Table Of ContentFarshad Darvishi Harzevili Editor
Synthetic
Biology
of Yeasts
Tools and Applications
Synthetic Biology of Yeasts
Farshad Darvishi Harzevili
Editor
Synthetic Biology
of Yeasts
Tools and Applications
Editor
FarshadDarvishiHarzevili
DepartmentofMicrobiology
AlzahraUniversity
Tehran,Iran
ISBN978-3-030-89679-9 ISBN978-3-030-89680-5 (eBook)
https://doi.org/10.1007/978-3-030-89680-5
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Preface
Yeasts are one of the most attractive microbial cell factories for the production
of a wide range of valuable products, including pharmaceuticals, nutraceuticals,
cosmetics, agrochemicals, biofuels, and so on. Tools of synthetic biology have
been developed to improve the metabolic engineering of yeasts in a faster and
more reliable manner. Nowadays, synthetic biology tools have been used to make
synthetic pathways and rewiring metabolism to produce valuable products at high
titer, rate, and yield.
This book covers recent advances and future trends in the synthetic biology
of yeasts. The book consists of two parts. The first part opens with an intro-
duction to rational metabolic pathway prediction and design using computational
toolsandtheirapplicationsforyeastsystemsandsyntheticbiology(Chap.“Ratio-
nal Metabolic Pathway Prediction and Design: Computational Tools and Their
Applications for Yeast Systems and Synthetic Biology”). After rational metabolic
pathwaydesign,synthesis,andengineeringtoolsforassemblyofstandardizedbio-
bricks, powerful genome editing and optimization of synthetic pathways are very
important in metabolic engineering of yeasts. Hence, construction and assem-
bly of standardized biobricks for synthetic pathways engineering in yeasts were
summarized in Chap. “Construction and Assembly of Standardized Biobricks
for Synthetic Pathways Engineering in Yeasts”.
Chapter “Cellular Engineering of Yarrowia lipolytica for Biomanufacturing
of High-Value Products from Oils and Fats” presented an example about cellular
engineering of yeasts. A combined cell morphology engineering and metabolic
pathway optimization of non-conventional yeast Yarrowia lipolytica is used to
biomanufacturing of high-value products from oils and fats as hydrophobic sub-
strates.Chapter“WholeCellYeast-BasedBiosensors”providedanoverviewabout
engineering of yeast cells to act as whole-cell yeast-based biosensors. The highly
modularnatureofyeast-basedbiosensorssuggeststhattheycanbeausefultoolfor
detectingawiderangeofbiologicallyrelevantanalytes,includingpharmaceuticals,
toxins,andchemicallyundefinedorcomplexmixturesrangingfromenvironmental
mutagens to bioavailable phosphorous.
The second part, Chaps. “Yeast Synthetic Biology Approaches for the Produc-
tion of Valuable Polyphenolic Compounds”–“Synthetic Biology in the Candida
v
vi Preface
(CTG) Clade”, covers applications of synthetic biology to produce diverse and
attractive products by some well-known yeasts. Chapter “Yeast Synthetic Biology
Approaches for the Production of Valuable Polyphenolic Compounds” summa-
rized yeast synthetic biology approaches for the production of valuable phenolic
compounds including hydroxycinnamic acids, flavonoids, stilbenoids, coumarins,
curcuminoids, and polyphenolic amides. Production of artemisinin as an anti-
malarialdrugwithanti-cancer,anti-inflammation,anti-viral,andanti-SARS-CoV-2
activitiesviayeastmetabolicengineeringwasdiscussedinChap.“YeastSynthetic
Biology for Production of Artemisinin as an Antimalarial Drug”. Chapter “Yeast
Synthetic Biology for the Production of Terpenoids Derived from Traditional
Chinese Medicinal Plants” reviewed yeast synthetic biology applications for the
production of terpenoids derived from traditional Chinese medicinal plants. The
synthetic biology of yeasts for the production of fragrant compounds like citrus
flavorswasreviewedinChap.ApplicationofYeastSyntheticBiologyforthePro-
ductionofCitrusFlavors.Synthesisofpolyolsandorganicacidsbymetabolically
engineeredYarrowialipolyticastrainsissummarizedinChap.“SynthesisofPoly-
ols and Organic Acids by Wild-Type and Metabolically Engineered Yarrowia
lipolytica Strains”. Chapter Recent Advances in Synthetic Biology Applications
of Pichia Species reviewed recent advances in synthetic biology applications for
Pichiaspecies.Kluyveromycesmarxianusasaplatforminsyntheticbiologyforthe
productionofusefulmaterialswasconsideredinChap.“Kluyveromycesmarxianus
asaPlatforminSyntheticBiologyfortheProductionofUsefulMaterials”.Inthe
last chapter, synthetic biology in the Candida (CTG) clade was summarized.
Overall, this book will serve as a suitable reference for students, scientists,
and researchers at universities, industries, corporations, and government agencies
interested in yeast synthetic biology, systems biology, and metabolic engineering
as well as all disciplines related to biotechnology, microbiology, bioengineering,
and chemical engineering.
