Readings

Course readings.
WEEK #	TOPICS	READINGS
1	Welcome and Introductions See the Lecture Summary	No readings
2	Cellulose Breakdown Basics See the Lecture Summary	Paper 1 Irwin, D. B., M. Spezio, L. P. Walker, and D. B. Wilson. "Activity Studies of Eight Purified Cellulases: Specificity, Synergism, and Binding Domain Effects." Biotechnology and Bioengineering 42 (1993): 1002-13. Paper 2 Himmel, M. E., S-Y Ding, D. K. Johnson, W. S. Adney, M. R. Nimlos, J. W. Brady, and T. D. Foust. "Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuel Production." Science 315 (2007): 804-7.
3	Cellulolytic Bacteria and Fungi See the Lecture Summary	Paper 1 Eberhardt, R. Y., H. J. Gilbert, and G. P. Hazlewood. "Primary Sequence and Enzymic Properties of Two Modular Endoglucanases, Cel5A and Cel45A, from the Anaerobic Fungus Piromyces equi." Microbiology 146 (2000): 1999-2008. Paper 2 Tajima, K., R. I. Aminov, T. Nagamine, H. Matsui, M. Nakamura, and Y. Benno. "Diet-Dependent Shifts in the Bacterial Population of the Rumen Revealed with Real-Time PCR." Applied and Environmental Microbiology 67 (2001): 2766-74.
4	Transcriptional Regulation See the Lecture Summary	Paper 1 Foreman, P. K., D. Brown, L. Dankmeyer, R. Dean, S. Diener, N. S. Dunn-Coleman, F. Goedegbuur, T. D. Houfeks, G. J. England, A. S. Kelley, H. J. Meerman, T. Mitchell, C. Mitchinson, H. A. Olivares, P. J. M. Teunissen, J. Yao, and M. Ward. "Transcriptional Regulation of Biomass-Degrading Enzymes in the Filamentous Fungus Trichoderma reesei." Journal of Biological Chemistry 278 (2003): 31988-97. (PDF) Paper 2 Suzuki, H., K. Igarashi, and M. Samejima. "Real-Time Quantitative Analysis of Carbon Catabolic Derepression of Cellulolytic Genes Expressed in the Basidiomycete Phanerochaete chrysosporium." Applied Microbiology and Biotechnology 80 (2008): 99-106.
5	Recombinant Cellulases See the Lecture Summary	Paper 1 Smith, J., and A. S. Robinson. "Overexpression of an Archaeal Protein in Yeast: Secretion Bottleneck in the ER." Biotechnology and Bioengineering 79 (2002): 713-23. Paper 2 Nielsen, D. R., E. Leonard, S-H Yoon, H-C Tseng, C. Yuan, and K. L. Jones Prather. "Engineering Alternative Butanol Production Platforms in Heterologous Bacteria." Metabolic Engineering 11 (2009): 262-73.
6	Synthetic Cellulosomes See the Lecture Summary	Paper 1 Tsai, S. L., G. Goyal, and W. Chen. "Surface Display of a Functional Minicellulosome by Intracellular Complementation using a Synthetic Yeast Consortium and its Applications to Cellulose Hydrolysis and Ethanol Production." Applied and Environmental Microbiology 76 (2010): 7514-20. (PDF - 1.2MB) Paper 2 Mitsuzawa, S., H. Kagawa, Y. Li, S. L. Chan, C. D. Paavola, and J. D. Trent. "The Rosettazyme: A Synthetic Cellulosome." Journal of Biotechnology 143 (2009): 139-44.
7	Guest speaker: Industrial Biomass Processing and Hydrolysis See the Lecture Summary	No readings
8	Metabolic Engineering See the Lecture Summary	Paper 1 Alper, H., J. Moxley, E. Nevoight, G. Fink, and G. Stephanopolous. "Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production." Science 314 (2006): 1565-8. Paper 2 Atsumi, S., T. Hanai, and J. C. Liao. "Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels." Nature 451 (2007): 86-90.
9	Engineering Cellulolytic Organisms See the Lecture Summary	Paper 1 Verdoes, J. C., P. J. Punt, and V. Camjj. "Molecular-Genetic Strain Improvement for the Overproduction of Fungal Proteins by Filamentous Fungi." Applied Microbiology and Biotechnology 43 (1995): 195-205. Paper 2 Shaw, A. J., K. K. Podkaminer, S. G. Desai, J. S. Bardsley, S. R. Rogers, P. G. Thorne, D. A. Hogsett, and L. R. Lynd. "Metabolic Engineering of a Thermophilic Bacterium to Produce Ethanol at High Yield." Proceedings of the National Academies of the Sciences 105 (2008): 13769-74. (PDF)
10	Directed Evolution and Protein Engineering See the Lecture Summary	Paper 1 Heinzelman, P., C. D. Snow, I. Wu, C. Nguyen, A. Villalobos, S. Govindarajan, J. Minshull, and F. H. Arnold. "A Family of Thermostable Fungal Cellulases Created by Structure-Guided Recombination." Proceedings of the National Academies of Sciences 106 (2009): 5610-15. Paper 2 Peralta-Yahya, P., B. T. Carter, H. Lin, H. Tao, and V. Cornish. "High-Throughput Selection for Cellulase Catalysts Using Chemical Complementation." Journal of the American Chemical Society 130 (2008): 17446-52.
11	Identifying New Cellulases from Nature See the Lecture Summary	Paper 1 Sommer, M. O. A., G. M. Church, and G. Dantas. "A Functional Metagenomic Approach for Expanding the Synthetic Biology Toolbox for Biomass Conversion." Molecular Systems Biology 6 (2010): 1-7. Paper 2 Warnecke, F., P. Luginbuhl, N. Ivanova, M. Ghassemian, T. H. Richardson, J. T. Stege, M. Cayouette, A. C. McHardy, G. Djordjevic, N. Aboushadi, R. Sorek, S. G. Tringe, M. Podar, H. Garcia Martin, V. Kunin, D. Dalevi, J. Madejska, E. Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N. C. Kyrpides, E. G. Matson, E. A. Ottesen, X. Zhang, M. Hernandez, C. Murillo, L. G. Acosta, I. Rigoutsos, G. Tamayo, B. D. Green, C. Chang, E. M. Rubin, E. J. Mathur, D. E. Robertson, P. Hugenholz, and J. R. Leadbetter. "Metagenomic and Functional Analysis of Hindgut Microbiota of a Wood-Feeding Higher Termite." Nature 450 (2007): 560-65.
12	Oral Presentations See the Lecture Summary	No readings