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Appl Microbiol Biotechnol (2013) 97:503–517

DOI 10.1007/s00253-012-4497-y

MINI-REVIEW

Biotechnology of non-Saccharomyces
yeasts—the ascomycetes
Eric A. Johnson

Received: 15 February 2012 / Revised: 3 October 2012 / Accepted: 6 October 2012 / Published online: 27 November 2012
# Springer-Verlag Berlin Heidelberg 2012

Abstract Saccharomyces cerevisiae and several other yeast Keywords Yeast . Biotechnology . Ascomycetes .
species are among the most important groups of biotechnolog- Non-Saccharomyces
ical organisms. S. cerevisiae and closely related ascomycetous
yeasts are the major producer of biotechnology products
worldwide, exceeding other groups of industrial microorgan- Prominent non-Saccharomyces ascomycetous yeast
isms in productivity and economic revenues. Traditional in- species of biotechnological importance
dustrial attributes of the S. cerevisiae group include their
primary roles in food fermentations such as beers, cider, wines, A landmark three-volume treatise “Yeasts: A Taxonomic
sake, distilled spirits, bakery products, cheese, sausages, and Study” was recently published that authoritatively describes
other fermented foods. Other long-standing industrial process- the taxonomy, ecology, physiology, and other aspects of the
es involving S. cerevisae yeasts are production of fuel ethanol, large and diverse world of yeasts (Kurtzman et al. 2011).
single-cell protein (SCP), feeds and fodder, industrial enzymes, This treatise has provided current updates on the taxonomic
and small molecular weight metabolites. More recently, non- designation of yeasts according to the International Code of
Saccharomyces yeasts (non-conventional yeasts) have been Taxonomy as well as chapters on ecological and applied
utilized as industrial organisms for a variety of biotechnolog- aspects, including developments in biotechnology (Johnson
ical roles. Non-Saccharomyces yeasts are increasingly being and Echavarri-Erasun 2011). The primary species of asco-
used as hosts for expression of proteins, biocatalysts and multi- mycetous non-Saccharomyces yeasts of current and poten-
enzyme pathways for the synthesis of fine chemicals and small tial importance in biotechnology are described in this Mini-
molecular weight compounds of medicinal and nutritional Review. Yeasts of basidiomycetous affinity and biotechno-
importance. Non-Saccharomyces yeasts also have important logical importance are described in the second Mini-Review
roles in agriculture as agents of biocontrol, bioremediation, and (Johnson 2013). An overview of various areas of yeast
as indicators of environmental quality. Several of these prod- biotechnology are provided in Fig. 1.
ucts and processes have reached commercial utility, while
others are in advanced development. The objective of this Debaryomyces hansenii
mini-review is to describe processes currently used by industry
and those in developmental stages and close to commerciali- The primary non-Saccharomyces ascomycetous yeasts of
zation primarily from non-Saccharomyces yeasts with an em- importance in biotechnology are listed in Table 1 and de-
phasis on new opportunities. The utility of S. cerevisiae in scribed in the following sections.
heterologous production of selected products is also described. Debaryomyces spp., particularly D. hansenii, have bio-
technological potential and utility in a diversity of areas
(Breuer and Harms 2006; Fleet 2007). Debaryomyces spp.
belong to the lipid-accumulating or “oleaginous” yeasts, and
E. A. Johnson (*) some strains can accumulate 20–70 % of their biomass as
Department of Bacteriology, Food Research Institute,
lipids (Cohen and Ratledge 2005; Papanilolaou and George
University of Wisconsin,
Madison, WI 53706, USA 2011a, b; Beopolous et al. 2011; Ratledge 2002). In addition
e-mail: eajohnso@wisc.edu to D. hansenii, other oleaginous yeasts include species of
504 Appl Microbiol Biotechnol (2013) 97:503–517

Fig. 1 An overview of various TRADITIONAL YEAST


areas of yeast biotechnology FERMENTATIONS
FOOD AND
ENVIRONMENTAL FEED INGREDIENTS
Beer, Wine, Sake, Soy Sauce,
BIOTECHNOLOGY Other Food Fermentations
Enzymes, Flavors,
Bioremediation, Pollutant Pigments, Amino acids,
Degradation Organic acids

BIOCONTROL BIOCATALYSIS

Crop protection, YEAST Pharmaceuticals, Chiral


Food and Feed Safety, BIOTECHNOLOGY Chemical Intermediates,
Probiotics Biotransformations

BIOMEDICAL HETEROLOGOUS
RESEARCH PROTEIN
PRODUCTION
Drug discovery, Drug FUNDAMENTAL
Resistance and Metabolism, BIOLOGICAL RESEARCH Protein Pharmaceuticals,
Elucidation of Disease Enzymes, Hormones,
Mechanisms Vaccines, Toxins
Molecular and Cellular Biology, Genomics,
Functional Genomics, Pathway Engineering,
Systems Biology Mechanisms

