Mining Saccharomyces diversity and experimental evolution for cellulosic biofuel
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This document summarizes research on using yeast diversity and experimental evolution to develop yeast strains for cellulosic biofuel production. Key points include: - There is genetic diversity within the Saccharomyces genus that can be exploited, including species with better tolerance to toxins produced during biomass hydrolysis. - Hybridization of tolerant non-S. cerevisiae species with engineered S. cerevisiae strains can combine beneficial traits. - Experimental evolution of hybrid strains under hydrolysis conditions leads to strains with improved growth and xylose consumption. - Genome sequencing shows adaptations involve new mutations, chromosomal rearrangements, and changes in gene copy number.
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Mining Saccharomyces diversity and experimental evolution for cellulosic biofuel
- 1. Mining Saccharomyces diversity and experimental evolution for cellulosic biofuel David Peris, Postdoctoral Research Associate 3rd June 2017 @djperis
- 2. Saccharomyces cerevisiae baker’s yeast Wine Ale beer Bakery
- 3. AFEX-Corn Stover (ACSH) Challenges Proteins, Oils, Ash (0-2%) Hemicellulose (19-34%) Lignin (21-32%) Cellulose (33-51%)
- 4. AFEX-Corn Stover (ACSH) Challenges Proteins, Oils, Ash (0-2%) Hemicellulose (19-34%) Lignin (21-32%) Cellulose (33-51%) Glucose Xylose Sugars (C6/C5) Piotrowski et al 2014
- 5. AFEX-Corn Stover (ACSH) Challenges Proteins, Oils, Ash (0-2%) Hemicellulose (19-34%) Lignin (21-32%) Cellulose (33-51%) Glucose Xylose HMF Ferulic acid p-coumaric acid Feruloyl amide Sodium acetate Acetamide Sugars (C6/C5) Hydrolysate Toxins Piotrowski et al 2014
- 6. S. cerevisiae S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum North America B North AmericaC Far East North America A Europe-A Asia- A Asia- B Asia- A Europe Near East Asia- B Oceania Asia- A SouthAmerica A Holarctic NA Holarctic EU South America B Australasia Patagonia B Holarctic Patagonia A Nakaseomycescastellii (outgroup) 0.02 West China Sichuan Redomestication of S. cerevisiae for biofuels The most tolerant of S. cerevisiae Engineered with xylose utilization genes Wohlbach et al. 2009 PNAS Sato et al. 2013 AEM Y732n CHASSIS Xylose
- 7. S. cerevisiae S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum North America B North AmericaC Far East North America A Europe-A Asia- A Asia- B Asia- A Europe Near East Asia- B Oceania Asia- A SouthAmerica A Holarctic NA Holarctic EU South America B Australasia Patagonia B Holarctic Patagonia A Nakaseomycescastellii (outgroup) 0.02 West China Sichuan Redomestication of S. cerevisiae for biofuels The most tolerant of S. cerevisiae Engineered with xylose utilization genes Wohlbach et al. 2009 PNAS Sato et al. 2013 AEM Y732n CHASSIS Xylose Hydrolysate toxins
- 8. S. cerevisiae S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum North America B North AmericaC Far East North America A Europe-A Asia- A Asia- B Asia- A Europe Near East Asia- B Oceania Asia- A SouthAmerica A Holarctic NA Holarctic EU South America B Australasia Patagonia B Holarctic Patagonia A Nakaseomycescastellii (outgroup) 0.02 West China Sichuan Redomestication of S. cerevisiae for biofuels The most tolerant of S. cerevisiae Engineered with xylose utilization genes Liti et al 2009 Y732n CHASSIS Xylose Hydrolysate toxins 0.8%
