Biofuels Production programs

Neurospora crassa as a Model for Mechanisms of Plant Biomass Conversion to Biofuels

This program is focused on studying the degradation of cellulosic biomass by the model fungus Neurospora crassa.  The group analyzes N. crassa growth on plant biomass using a combination of systems biology, synthetic biology, and mechanistic enzymology.

program Highlights

2014 Highlights

We are using systems biology and mechanistic enzymology to understand how Neurospora crassa, a model filamentous fungus, grows on plant biomass. From these experiments, we aim to improve the industrial process microbial fermentation by yeasts to convert plant biomass into biofuels. We are now assessing the fundamental question whether Simultaneous Saccharification and Co-Fermentation (SSCF) or Separate Hydrolysis and Co-Fermentation (SHCF) of plant biomass will be economically viable for biofuel production. Presently, the SSCF approach is not feasible, as industrially relevant cellulase cocktails function better at ~50 °C, whereas industrial strains of the workhorse yeast S. cerevisiae only ferment well up to ~35 °C. We are using our understanding of the biology and biochemistry of N. crassa to optimize S. cerevisiae for SHCF processes. We are also exploring thermotolerant relatives of N. crassa and S. cerevisiae for use in SSCF and SHCF processes at higher temperatures.

2013 Highlights

We are using systems biology and mechanistic enzymology to understand how Neurospora crassa, a model filamentous fungus, grows on plant biomass.  Based on these experiments, we are learning how to improve the industrial process of conversion of plant biomass into biofuels, centered on microbial fermentation by the yeast Saccharomyces cerevisiae. We are now assessing the fundamental question whether Simultaneous Saccharification and Co-Fermentation (SSCF) of plant biomass will be an economically viable approach to biofuel production, or whether Separate Hydrolysis and Co-Fermentation (SHCF) will be more economical.  In the SSCF scenario, the lignocellulolytic enzymes used to quantitatively convert cellulose and hemicellulose into soluble sugars and the organism used for fermentation must function optimally in the same reaction conditions and at the same reaction temperature.  Presently, this is not possible, as industrially relevant cellulase cocktails function better at ~50 °C, whereas industrial strains of the workhorse fermentation organism S. cerevisiae only ferment well up to ~35 °C.  We are using our understanding of the biology and biochemistry of N. crassa to optimize S. cerevisiae for SHCF processes.  We are also laying the groundwork for studying thermotolerant relatives of N. crassa and S. cerevisiae that can be used in SSCF and SHCF processes at higher temperatures.

2012 Highlights

We are using systems biology and mechanistic enzymology to understand how Neurospora crassa, a model filamentous fungus, grows on plant biomass. Based on these experiments, we are learning how to improve the industrial process of conversion of plant biomass into biofuels, centered on microbial fermentation by the yeast Saccharomyces cerevisiae. Based on discoveries by our groups of N. crassa strategies for consuming plant biomass, we are now assessing the fundamental question whether Simultaneous Saccharification and Co-Fermentation (SSCF) of plant biomass will be an economically viable approach to biofuel production, or whether Separate Hydrolysis and Co-Fermentation (SHCF) will be more economical. In the SSCF scenario, the lignocellulolytic enzymes used to quantitatively convert cellulose and hemicellulose into soluble sugars and the organism used for fermentation must function optimally in the same reaction conditions and at the same reaction temperature. Presently this is not possible, as industrially relevant cellulase cocktails function better at ~50 °C, whereas industrial strains of the workhorse fermentation organism Saccharomyces cerevisiae only ferment well up to ~35 °C. We are using our understanding of the biology and biochemistry of N. crassa to optimize S. cerevisiae for SHCF processes. We are also laying the groundwork for studying thermotolerant relatives of N. crassa and S. cerevisiae that can be used in SSCF and SHCF processes at higher temperatures.

Publications

Published in 2014

Leveraging Transcription Factors to Speed Cellobiose Fermentation by Saccharomyces cerevisiae, Yuping Lin, Kulika Chomvong, Ligia Acosta-Sampson, Raíssa Estrela Curado, Jonathan M. Galazka, Soo Rin Kim, Yong-Su Jin, Jamie H. D. Cate, Biotechnology and Biofuels, V. 7, pp. 126, doi:10.1186/s13068-014-0126-6, August 27, 2014.