Candida, Cryptococcus, Pichia (Hansenula), Lipomyces, offers the commercial potential for production of lipids or
Pseudozyma, Rhodosporidium, Rhodotorula, Trichosporon, “single-cell oils” (Beopolous et al. 2011; Fickers et al. 2005;
Trigonopsis, Yarrowia, Saccharomycopsis, and potentially Papanikolaou et al. 2002; Papanilolaou and George 2011a, b),
Phaffia rhodozyma, and Xanthophyllomyces dendrorhous. biodiesel generation (Dai et al. 2007), and accumulation of
Several of these yeast species are of basidiomycetous affinity lipid-soluble fine chemicals of high value, such as carote-
and are covered in the accompanying Mini-Review. The abil- noids, surfactants, and flavorants.
ity of oleaginous yeasts to accumulate high quantities of lipids Debaryomyces spp. are remarkable (Gunde-Cinerman et
al. 2009), being able to grow in culture media and complex
Table 1 Principal ascomycetous yeast species of biotechnology substrates such as foods containing up to 4 M NaCl (∼10 % w/
importance w) and glucose (∼5 % w/w). In contrast, the most osmotolerant
strains of S. cerevisiae are restricted in growth to media con-
Yeast species Updated nomenclaturea
taining less than 1.7 M NaCl (Onishi 1963). Consequently,
Candida spp. Variousa Debaryomyces spp. are frequently found in salted, sugared,
Debaryomyces hansenii Unchanged
and fermented foods of high osmolarity as well as in marine
Hansenula spp. Ogataea spp.
environments (Kutty and Philp 2008). Osmotolerance of
Kluyveromyces lactis Unchanged
Debaryomyces is desirable from a biotechnological perspec-
tive as the yeast can be grown in media that are resistant to
Kluyveromyces marxianus Unchanged
contamination, thus reducing costs of the fermentation
Lipomyces spp. Unchanged
(Breuer and Harms 2006). It is intriguing that D. hansenii also
Pichia stipitis Schefferomyces stipitis
has high resistance to chlorine dioxide (ClO2) (Ramirez-
Pichia spp. Komagataella spp.
Orozco et al. 2001), a property that could be exploited to
Saccharomyces cerevisiae Unchanged
maintain asepsis in fermentations. D. hansenii produces killer
Schizosaccharomyces pombe Unchanged
toxins active against various yeast species, which may be of
Saccharomycopsis spp. Unchanged
value in maintaining aseptic conditions in industrial fermen-
Schwanniomyces occidentalis Unchanged
tations and for potential control of yeast infections (Buzzini
Yarrowia lipolytica Unchanged
and Martini 2001). The ability of D. hansenii to tolerate
These yeasts were chosen on the basis of the potential and realized extreme stresses could be highly advantageous in the imple-
importance in industrial fermentations and biotechnological processes. mentation of low-cost fermentation processes (Breuer and
The list does not encompass the large number of yeast species involved Harms 2006).
in food spoilage and defects (Fleet 2007), or in human and animal
D. hansenii produces xylitol from D-xylose in wood
disease
hydrolysates, yielding relatively high xylitol:ethanol ratios
Candida is an extremely heterogenous genus encompassing ascomy-
cetous and basidiomycetous yeasts for which the teleomorphic state (Breuer and Harms 2006). This capability is of potential
has not been demonstrated (Lachance 2011) importance in biomass conversion since a major bottleneck
a
For updated nomenclature, see Kurtzman et al. (2011) in this process is the bioconversion of pentoses to ethanol
Appl Microbiol Biotechnol (2013) 97:503–517 505

(Hahn-Hägerdahl et al. 2007; Jeffries 2006; Saha 2003). D. active against certain ascomycetous yeasts (Jablonowski
hansenii also produces other sugar alcohols from pentoses, and Schaffrath 2007). Since K. lactis is present in many
including arabinose (Breuer and Harms 2006). D. hansenii dairy products that are consumed by humans, it is consid-
synthesizes several exo-enzymes including β-glucosidases, ered to be generally recognized as safe (GRAS), and the
esterases, and inulinases, enzyme systems of current and yeast can be utilized for production of food ingredients,
growing industrial importance (Ricca et al. 2007; Sandhya flavors and fragrances, and as a dietary supplement
and Pandey 2006). The draft genome sequence of (Gounaris 2010; van Ooyen et al. 2006). The potential for
Debayomyces hansenii has become available (Kumar et al. production of lactic acid by Kluyveromyces and other yeasts
2012) which should enable increased understanding of salt has been assessed (Sauer et al. 2010).
tolerance and exploitation of this ascomycetous yeast in
biotechnology. Methanol-utilizing yeasts—K. (P.) pastoris, other Komagataella
spp., Ogataea (Hansenula) polymorpha, Ogataea minuta,
Kluyeromyces lactis and Kluyveromyces marxianus and Candida spp.

The systematics of Kluyveromyces spp. has been extensively The methylotrophic yeasts were initially isolated in the late
studied, particuarly by two prominent yeast biologists 1960s and early 1970s (Kato et al. 1974; Ogata et al. 1969),
(Lachance 2003, 2007; van der Walt 1970). Kluyveromyces and methanol-assimilating yeasts have been continued to be
is an ascomycetous yeast that readily forms asci. Several isolated from various habitats (Ji and Bai 2008; Peter et al.
genetic techniques have been developed for manipulation of 2011). These yeasts have the intriguing property of being
K. lactis for basic studies and industrial development (Spencer able to very efficiently use methanol as a sole source of
et al. 2002; van Ooyen et al. 2006). The availability of genetic carbon and energy. Methanol utilization is associated with
and molecular tools and genomic information for for K.lactis the strong expression of the enzyme methanol oxidase
and K. marxianus (Dujon 2006; Dujon et al. 2004) has facil- (Mox) (also referred to as alcohol oxidase), and the mox
itated the development of the yeast for heterologous protein promoter governing the expression of the gene has been
production and potentially other industrial applications (van exploited for high-level expression of native and heterolo-
Ooyen et al. 2006). gous genes (Boettner et al. 2007; Cregg 2007; Gellissen et
Species of Kluyveromyces produce β-galactosidase al. 2005; Houard et al. 2002; Porro et al. 2005). The heter-
(lactase) that enables the utilization of lactose as a primary ologous proteins accumulate in peroxisomes, and at high
carbon source (Ansari and Satar 2012; Oliveira et al. 2011; levels of expression, peroxisomes can occupy as much as
Rubio-Texeira 2006), an attribute of particular importance 80 % of the cell volume, imparting a striking cellular mor-
for the dairy industry. Kluyveromyces spp. can be grown on phology (Gellisen 2002; Tanaka and Ueda 1993; Veenhuis
inexpensive substrates and waste streams containing lactose et al. 1983).
such as cheese whey (Siso 1996). This yeast genus also has Initially, the methylotrophic yeasts were considered for
industrial potential for production of single-celled protein, the production of biomass and single-cell protein from an
exopolysaccharides, and fine chemicals (Antoni et al. 2003; inexpensive source of carbon (methanol). Industrial devel-
van Ooyen et al. 2006). opment of the yeast was performed at Phillips Petroleum
Kluyveromyces lactis has been investigated for produc- Company for the production of single-cell protein for feeds
tion of heterologous proteins, and has the capability for (Sreekrishna and Kropp 1996; Wegner 1983). High levels of
efficient expression and secretion of a variety of peptides biomass (ca. 130 g DCW per liter) and high yeast produc-
and high molecular weight proteins in attractive yields tivity (>10 g DCW/l-h) was achieved with a specialized
(Fleer 1992; Romanos et al. 1992; van Ooyen et al. 2006). fermentation system including injection of pure oxygen
High cell densities have been obtained in fermentations, and high mass transfer conditions. A similar process was
reaching approximately 100 g dry cell weight (DCW) per developed by Imperial Chemical Industries using the bacte-
liter concomitant with secretion of recombinant human se- rium Methylophilus methylotrophus for the production of
rum albumin in several grams per liter (Fleer 1992; Pruteen (Macauley-Patrick et al. 2005). However, the eco-
Romanos et al. 1992). A drawback to the use of K. lactis nomics of protein production became unfavorable compared
for the production of heterologous human proteins is that the to proteins from soybean and other sources, and efforts were
glycosylation does not conform to the human pattern. It may turned to the development of K. pastoris and O. polymorpha
be possible to adapt a “humanized” glycosylation system to for heterologous protein production (Macauley-Patrick et al.
K. lactis, such as that developed for Komagataella (Pichia) 2005; Romanos et al. 1992; Wegner 1990).
pastoris and Saccharomyces cerevisiae (Hamilton and Of the methylotrophic yeasts, K. pastoris and O. poly-
Gerngross 2007; Li et al. 2007; Wildt and Gerngross morpha have been intensely investigated for heterologous
2005). K. lactis also forms the killer toxin zymocin that is protein production (Cregg 2007; Jahic et al. 2006; http://
506 Appl Microbiol Biotechnol (2013) 97:503–517