Harzevil, Gilan, Iran Farshad Darvishi Harzevili
Contents
SyntheticBiologyToolsandCellularEngineering
RationalMetabolicPathwayPredictionandDesign:Computational
Tools and Their Applications for Yeast Systems and Synthetic
Biology .................................................................. 3
Pedro A. Saa
ConstructionandAssemblyofStandardizedBiobricksforSynthetic
PathwaysEngineeringinYeasts ......................................... 27
Paulina Korpys-Woz´niak, Monika Kubiak, Monika Borkowska,
and Ewelina Celin´ska
CellularEngineeringofYarrowialipolyticaforBiomanufacturing
ofHigh-ValueProductsfromOilsandFats .............................. 63
Na Liu, Ya-Hue Valerie Soong, Andrew Olson, and Dongming Xie
WholeCellYeast-BasedBiosensors ...................................... 91
Heather A. M. Shepherd, Emilia-Maria A. Bondarenko,
Katherine M. Jennings, Rachel A. Miller, and Holly V. Goodson
ApplicationsofYeastSyntheticBiology
YeastSyntheticBiologyApproachesfortheProductionofValuable
PolyphenolicCompounds ............................................... 119
Daniela Gomes, João Rainha, Ligia R. Rodrigues,
and Joana L. Rodrigues
Yeast Synthetic Biology for Production of Artemisinin
asanAntimalarialDrug ................................................. 157
Arman Beyraghdar Kashkooli, Karim Farmanpour-Kalalagh,
and Alireza Babaei
YeastSyntheticBiologyfortheProductionofTerpenoidsDerived
fromTraditionalChineseMedicinalPlants .............................. 181
Yongjun Wei
vii
viii Contents
ApplicationofYeastSyntheticBiologyfortheProductionofCitrus
Flavors .................................................................. 207
Karim Farmanpour-Kalalagh, Arman Beyraghdar Kashkooli,
and Alireza Babaei
Synthesis of Polyols and Organic Acids by Wild-Type
andMetabolicallyEngineeredYarrowialipolyticaStrains ............... 227
Chong Li, Weichao Lin, Khai Lun Ong, Jinhua Mou,
Carol Sze Ki Lin, and Patrick Fickers
RecentAdvancesinSyntheticBiologyApplicationsofPichiaSpecies ... 251
Wan Sun, Yimeng Zuo, Zhanyi Yao, Jucan Gao, Zengyi Shao,
and Jiazhang Lian
Kluyveromyces marxianus as a Platform in Synthetic Biology
fortheProductionofUsefulMaterials .................................. 293
Noppon Lertwattanasakul, Mochamad Nurcholis,
Nadchanok Rodrussamee, Tomoyuki Kosaka, Masayuki Murata,
and Mamoru Yamada
SyntheticBiologyintheCandida(CTG)Clade .......................... 337
Dalal Kasir, Sébastien Besseau, Marc Clastre, Audrey Oudin,
Monzer Hamze, Vincent Courdavault, Marwan Osman,
and Nicolas Papon
Synthetic Biology Tools and Cellular
Engineering
Rational Metabolic Pathway
Prediction and Design:
Computational Tools and Their
Applications for Yeast Systems
and Synthetic Biology
Pedro A. Saa
Abstract
Continuous progress in metabolic engineering of microbial cell factories like
yeast requires the support of computational tools for finding novel unintuitive
biotransformationsroutes.Inthischapter,asuccinctoverviewisprovidedofthe
mostrelevantcomputationaltoolsforpathwaypredictionbyretro-biosynthesis,
and pathway design through stoichiometry-based optimization methods. Illus-
trative case studies are also presented showcasing different strategies for
pathwayoptimizationinyeast,namelyredoxcofactorbalancing,improvedpre-
cursorsupply,andheterologousexpressionofcarbonfixationpathways.Finally,
challenges and limitations hindering the broad adoption and implementation of
these tools for metabolic engineering will be discussed.
Keywords
Pathway design (cid:129) Pathway analysis (cid:129) Metabolic engineering (cid:129) Yeast
1 Introduction
Advancementsinmetabolicengineeringandsyntheticbiologyhaveenabledaccel-
erated engineering of microbial factories for the production of valuable chemicals
(Smolke and Tyo 2012; Lee and Kim 2015; Isaacs et al. 2011), realizing the
B
P.A.Saa( )
DepartamentofChemicalandBioprocessEngineering,PontificiaUniversidadCatólicadeChile,
Santiago,Chile
e-mail:[email protected]
InstituteforMathematicalandComputationalEngineering,PontificiaUniversidadCatólicade
Chile,Santiago,Chile
©TheAuthor(s),underexclusivelicensetoSpringerNatureSwitzerlandAG2022 3
F.DarvishiHarzevili(ed.),SyntheticBiologyofYeasts,
https://doi.org/10.1007/978-3-030-89680-5_1
