1. Mining Saccharomyces diversity and experimental
evolution for cellulosic biofuel and beer applications
David Peris, Postdoctoral Research Associate
Department of Genetics, University of Wisconsin-Madison
27th June 2017
@djperis
2. Domesticated Saccharomyces cerevisiae for alcoholic beverage production
Carbon sources
Glucose
Fructose
Glu Glu
Maltose
Glu Glu Glu
Maltotriose
glycolysis
Carbon products
Ethanol
Other
compounds
fermentation
3. Most S. cerevisiae can not consume xylose
Proteins,
Oils, Ash (0-2%)
Hemicellulose
(19-34%)
Lignin
(21-32%)
Cellulose
(33-51%)
Glucose
Xylose
Sugars (C6/C5)
Piotrowski et al 2014 Front Microbiol
4. Toxins inhibits the ethanol production
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 Front Microbiol
Ethanol
5. Engineering chassis S. cerevisiae for xylose consumption
The most tolerant of a panel of S. cerevisiae
Engineered with xylose utilization genes
Wohlbach et al. 2009 PNAS
Sato et al. 2013 AEM
Y732n
CHASSIS
Xylose
6. S. cerevisiae is still not happy with the toxins
Wohlbach et al. 2009 PNAS
Sato et al. 2013 AEM
Y732n
CHASSIS
Xylose Hydrolysate toxins
The most tolerant of a panel of S. cerevisiae
Engineered with xylose utilization genes
7. The diversity in S. cerevisiae is low
Liti et al 2009 Nature
S. cerevisiae
0.8% nucleotide diversity
8. America C
Surveying the diversity of Saccharomyces genus
Phylogenomic tree
Strains from 23 available lineages
0.05
n = 980 strains
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
EU & America A
Far East
America B
Holarctic &
Patagonia B
Peris et al 2017 BFB
9. America C
The Saccharomyces diversity is huge
0.05
n = 980 strains
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
EU & America A
Far East
America B
Holarctic &
Patagonia B
Phylogenomic tree
Strains from 23 available lineages
Dujon 2006 TIG
10. America C
S. mikatae & S. paradoxus are more tolerant to ACSH conditions
0.05
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
EU & America A
Far East
America B
Peris et al 2017 BFB
11. S. uvarum can consume xylose
0.05
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
Peris et al 2017 BFB
12. Improvement of S. cerevisiae chassis strain
The most tolerant of a panel of S. cerevisiae
Engineered with xylose utilization genes
Engineered with Hydrolysate tolerance traits
Y732n
CHASSIS v2.0
Xylose Hydrolysate toxins
13. 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
14. Generation of hybrids to combine genetic traits and generate diversity
S.mikatae
XHaploid (n)
S. cerevisiae
CHASSIS
Peris et al 2017 BFB
Haploid (n)
MATa MAT
MATa/MAT
15. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
0
1
2
3
4
5
0
1
2
3
4
5
RC/MRC
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
sppIDer (species IDentifier) 1:1 chromosome of each parent
Chromosome
Peris et al 2017 BFB
Quinn et al In preparation
Chromosome
Sequencing
coverage S. cerevisiae
S. mikatae
16. Adaptive evolution of the unstable hybrid: new mutations
Peris et al 2017 BFB
R1
30ºC
14days
17. Bottlenecks and new passages in fresh media
R1 …
30ºC
14days
Peris et al 2017 BFB
18. The best variants will survive
R1 R9…
50 Generation
30ºC
14days
ACSH
Peris et al 2017 BFB
19. One of the evolved hybrids retain the genetic traits of the parents
Peris et al 2017 BFB
The evolved hybrids consume similar levels of xylose
The growth rate of the evolved hybrid is similar to the parents
More generation might generate a better strain than the
parents.
20. One of the evolved hybrids retain the genetic traits of the parents
Peris et al 2017 BFB
The evolved hybrids consume similar levels of xylose
The growth rate of the evolved hybrid is similar to the parents
More generation might generate a better strain than the
parents.
Chromosome
Chromosome
Sequencing
coverage S. cerevisiae
S. mikatae
22. HyPr promotes gene conversion in the MAT locus
a/ a/
a/a /
NATMX HYGMX
NATMX HYGMX
HO
expression
Alexander et al 2016 FGB
23. Convert the rare-mating to frequent-mating with HyPr
a/ a/
a/a /
X
NATMX HYGMX
NATMX HYGMX
NATMX HYGMX
HO
expression
a/a//
Alexander et al 2016 FGB
24. Marker-free hybrids
a/ a/
a/a /
X
NATMX HYGMX
NATMX HYGMX
NATMX HYGMX
HO
expression
a/a//
a/a//
Remove selection
pressure
Alexander et al 2016 FGB
25. Ryan Moriarty
X X X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
Proof of concept: higher order hybrids using HyPr?
26. Double hybrids were done!
X X X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
27. A four species hybrid was done!
X
X
X X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
30. We have evidence for a six species hybrid!
X
X
X X
X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
31. Restriction fragment Length Polymorphism give some clues
M349-Sc
M456–Sc
M495–ScxSpxSaxSu
M359-Sa
M356-Su
M461–Sax
Su
BRE5
S.cerevisiae
S.paradoxus
S.mikatae
S.kudriavzevii
S.uvarum
S.arboricola
Hybrid(6x->12n)
X
X
32. Complex hybrids generate diversity for industrial applications
X
X
X X
X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
33. Conclusions
There is a huge diversity in yeasts in general, and Saccharomyces in particular
waiting to be discovered and exploited
34. Conclusions
There is a huge diversity in yeasts in general, and Saccharomyces in particular
waiting to be discovered and exploited
Hybridization is a short-term solution to combine interesting strain with interesting
industrial traits and a method for characterizing those traits
35. Conclusions
There is a huge diversity in yeasts in general, and Saccharomyces in particular
waiting to be discovered and exploited
Hybridization is a short-term solution to combine interesting strain with interesting
industrial traits and a method for characterizing those traits
With HyPr we are able to generate higher order hybrids and diversity to address
important genetic questions and fix industrial problems
36. Thank you
Chris T. Hittinger
Ryan V. Moriarty
Quinn Langdon
William Alexander
Meihua Kuang
Kayla Sylvester
Emily Baker
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