faculty.kgi.edu/cregg). In O. polymorpha, several heterolo- cytochrome P450 monooxygenases for biocatalysis, produc-
gous proteins including membrane-bound and labile tion of SCP from a variety of substrates including hydro-
enzymes have been efficiently produced (Cregg 2007; carbons, formation of D-amino acids from racemic mixtures,
Gellisen 2002, 2005). The yield of heterologous protein production of hydrophobic intermediates of the alkane oxi-
production in K. pastoris and O. polymorpha is often higher dation pathway such as fatty alcohols, fatty acids, and
than other yeasts including S. cerevisiae, and grams per liter especially dicarboxylic acids of commercial interest, reduc-
can be obtained for certain proteins. Secretion is generally tion of xylose to xylitol, and reclamation of chemicals,
more efficient and protein degradation diminished in these paricularly solvents (Guo et al. 2006; Klein and Favreau
yeasts compared to S. cerevisiae. Expression systems, fer- 1995; Spencer et al. 2002; Wolf 1996; Yadav et al. 2012).
mentation conditions, downstream processing, and other Several Candida spp. grow on a diversity of substrates
aspects of heterologous protein production in K. pastoris including n-alkanes, fatty acids, xylose, and several other
and O. polymorpha have been extensively reviewed carbohydrates (Kapoor and Gupta 2012; Tanaka and Ueda
(Boettner et al. 2007; Cregg 2007; Daly and Hearn 2005; 1993; Klein and Favreau 1995; Wolf 1996).
Gellisen 2002; Gellissen et al. 2005; Macauley et al. 2005). Candida species developed for industrial processes in-
Heterologous protein production in K. pastoris, particularly clude alkane and phenol-utilizing species, particularly
optimization of glycosylation, is discussed more thoroughly Candida maltosa and Candida tropicalis (Klein and
below. The genome sequence of P. pastoris has become Favreau 1995). C. maltosa is able to utilize aromatic and
available (Kuberi et al. 2011) which will enable more de- certain other amino acids as the sole nitrogen source and has
finitive studies of factors controlling heterologous protein been utilized for the resolution of D- and L-racemic mixtures
synthesis. of amino acids by metabolism of the undesired isomer. The
utilization of n-alkanes and certain other lipid compounds
Yarrowia (Candida) lipolytica requires cytochrome P450 (P450, CYP) enzymes, which are
increasingly being utilized as biocatalysts (Becher and
Y. lipolytica is an ascomycetous yeast that is the teleomorph Wirsel 2012; Faber 2004; Kristan and Rizner 2012; Li et
of C. lipolytica. Industrial interest in Y. lipolytica derived al. 2012; Panke et al. 2004; Patel 2007; Straathof and
initially from its unique physiological capabilities to utilize Aldercreutz 2000; Straathof et al. 2002). Two species that
polyalcohols, organic acids, and long-chain hydrocarbons as have yielded valuable industrial biocatalysts and are exten-
substrates (Fickers et al. 2005; Gellissen et al. 2005; Khanna sively described in the chemical literature are Pseudozyma
et al. 2012; Papanikolaou and Aggelis 2011a, b). Y. lip- antarctica and Candida cylindracea. Other species investi-
olytica also produces high levels of lipolytic enzymes, sev- gated for their P450 systems include C. tropicalis, C. mal-
eral of which have industrial utility (Beopolous et al. 2011; tosa, and Candida rugosa. C. tropicalis and Candida utilis
Fickers et al. 2011). The yeast has been evaluated as a have also been used industrially for the synthesis of SCP
source of single cell protein (SCP) from lipid substrates, (Hagel et al. 2012; Idris and Bukhari 2012; Klein and
such as crude oils and hydrocarbons (Cohen and Ratledge Favreau 1995). These organisms grow and produce biomass
2005; Khanna et al. 2012; Ratledge 2002). The yeast pro- on a variety of substrates and waste streams including oils,
duces relatively large quantities of organic acids (e.g., py- plant hydrolysates, apple pomace, sulfite waste liquor, and
ruvate, citric acid, and isocitrate) from various carbon many others (Halász and Lásztity 1991; Klein and Faveau
sources (Zhou et al. 2012). Y. lipolytica also produces higher 1995; Bekatorou 2006).
value compounds, such as lactones as flavorants (Garcia et
al. 2007; Waché et al. 2006; Ye et al. 2012) and enzymes Scheffersomyces (Pichia) stipitis
including cytochrome P450s and lipases with commercial
uses in biotransformations of steroids, synthesis of pharma- S. (P.) stipitis is an ascomycetous yeast that has been exten-
ceutical intermediates, and production of fine chemicals sively investigated for the fermentation of xylose in hemi-
(Fickers et al. 2005). The availability of the genome se- cellulose to ethanol, L-lactic acid, and other products (Hahn-
quence (Dujon 2006) should lead to advances in genetic Hägerdal et al.2007; Ilmén et al. 2007; Jeffries 2006; Jordan
manipulation of this yeast. et al. 2012). Hemicellulose is the second most abundant
component of cellulosic biomass. Laboratory strains of S.
Candida spp. stipitis, which are amenable to genetic and physiological
manipulation, have been developed by metabolic engineer-
Candida is an extremely heterogenous genus that comprises ing for xylose utilization (Jeffries 2006; Jeffries et al. 2007;
a wide diversity of yeasts of ascomycetous affinity that lack Hahn-Hägerdahl et al. 2007). The genome sequence recent-
known sexual states (Lachance 2011). The commercial util- ly obtained for S. stipitis will provide a valuable resource for
ity and potential of Candida spp. includes synthesis of enhancement of xylose utilization (Jeffries et al. 2007).
Appl Microbiol Biotechnol (2013) 97:503–517 507