 

Selection of Chromosomal DNA Libraries Using a Multiplex CRISPR System in Saccharomyces cerevisiae, O. W. Ryan, J. M. Skerker, M. J. Maurer, X. Li, J. C. Tsai, S. Poddar, M. E. Lee, W. DeLoache, J. E. Dueber, A. P. Arkin, J. H. Cate, eLife, doi: 10.7554/eLife.03703, PMID: 25139909, August 19, 2014. 

 

Overcoming Inefficient Cellobiose Fermentation by Cellobiose Phosphorylase in the Presence of Xylose, K. Chomvong, V. Kordic, X. Li, S. Bauer, A. E. Gillespie, S. J. Ha, E. J. Oh, J. M. Galazka, Y. S. Jin, J. H. Cate, Biotechnology and Biofuels, V. 7 (85). doi: 10.1186/1754-6834-7-85, PMID: 24944578, PMCID: PMC4061319, June 7, 2014. 

 

The Proteome and Phosphoproteome of Neurospora crassa in Response to Cellulose, Sucrose and Carbon Starvation, Y. Xiong, S. T. Coradetti, X. Li, M. A. Gritsenko, T. Clauss, V. Petyuk, D. Camp, R. Smith, J. H. Cate, F. Yang, N. L. Glass, Fungal Genetic Biology, pii: S1087-1845(14)00083-8, doi: 10.1016/j.fgb.2014.05.005. PMID: 24881580, November 2014. 

 

2,3-Butanediol Production from Cellobiose by Engineered Saccharomyces cerevisiae, H. Nan, S. O. Seo, E. J. Oh, J. H. Seo, J. H. Cate, Y. S. Jin, Applied Microbiology and Biotechnology, V. 98, pp. 5757-64, PMID: 24743979, June 2014. 

 

Construction of a Quadruple Auxotrophic Mutant of an Industrial Polyploid Saccharomyces cerevisiae Strain by Using RNA-Guided Cas9 Nuclease, G. C. Zhang, I. I. Kong, H. Kim, J. J. Liu, J. H. Cate, Y. S. Jin, Applied and Environmental Microbiology, V. 80, pp. 7694-7701, PMID: 25281382, October 2014. 

 

Multiplex Engineering of Industrial Yeast Genomes Using CRISPRm Method, O. W. Ryan, J. H. Cate, Methods in Enzymology, V. 546, pp. 473-489, PMID: 25398354, 2014. 

 

Microbial Biosynthesis of Medium-chain 1-Alkenes by a Non-Heme Iron Oxidase, Z. Rui, X. Li, X. Zhu, J. Liu, B. Domigan, I. Barr, J. H. D. Cate, W. Zhang, Proceedings of the National Academy of Sciences, PNAS 111(51), pp. 18237-18242, doi: 10.1073/pnas. 1419701112, November 2014. 

 

 

Published in 2013

Energetic Benefits and Rapid Cellobiose Fermentation by Saccharomyces cerevisiae Expressing Cellobiose Phosphorylase and Mutant Cellodextrin Transporters, Suk-Jin Ha, Jonathan Galazka, Eun Joong Oh, Vesna Kordic, Heejin Kim, Yong-Su Jin, Jamie Cate, Metabolic Engineering 15, pp. 134-143,  http://dx.doi.org/10.1016/j.ymben.2012.11.005, January, 2013.

 

Draft Genome Sequence of the Cellulolytic Bacterium Clostridium Papyrosolvens C7 (Atcc 700395), V. Zepeda, B. Dassa, I. Borovok, R. Lamed, E. A. Bayer, J. H. Cate, Genome Announcements, doi: 10.1128/genomeA.00698-13, September 14, 2013.

 

Evidence for Transceptor Function of Cellodextrin Transporters in Neurospora crassa, Elizabeth A. Znameroski, Xin Li, Jordan Tsai, Joathon M. Galazka, N. Louise Glass, Jamie H.D. Cate, Journal of Biological Chemistry 289, pp. 2610-2619, doi: 10.1074/jbc.M113.533273, December 16, 2013.

 

Determinants of Regioselective Hydroxylation in the Fungal Polysaccharide Monooxygenases, V.V. Vu, W.T. Beeson, C.M. Phillips, J.H. Cate, and M.A. Marletta, Journal of the American Chemical Society, doi: 10.1021/ja409384b, December 26, 2013.