- 9. Surfing the diversity of Saccharomyces genus Phylogenomic tree 23/30 Lineages represented Whole Genome sequences Lineages not available S. cerevisiae S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum North America B North AmericaC Far East North America A Europe- Asia- A Asia- B Asia- A Europe Near East Asia- B Oceania Asia- A SouthAmerica A Holarctic NA Holarctic EU South America B Australasia Patagonia B Holarctic Patagonia A Nakaseomycescastellii (outgroup) 0.02 West China Sichuan Peris et al in preparation
- 10. High genetic diversity in the Saccharomyces genus S. cerevisiae S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. eubayanus S. uvarum North America B North AmericaC Far East North America A Europe- Asia- A Asia- B Asia- A Europe Near East Asia- B Oceania Asia- A SouthAmerica A Holarctic NA Holarctic EU South America B Australasia Patagonia B Holarctic Patagonia A Nakaseomycescastellii (outgroup) 0.02 West China Sichuan
- 11. Non-cerevisiae species have better tolerance to ACSH Peris et al 2017a
- 12. New genetic traits associated with Hydrolysate toxin tolerance Peris et al 2017a
- 13. Improvement of S. cerevisiae chassis strain The most tolerant of S. cerevisiae Engineered with xylose utilization genes Engineered with Hydrolysate tolerance traits Y732n CHASSIS v2.0 Xylose Hydrolysate toxins
- 14. Industrial Saccharomyces hybrids Gonzalez et al. 2008 Dunn et al. 2008 Peris et al. 2012a,b,c,2014,2016,2017b Libkind et al. 2011 Almeida et al 2014 S. pastorianus S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. uvarum S. cerevisiae S. eubayanus S. bayanus
- 15. Generation of hybrids to combine genetic traits S.mikatae XHaploid (n) S. cerevisiae CHASSIS Alexander et al 2016 Peris et al 2017a Haploid (n)
- 16. Genome composition of the new hybrid, 1:1 chromosome copies Chromosome Peris et al 2017a Chromosome Sequencing coverage
- 17. Adaptive evolution of the new hybrid: new mutations Peris et al 2017a R1 30ºC 14days
- 18. Bottlenecks and new passages in fresh media Peris et al 2017a R1 … 30ºC 14days
- 19. The best variants will survive Peris et al 2017a R1 R9… 50 Generation 30ºC 14days ACSH
- 20. Regions with interesting traits are retained or amplified Peris et al 2017a Chromosome Chromosome Sequencing coverage
- 21. Improvement by gross chromosomal rearrangements Peris et al 2017a Chromosome Chromosome Sequencing coverage Grows well in ACSH
- 22. Hybrid vigor in ACSH conditions Peris et al 2017a Chromosome Chromosome Sequencing coverage Grows well in ACSH Consumes xylose
- 23. Conclusions There is a huge diversity in yeasts in general, and Saccharomyces in particular waiting to be discovered and exploited
- 24. Conclusions There is a huge diversity in yeasts in general, and Saccharomyces in particular waiting to be discovered and exploited S. mikatae and S. paradoxus species have hydrolysate toxin tolerance
- 25. Conclusions There is a huge diversity in yeasts in general, and Saccharomyces in particular waiting to be discovered and exploited S. mikatae and S. paradoxus species have hydrolysate toxin tolerance Hybridization is a short-term solution to combine interesting strain specific industrial traits and characterize them
- 26. Thank you Chris T. Hittinger Ryan V. Moriarty Kayla Sylvester William Alexander Emily Baker Meihua Kuang Quinn Langdon Hittinger Lab Members Wild YEAST program Trey Sato Li Hinchman Lucas Parreiras Jeff Piotrowski Diego Libkind Jose Paulo Sampaio Paula Gonçalves Christian Landry Jean-Baptiste Leducq Guillaume Charron Justin Fay Katie Hyma Fengyan Bai Qi Ming Wang Yaoping Zhang Alex Reau Haibo Li David Benton Yury Bukhman HPLC Service Mick McGee Audrey Gasch Maria Sardi UW & GLBRC Collaboration