Genes from S. stipitis have been introduced into S. cerevi- other pentoses, which constitute about 25 % of biomass, are
siae to enable fermentation of pentoses but with variable not efficiently fermented to ethanol by S. cerevisiae and
yields (Cai and Zhang 2012; Hahn-Hägerdahl et al. 2007; other yeasts, such as S. stipitis, which only slowly use
Jeffries 2006; Jeffries et al. 2007). xylose and other pentoses resulting in low cell and ethanol
productivity (Gray et al. 2006; Hahn-Hägerdahl et al. 2007;
Jeffries 2006; Lynd et al. 2002; Saha 2003). Two primary
Selected industrial processes of ascomycetous yeasts strategies are being pursued for fermentation of cellulosic
biomass by yeast: (a) enhance and optimize xylose and other
Bioethanol pentose utilization by S. stipitis or other pentose-fermenting
yeasts or (b) introduction of the pathways for fermentation
Rapid global population growth is occurring concurrently of xylose and other pentoses into S. cerevisiae to be
with increased demands for food, fuel, and energy exploited by its well-known strong fermentation capacity
(Goldemberg et al. 2007; Nass et al. 2007; Ragauskas et and high ethanol tolerance (Chu and Lee 2007; Jeffries
al. 2006). World oil production will not keep pace with 2006; Lynd et al. 2002; Ostergaard et al. 2000; Saha 2003;
increase in demand for petrochemical fuels (Kendon et al. van Maris et al. 2006). Metabolic engineering and modeling
1986). Limited oil reserves, pollution concerns, global of the biochemical pathways involved in the fermentation of
warming, and political instability have renewed interest pentoses and other carbon sources are being exploited to
and led to financial support for the generation of sustainable enhance fermentation productivity, as well as other limiting
sources of energy (Agrawal et al. 2007; Antoni et al. 2007; factors such as ethanol resistance (Alper et al. 2006; Flores
Cai and Zhang 2012; Farell et al. 2006; Hill et al. 2006; et al. 2000; Ostergaard et al. 2000; Stephanopolous 2007).
Kuhad et al. 2011; Ragauskas et al. 2006). Due to the The availability of the genome sequence from S. stipitis
outstanding capacity of S. cerevisiae and certain other yeasts (Jeffries et al. 2007) and other yeasts has provided important
to produce ethanol and other organics products, yeasts will resources for improvement of biomass utilization. Marked
continue to be developed for manufacture of ethanol and improvements have been made in fermentation of cellulosic
other alcohols. hydrolyzates by yeasts, yet the processes have not reached
Biofuels including bioethanol and biodiesel rely on the the stage of economic viability and industrialization.
conversion of renewable feedstocks to fuels, with current
emphasis mainly on digestion of biomass and lignocellulose Selected yeast enzymes for industrial processes
sources such as crop residues, perennial grasses, and other
abundant materials. These materials are plentiful in many The term “enzyme” (literally “in yeast”) was coined by Kühne
terrestrial environments, and it has been estimated that more in 1876 (Aehle 2004). Enzyme technology utilizing cell-free
than 1.3 billion tons of biomass could be produced annually in enzymes and whole-cell biocatalysts is integral to several
the United States on a sustainable basis (Himmel et al. 2007). large-scale chemical, pharmaceutical, and agricultural biopro-
Recently, the U.S. government set forth the Biofuel Initiative, cesses (Aehle 2004; Pandey et al. 2006; Panke et al. 2004).
which has the goal of replacing 75 % of the current fossil fuel The economic value of the industrial enzyme market in 2005
resources with biofuel by 2025 (Luque et al. 2008). was approximately $3 billion and was expected to reach more
A primary limitation in biomass fermentations is that than $8 billion by 2009 (Porro et al. 2005).
yeasts cannot directly convert cellulose, hemicellulose, lig- In recent years, growth of the bulk enzyme industry has
nin, and associated components inherent in biomass to eth- been particularly robust in the baking and animal feed
anol (Hahn-Hägerdahl 2006; Jeffries 2006; Jeffries et al. sectors, in organic syntheses for fine chemicals and pharma-
2007; Cai and Zhang 2012; Kuhad et al. 2011; Lynd et al. ceuticals, and to a lesser degree for paper and pulp process-
2002; Weber et al. 2010). The lignin component in terrestrial ing, production of biofuels, and for personal care (Aehle
biomass is exceptionally recalcitrant to digestion and con- 2004; Kirk et al. 2002). The bulk enzyme market is domi-
version to bioproducts by most microorganisms, except for nated by enzymes produced by bacteria and filamentous
white rot fungi, but degradation by these fungi is slow and fungi cultivated in submerged culture, particularly Bacillus
inefficient. Cellulose and hemicellulose utilization requires and Aspergillus species (Aehle 2004; Pandey et al. 2006).
digestion to fermentable sugars before they can be fer- Only a limited number of yeast enzymes are currently used
mented by yeasts (Hahn-Hägerdahl 2006; Jeffries 2006; as bulk enzymes in commodity processes, the majority
Jeffries et al. 2007; Kuhad et al. 2011; Lynd et al. 2002; derived from ascomycetous yeasts (Tables 2 and 4).
Walker 2011). The current rate of enzymatic cellulosic bio- However, several yeast enzymes have found application in
mass conversion to sugars is about two orders of magnitude the production of high-value specialized fine chemicals and
slower than the average fermentation rate of simple sugars for biotransformation of pharmaceutical intermediates (see
with yeast (Antoni et al. 2007). In addition, xylose and most below). Enzymes and whole cells used as biocatalysts for
508 Appl Microbiol Biotechnol (2013) 97:503–517

