  • 2014-06-03. Side by Side Comparison of Chemical Compounds Generated by Aqueous Pretreatments of Maize Stover, Miscanthus and Sugarcane Bagasse in BIOENERGY RESEARCH
  • 1989-10. Enzymes limiting butanol and acetone formation in continuous and batch cultures of Clostridium acetobutylicum in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 1969-06. The occurrence of a modified Entner-Doudoroff pathway in Clostridium aceticum in ARCHIVES OF MICROBIOLOGY
  • 2011-10-18. Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose in PROTEOME SCIENCE
  • 2008-02. Morphological plasticity as a bacterial survival strategy in NATURE REVIEWS MICROBIOLOGY
  • 1991-12. Dehydrogenase activation by Ca2+ in cells and tissues in JOURNAL OF BIOENERGETICS AND BIOMEMBRANES
  • 2007-02-27. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry in NATURE METHODS
  • 1985-06. Effect of increased hydrogen partial pressure on the acetone-butanol fermentation by Clostridium acetobutylicum in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2015-01-22. Designer synthetic media for studying microbial-catalyzed biofuel production in BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
  • 1991-11. Enzymatic characterization of a nonmotile, nonsolventogenicClostridium acetobutylicum ATCC 824 mutant in CURRENT MICROBIOLOGY
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        "description": "BackgroundClostridium acetobutylicum has been a focus of research because of its ability to produce high-value compounds that can be used as biofuels. Lignocellulose is a promising feedstock, but the lignin\u2013cellulose\u2013hemicellulose biomass complex requires chemical pre-treatment to yield fermentable saccharides, including cellulose-derived cellobiose, prior to bioproduction of acetone\u2013butanol\u2013ethanol (ABE) and hydrogen. Fermentation capability is limited by lignin and thus process optimization requires knowledge of lignin inhibition. The effects of lignin on cellular metabolism were evaluated for C. acetobutylicum grown on medium containing either cellobiose only or cellobiose plus lignin. Microscopy, gas chromatography and 8-plex iTRAQ-based quantitative proteomic technologies were applied to interrogate the effect of lignin on cellular morphology, fermentation and the proteome.ResultsOur results demonstrate that C. acetobutylicum has reduced performance for solvent production when lignin is present in the medium. Medium supplemented with 1\u00a0g\u00a0L\u22121 of lignin led to delay and decreased solvents production (ethanol; 0.47\u00a0g\u00a0L\u22121 for cellobiose and 0.27\u00a0g\u00a0L\u22121 for cellobiose plus lignin and butanol; 0.13\u00a0g\u00a0L\u22121 for cellobiose and 0.04\u00a0g\u00a0L\u22121 for cellobiose plus lignin) at 20 and 48\u00a0h, respectively, resulting in the accumulation of acetic acid and butyric acid. Of 583 identified proteins (FDR\u00a0<\u00a01\u00a0%), 328 proteins were quantified with at least two unique peptides. Up- or down-regulation of protein expression was determined by comparison of exponential and stationary phases of cellobiose in the presence and absence of lignin. Of relevance, glycolysis and fermentative pathways were mostly down-regulated, during exponential and stationary growth phases in presence of lignin. Moreover, proteins involved in DNA repair, transcription/translation and GTP/ATP-dependent activities were also significantly affected and these changes were associated with altered cell morphology.ConclusionsThis is the first comprehensive analysis of the cellular responses of C. acetobutylicum to lignin at metabolic and physiological levels. These data will enable targeted metabolic engineering strategies to optimize biofuel production from biomass by overcoming limitations imposed by the presence of lignin.", 
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    23 schema:description BackgroundClostridium acetobutylicum has been a focus of research because of its ability to produce high-value compounds that can be used as biofuels. Lignocellulose is a promising feedstock, but the lignin–cellulose–hemicellulose biomass complex requires chemical pre-treatment to yield fermentable saccharides, including cellulose-derived cellobiose, prior to bioproduction of acetone–butanol–ethanol (ABE) and hydrogen. Fermentation capability is limited by lignin and thus process optimization requires knowledge of lignin inhibition. The effects of lignin on cellular metabolism were evaluated for C. acetobutylicum grown on medium containing either cellobiose only or cellobiose plus lignin. Microscopy, gas chromatography and 8-plex iTRAQ-based quantitative proteomic technologies were applied to interrogate the effect of lignin on cellular morphology, fermentation and the proteome.ResultsOur results demonstrate that C. acetobutylicum has reduced performance for solvent production when lignin is present in the medium. Medium supplemented with 1 g L−1 of lignin led to delay and decreased solvents production (ethanol; 0.47 g L−1 for cellobiose and 0.27 g L−1 for cellobiose plus lignin and butanol; 0.13 g L−1 for cellobiose and 0.04 g L−1 for cellobiose plus lignin) at 20 and 48 h, respectively, resulting in the accumulation of acetic acid and butyric acid. Of 583 identified proteins (FDR < 1 %), 328 proteins were quantified with at least two unique peptides. Up- or down-regulation of protein expression was determined by comparison of exponential and stationary phases of cellobiose in the presence and absence of lignin. Of relevance, glycolysis and fermentative pathways were mostly down-regulated, during exponential and stationary growth phases in presence of lignin. Moreover, proteins involved in DNA repair, transcription/translation and GTP/ATP-dependent activities were also significantly affected and these changes were associated with altered cell morphology.ConclusionsThis is the first comprehensive analysis of the cellular responses of C. acetobutylicum to lignin at metabolic and physiological levels. These data will enable targeted metabolic engineering strategies to optimize biofuel production from biomass by overcoming limitations imposed by the presence of lignin.
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    36 ResultsOur results
    37 ability
    38 absence
    39 absence of lignin
    40 accumulation
    41 acetic acid
    42 acetobutylicum
    43 acetobutylicum ATCC 824
    44 acid
    45 activity
    46 altered cell morphology
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    56 cellular metabolism
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    69 engineering strategies
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