 

Published in 2012

 

Energetic Benefits and Rapid Cellobiose Fermentation by Saccharomyces cerevisiae Expressing Cellobiose Phosphorylase and Mutant Cellodextrin Transporters, Suk-Jin Ha, Jonathan Galazka, Eun Joong Oh, Vesna Kordic, Heejin Kim, Yong-Su Jin, Jamie Cate, Metabolic Engineering, http://dx.doi.org/10.1016/j.ymben.2012.11.005, November 22, 2012.

 

Enhanced Xylitol Production Through Simultaneous Co-Utilization of Cellobiose and Xylose by Engineered Saccharomyces cerevisae,  Eun Joong Oh, Suk-Jin Ha, Soo Rin Kim, Won-Heong Lee, Jonathan M. Galazka, Jamie H.D. Cate, Yong Su-Jin, Metabolic Engineering, http:/dx.doi.org/PDF/10.1016/j.ymben.2012.09.003, November 2, 2012.

 

Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases, Xin Li, William Beeson, Christopher Phillips, Michael A. Marletta, Jamie H. D. Cate, Structure, doi: 10.1016, j. str.2012.04.002, May 10, 2012.

 

Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins, Elizabeth A. Znameroski, Samuel T. Coradetti, Christine M. Roche, Jordan C. Tsai, Anthony T. Iavarone, Jamie H. D. Cate, and N. Louise Glass, Proceedings of the National Academy of Sciences 109, pp. 6012-6017, doi: 10.1073/pnas.1118440109, April 17, 2012.

 

Model-Guided Strain Improvement: Simultaneous Hydrolysis and Co-Fermentation of Cellulose Sugars , Yong-Su Jin, Jamie Cate, Biotechnology Journal, 7(3), pp. 328-329, doi: 10.1002/biot.2011004489, March 2, 2012.

Published in 2011

Oxidative Cleavage of Cellulose by Fungal Copper-Dependent Polysaccharide Monooxygenases, William Beeson, Christopher Phillips, Jamie Cate, Michael Marletta, Journal of the American Chemical Society, doi: 10.1021/ja210657t, December 20, 2011.

 

Improving the Bioconversion of Plant Biomass to Biofuels: A Multidisciplinary Approach, John Galazka and Jamie Cate, Energy and Environmental Science, 4, pp. 3329-3333, doi:10:1039/CIEE01569A, July 29, 2011.

 

A Quantitative Proteomic Approach for Cellulosic Degradation by Neurospora crassa, Chris Phillips, Anthony Iavarone, Michael Marletta, Journal of Proteome Research, doi: 10.1021/pr200329b, July 11, 2011.

 

A New Diet for Yeast to Improve Biofuel Production, Jonathan Galazka, Jamie Cate, Bioengineered Bugs, 2(4), pp. 199-202, doi: 10:4161/bbug.2.4.15624, July 2011

 

Engineered Saccharomyces cerevisiae Capable of Simultaneous Cellobiose and Xylose Fermentation, Suk-Jin Ha, Jonathan Galazka, Soo Rin Kim, Jin-Ho Choi, Xiaomin Yang, Jin-Ho Seo, N. Louise Glass, Jamie H. D. Cate, Yong-Su Jin, Proceedings of the National Academy of Sciences, DOI: 10.1073, January 11, 2011.

 

Cellobiose Dehydrogenase and a Copper-Dependent Polysaccharide Monooxygenase Potentiate Cellulose Degradation by Neurospora crassa, Christopher Phillips, William Beeson, Jamie Cate, Michael Marletta, ACS Chemical Biology, 6(12), pp. 1399-1406, doi:10.1021/cb200351y, October 17, 2011.

Published in 2010

Extracellular Aldonolactonase from Myceliophthora thermophilia, William Beeson, Anthony Iavarone, Corinne Hausmann, Jamie Cate, Michael Marletta, Applied and Environmental Microbiology, DOI: 10.1128/AEM.01922-10, November 12, 2010.

 

Cellodextrin Transport in Yeast for Improved Biofuel Production, Jonathan Galazka, Chaoguang Tian, William Beeson, Bruno Martinez, N. Louise Glass, Jamie Cate, Science, DOI: 10.1126/science1192838, August 25, 2010. 

Published in 2009

Systems Analysis of Plant Cell Wall Degradation by the Model Filamentous Fungus Neurospora crassa, Chaoguong Tian, William T. Beeson, Anthony T. Iavarone, Jianping Sun, Michael A. Marletta, Jamie H. D. Cate, N. Louise Glass, Proceedings of the National Academy of Sciences, 106(52): pp. 22157-22162, Dec. 15, 2009.

 


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