Table 2 Industrial enzymes from yeasts Table 3 Examples of industrial recombinant enzymes produced in
yeasts
Enzyme Yeast Industry
Enzyme Recombinant yeast host
Chymosin Kluyeromyces spp. Food processing
Saccharomyces cerevisae Chymosin Kluyveromyces marxianus var. lactis
α-Galactosidase Saccharomyces spp. Feed applications Glycolate oxidase Komagataella pastoris
L-Glutaminase Zygosaccharomyces rouxii Therapeutic Phytase Komagataella pastoris
Analytical
Sources: Cowan 1996; Cregg 2007; see text for additional references
Inulinases Candida spp. Food applications
Kluyveromyces marxianus
Invertase Saccharomyces cerevisiae Food applications Biocatalysts for pharmaceutical and fine chemical
Lactase Candida pseudotropicalis Food processing production
Kluyveromyces spp.
Lipase Candida rugosa Food processing
Catalysis in the chemical and pharmaceutical industries has
Pseudozyma antactica A, B Flavors
traditionally been dominated by chemical syntheses using
Candida lipolytica Detergent
non-biological catalysts (Bernhardt 2006; Blaser 2003;
Geotrichum candidum Wastewater
Blaser et al. 2005; Bonrath and Netscher 2005; Kuoda and
Trichosporon fermentum Degreasing
Ueda 2011). However, several disadvantages are inherent to
Bioremediation certain industrial chemical synthetic processes, including rel-
Yarrowia lipolytica Therapeutic atively low catalytic efficiency for many reactions, lack of
L-Phenylalanine Rhodotorula spp. Pharmaceutical enantiomeric specificity for chiral syntheses, the need for
ammonia lyase Rhodosporidium spp.
reaction conditions of high temperature, low pH and high
Phenylalanine Candida boidinii Pharmaceutical
dehydrogenase pressure requirements, as well as the extensive use of organic
Phytase Ogataea polymorpha Feed solvents with consequent formation of organic waste and
Nutrition pollutants. These concerns and drawbacks have stimulated
keen interest in biocatalytic processes using enzymes
Sources: Aehle 2004; Hasan et al. 2006; Hilterhaus and Liese 2007; (Bonrath and Netscher 2005; Rozzell 1999). Advantages of
Pandey et al. 2006; Vakhlu and Klur 2006. Also see text for additonial
references
enzymes for chemical processes include mild reaction con-
ditions, i.e., operation at temperatures from 20 °C to 80 °C, at
neutral or slightly acidic pHs, and under atmospheric condi-
tions (Koeller and Wong 2001; Rozell 1999). In contrast to
high-value pharmaceuticals and fine chemicals is a rapidly organic catalysts, enzymes typically catalyze reactions with-
growing sector of the enzyme industry. out substrate functional-group protection, and many enzymes
Currently, about 90 % of industrial enzymes are produced have a long half-life, typically several days to months. Other
as heterologous proteins by recombinant methods (Cherry beneficial properties are the stereoselectivity of enzymes for
and Fidanstef 2003). Certain yeasts, especially K. pastoris their substrates that yields stereo- and regiochemically defined
and S. cerevisiae, are increasingly being utilized for heter- reaction products at the enormous rate acceleration of 105 to
ologous production of enzymes and a variety of other pro- 108 (Aehle 2004; Koeller and Wong 2001; Rozell 1999). They
teins (Aehle 2004; Cregg 2007; van Beilen and Li 2002). also catalyze reactions on unnatural substrates, leading to
Blastobotrys adeninivorans, O. polymorpha, K. lactis, enormous compound diversity.
Schizosaccharomyces pombe, Y. lipolytica, Pseudozyma Another advantage of enzymes as industrial catalysts is
spp., and other yeast species have also been developed for that they can be genetically selected and chemically modi-
the production of heterologous proteins (Avis et al. 2005; fied to enhance stability, substrate specificity, and specific
Buckholz and Gleeson 1991; Gellissen 2005; Gellissen et al. activity (Aehle 2004; Koeller and Wong 2001; Rozell
2005; Madzak et al. 2004; van Ooyen et al. 2006). Industrial 1999). Several enzymes are active in organic solvents, su-
recombinant enzymes and those close to commercialization percritical fluids, high pressures, and ionic solvents (“Green
produced by yeasts are presented in Tables 3 and 4. Yeasts are solvents”) (Klibanov 2001; Rezaei et al. 2007; Yang and
desirable hosts of enzymes for food uses because of their lack Pan 2005). Hydrophobic environments and ionic solvents
of production of toxic secondary metabolites (Olempska-Beer are optimal for some hydrophobic reactions using biocata-
et al. 2006). K. lactis is currently approved by the FDA for lysts, such as those catalyzed by lipases (Park et al. 2009;
production of recombinant enyzmes (chymosin) for uses in Yang and Pan 2005). Immobilized enzyme processes can
foods. A much more detailed description of industrial enzymes have advantages over enzymes in solution including stability,
from yeasts is described in Johnson and Echavarri (2011). process duration, and catalytic efficiency (Sheldon 2007). A
Appl Microbiol Biotechnol (2013) 97:503–517 509

Table 4 Yeast enzymes/whole cells used in biocatalytic processes (adapted from Hilterhaus and Liese 2007; see text for additional references)

Enzyme class Enzyme Yeast source

I. Oxidoreductases EC 1 Dehydrogenase Zygosaccharomyes rouxii


Dehydrogenase Geotrichum candidum
Dehdrogenase Candida sorbophila
Reductase Ogataea methanolica
Reductase Aureobasidium pullulans
Reductase Saccharomyces cerevisiae
D-amino acid oxidase Trigonopsis variabilis
β-Galactosidase Kluyveromyces lactis
Formate dehydrogenase Candida boidinii
Transferases EC2 Lipase Candida cylindracea
Lipase Candida antarctica A, B0Pseudozyma antarctica
Hydrolases EC 3 β-Galactosidase Kluyveromyces lactis
Lactamase/racemase Cryptococcus laurentii
Lyases EC 4 Pyruvate carboxylase Saccharomyces cerevisiae
Enoyl-CoA hydratase Candida rugosa
L-Phenylalanine ammonia lyase Rhodotorula rubra
Isomerases EC 5 No significant commercial sources from yeasts
Ligases EC6 No significant commercial sources from yeasts

drawback to certain enzyme syntheses is that they require metabolites for use in industrial biotechnology has been vital-
cofactors, but this problem can be minimized by various ized through metagenomics (Ferrer et al. 2007a, b; Lorenz and
approaches, including cofactor recycling (Straathof and Eck 2005). This approach has led to the discovery of enzymes,
Aldercreutz 2000) and the use of whole cells, such as engi- antimicrobials, and other compounds of industrial potential
neered S. cerevisiae (Faber 2004). (Ferrer et al. 2007a, b; Lorenz and Eck 2005; Podar and
Although a large number of studies and a voluminous Reysenbach 2006). However, most metagenomic studies have
literature have been devoted to the production of fine chem- been directed towards understanding bacterial diversity, and
icals using enantioselective catalysis by enzymes, relatively not yeasts, filamentous fungi, and other eukaryotes (Lorenz
few enzymatic processes are currently used on an industrial and Eck 2005). The paucity of metagenomic studies conducted
scale (Blaser 2003; Bonrath and Netscher 2005; De Mot and in yeasts, filamentous fungi, and other eukaryotes, such as
Verachtert 1982). It has been estimated that about 150 protozoa, is primarily due to the comparatively large size of
industrial syntheses currently utilize enzymes or microbial genomes in fungi compared to bacteria and viruses and the
whole cell catalysts (Straathof et al. 2002; Woodley 2006; relatively large nucleotide sequencing efforts required to obtain
Yazbeck et al. 2004), but the use of enzymes in syntheses is a representation of species diversity (Hall 2007). It is antici-
increasing particularly for complex and chiral molecules. pated that more metagenomic studies will be devoted to fungi
Several yeasts produce enzymes and bioacatalysts of and yeasts due to advances in technology in sequencing and
realized and potential value in the traditional enzyme indus- will be devoted to fungi because of their enormous biodiversity
try and as chiral-specific biocatalysts for the fine chemical and ability to produce a multitude of secondary metabolites.
and pharmaceutical industries (Table 5) (Aehle 2004; Liese
et al. 2000; Matsuda et al. 2009; Pandey et al. 2006; Patel Heterologous protein production in yeasts
2004, 2007; Straathof and Adlercreutz 2000). Useful case
studies of commercial enzymatic and microbial biotransfor- Since the early 1980s, yeasts have been utilized for heterol-
mations, including several involving yeasts, have been de- ogous production of a variety of proteins (Cregg 2007;
scribed (Table 5) (Cheetham 2004). Lipases and esterases, Gellissen 2005; Gellissen et al. 2005; Hitzeman et al.
commonly produced by yeasts, are the most frequently used 1981; Hou et al. 2012; Smith et al. 1985; Romanos et al.
biocatalysts in industrial organic syntheses (Chenevert et al. 1992). The production of heterologous proteins in yeasts
2006; Li et al. 2012; Pscheldt and Glieder 2008). holds enormous potential for biotechnological processes. A
Despite the advantages of biocatalysts, enzymes and whole breakthrough in heterologous protein expression in yeast
yeast cells are still an underutilized technology (Bernhardt was the cloning, expression, processing, and secretion of
2006; Rozzell 1999). Recently, the discovery of enzymes and human proinsulin in S. cerevisiae in the 1980s (Cousens et
510 Appl Microbiol Biotechnol (2013) 97:503–517

Table 5 Examples of yeast enzymes used in biotransformation/biocatalytic processes in the pharmaceutical and fine chemicals industries

Yeast Enzyme or Whole Cell Product Reference

Lipasea Taxol Koeller and Wong 2001


Monooxygenase (S. cerevisiae) Cyclic lactones Stewart et al. 1998
Nuceloside phosphorylasea Antiviral Ribavarin Koeller and Wong 2001
Zygosaccharomyces rouxii (dehydrogenase) Benzodiazepines Rozell 1999
Hilterhaus and Liese 2007
Dehydrogenasesa Optically active Sturmer and Breuer 2006
Alcohols
Dehdrogenasesa Ephedrine Sturmer and Breuer 2006
Esterasea Racemic alcohols Koul et al. 2005
Reductasea Ataxanavir (HIV protease inhibitor) Patel 2004
Lipase (Candida cylindraceae) Lobucavir (antiviral) Patel 2004, 2007
Lipase (C. cylindraceae) Hepatitis B antiviral Patel 2004, 2007
Lipase (Candida antarctica) Ribavarin (antiviral) Patel 2004
Reductase (Pichia spp.) Pacliataxel (anticancer drug) Patel 2004, 2007
Reductase (Aureobasidium pullulans, Candida spp.) Retinoid receptor agonists Patel 2004
Lipase (Candida cylindracea) Pharmaceutical intermediate Patel 2004
Reductase (Candida spp.) Pichia spp., Rhodotorula spp., Pharmaceutical intermediate Patel 2004
Saccharomyces spp.)
Epoxide hydrolase (Rhodotorula glutinis) Melantonin receptor agonist Patel 2004
Whole cell racemate resolution (Candida boidinii, Pharmaceutical intermediate Patel 2004, 2007
Ogataea methanolica, Ogataea polymorpha)
Reductase (Geotrichum candidum) Hydroxy methyl glutaryl Patel 2004
CoA inhibitors (cholesterol lowering agents)
Lipase (Pseudozyma antarctica), Hyphozyma Tachykinin receptor agonists) Patel 2004
sp., Cryptococcus tsukubaensis
(S)-2-pentanol, (S)-2-heptanol Anti-Alzheimer drugs Patel 2007
(R)–(S) oxidase Mixed racemate resolution Patel 2007
(Ogataea polymorpha)
(Candida boidinii)
(Ogataea methanolica)
Lipase, reductase (Pseudozyma antarctica Beta-blockers Zelaszczyk and Kiec-Kononowicz 2007
S. cerevisiae)
a
Yeast species not referenced. See text for additional references

al. 1987; Hadfield et al. 1993; Ladisch and Kohlmann 1992; perform eukaryotic post-translational modifications includ-
Thim et al. 1986). Insulin from S. cerevisiae had increased ing intron splicing, proteolytic processing, folding, forma-
pharmacological efficacy and reduced side effects compared tion of disulfide linkages, glycosylation, and mainentance of
to porcine insulin. Subsequent studies showed that S. cer- quality suitable for biochemical and structural analyses
evisiae effectively synthesized and secreted many mamma- (Gellissen 2005; Gellissen et al. 2005).
lian and human proteins including α-interferon, epidermal Yeast species investigated for heterologous protein pro-
growth factor, human serum albumin, hepatitis B surface duction included the non-methylotrophs S. cerevisiae,
antigen, epidermal growth factor, β-endorphin, and prochy- Schizosaccharomyces pombe, K. lactis, Y. lipolytica,
mosin. Several of of these proteins have been developed and Zygosaccharomyces rouxii, Zygosaccharomyces bailii, and
commercialized as high-value human pharmaceuticals or B. adeninivorans (Böer et al. 2007; Gellissen 2005;
enzymes (Hadfield et al. 1993; Romanos et al. 1992; Gellissen et al. 2005; Madzak et al. 2004; Porro et al. 2005;
Smith et al. 1985; Gellissen 2002; Gellissen et al. 2005; van Ooyen et al. 2006), and the methylotrophs K. pastoris, O.
Hou et al. 2012). Yeasts have several advantages as hosts for polymorpha, Candida boidinii, Ogataea methanolica, and
native and heterologous production, including ease and Schwanniomyces occidentalis (Table 4)(Böer et al. 2007;
rapidity of growth, excellent methods of genetic manipula- Gellissen 2002; Houard et al. 2002; Jahic et al. 2006;
tion, high expression with optimized systems, the ability to Labuschagne and Albertyn 2007). Of these yeasts, S.
Appl Microbiol Biotechnol (2013) 97:503–517 511

cerevisiae and K. pastoris have been most extensively devel- containing N-glycans (Gemmill and Trimble 1999). To re-
oped for heterologous protein production. More than 500 solve the problem of glycosylation, yeasts are being devel-
heterologous proteins have been producted in K. pastoris, oped for “humanization” of post-translational modifications
including plant, animal and human proteins, as well as (Li et al. 2007; Wildt and Gerngross 2005). Emphasis in this
membrane-associated proteins which are often difficult to area has been with K. pastoris, which is being optimized by
functionally express in many other systems (Cregg 2007; “glycoengineering” through gene alterations to eliminate un-
Labarre et al. 2007; Macauley-Patrick et al. 2005; Porro et desirable protein modifications (Gerngross 2004; Hamilton
al. 2005; http://faculty.kgi.edu/cregg). K. pastoris has the and Gerngross 2007).
exceptional ability to produce high quantities of proteins, Yeasts are currently commercially used or are close to
glycosylate them in patterns similar to that of humans, commercialization for the production of a variety of heter-
efficiently secrete them into the medium, and avoid ag- ologous protein pharmaceuticals. High-level expression of
gregation and proteolysis during recovery for many pro- human insulin (Cousens et al. 1987), interferons (Gasmi et
teins. Proteins can be expressed in sufficient quantity and al. 2011), tetanus fragment C (Clare et al. 1998), HIV-1
quality for applications in protein engineering and stuc- envelope glycoprotein gp120 (Jordan and Gibbins 2006),
tural analyses (Daly and Hearn 2005). and others have been achieved in S. cerevisiae, K. pastoris,
Y. lipolytica, and other yeast species (Hadfield et al. 1993).
Protein pharmaceuticals from yeasts Monoclonal antibodies (mAbs) are the most prevalent
and high-value classes of protein drugs (Gasser and
Proteins currently constitute about 25 % of new approved Mattanovich 2007; Maggon 2007; Pavlou and Reichert
drugs in the USA, with the majority being monoclonal 2005), which presently have a global market of approx.
antibodies (Gellissen 2005; Sethuraman and Stadheim $30 billion (Evans and Das 2005; Gasser and Mattanovich
2006; Walsh 2005, 2006). As of 2006, more than 165 2007). mAbs have traditionally been produced in mamma-
protein biopharmaceuticals have been approved by lian cell lines, mostly recombinant CHO cells and other
European and US regulatory agencies, and more than 500 lines, but this process is slow and expensive (Farrid 2006).
product candidates are in preclinical and clinical develop- The production of antibodies in yeasts and fungi is also
ment (Walsh 2006). In 2004, the global market for recom- being actively pursued, but it has been very challenging to
binant protein therapeutics and nucleic acid-based products develop antibody-producing systems in yeasts (Gasser and
was more than than $33 billion and was expected to reach Mattanovich 2007).
$60–70 billion by 2010 (Evans and Das 2005; Pavlou and
Reichert 2005; Schmidt 2004; Walsh 2006). Probiotics and prebiotics
Yeasts are intensively being developed as protein expres-
sion systems, which in comparison to mammalian cell lines Certain yeast species have been used as prebiotic and pro-
have higher productivity, higher cell yields, shorter fermen- biotic agents for preventing or treating various intestinal,
tation cycles, and can be cultured in defined media under nutritional, and toxicological disorders (Mosiehi-Jenabian et
relatively inexpensive conditions. In addition, yeasts can al. 2010; Williams 2010). In particular, Saccharomyces
efficiently secrete proteins, possess posttranslational modi- boulardii, originally isolated from fruit in Indochina, has
fication pathways, and are nonpathogenic and non- been used for treatment of intestinal diseases in children and
pyrogenic (Schmidt 2004). The primary yeast species being adults since 1950 (Buts and Bernasconi 2005; Edwards-
developed for protein pharmaceutical and enzyme produc- Ingram et al. 2007). Recent studies have shown that it is
tion are S. cerevisiae, K. pastoris, O. polymorpha, B. adeni- conspecific with S. cerevisiae, but S. boulardii appears to
nivorans, Y. lipolytica, and K. lactis (Schmidt 2004). Certain have certain genotypic and phenotypic properties that may
peptide and protein therapeutics produced in S. cerevisiae contribute to its probiotic properties (Edwards-Ingram et al.
and more recently O. polymorpha and K. pastoris have been 2007). Controlled clinical trials have shown efficacy of S.
commercialized (Table 5) (Gerngross 2004; Walsh 2003). boulardii for prevention or elimination of several intestinal
One disadvantage to the synthesis of protein biopharma- disorders, including infection by Clostridium difficile asso-
ceuticals in yeasts is that the resulting products often have a ciated with antibiotic-induced diarrhea (Fric 2007). Yeasts
non-human glycosylation pattern (Gemmill and Trimble have also been hypothesized to prevent other intestinal
1999; Gerngross 2004; Schmidt 2004; van Ooyen et al. infections, including inflammatory bowel disease and
2006). Non-human glycosylation of therapeutic proteins can Crohn's disease (Besirbellioglu et al. 2006; Buts 2009;
affect various biological properties including half-life, tissue Dalmasso et al. 2006; Edwards-Ingram et al. 2007;
distribution, pharmacokinetics, and immunogenicity Sougioultzis 2006; Villarruel et al. 2007). The mechanisms
(Hamilton and Gerngross 2007). Most yeast species have the of probiotic activity have not been elucidated but may
propensity to glycosylate proteins with high mannose- involve alteration of inflammatory and immune responses
512 Appl Microbiol Biotechnol (2013) 97:503–517

or destruction of toxic factors (Ozkan et al. 2007). Although neoformans, and certain other yeasts (Cooper 2011), select-
yeasts may be promising therapeutic agents, they need to ed strains of S. cerevisiae, Candida, Trichosporon, and
undergo controlled clinical trials to critically evaluate their Cryptococcus have shown pathogenic potential (Murphy
efficacy. and Kavanagh 1999; Wei et al. 2007), and careful assess-
Preliminary evidence indicates that certain yeasts can ment of safety is needed for applications in food and bio-
produce prebiotics, which are compounds (generally oligo- technology uses (Flamm 1991; Olemska-Beer et al. 2006;
saccharides) that stimulate the growth of bifidobacteria and Pariza and Johnson 2001; Spok 2006). Allergenicity has
other beneficial bacteria in the gut of humans and animals or been a major concern of uses of yeasts in human diets
oligopeptides that have beneficial health benefits by stimu- (Airola et al. 2006; Lehrer 1996; Smith et al. 1996).
lation of immune response. Prebiotics are often sugar deriv- The advent of functional genomics has created opportu-
atives such as fructooligosaccharides (Maugeri and nities for in depth understanding, analysis, and improvement
Hernalsteens 2007), of which certain yeasts can catabolize of yeasts in foods and other industrial applications.
due to their formation of inulinases. K. lactis was found to Scientific, public, and regulatory concerns with GMOs, such
synthesize prebiotic oligosaccharides and immunostimula- as spread of antibiotic resistance genes, insecticide or other
tory peptides from whey (Belem and Lee 1998). resistance genes can be obviated with modern genetic
manipulations (Lehrer et al. 1996; Pariza and Johnson
Yeast glucans and cell wall polysaccharides 2001; Plahuta and Raspor 2007; Pretorius and Bauer 2002;
Stewart 2006). S. cerevisiae is also used for the production
Yeast cell wall polysaccharides have been used as adjuncts of insulin, hepatitis B vaccine, and other products for human
for animal and fish feeds (Sauerwein et al. 2007; Singh et al. treatment, and it is of utmost importance that these strains
2008). These polysaccharides have been shown to promote and their by products do not pose a risk for human health.
animal growth and health by various mechanisms including
immunomodulation, oxidative status, binding of toxins and
pathogens, and interactions with gut constituents. Glucans Summary and perspectives
and mannans have also been found to have a myriad of
biological functions in animal models and potentially in Yeasts have a rich history and a bright future in biotechnol-
humans, including modulation of histamine release (Holck ogy. Their involvement and importance in traditional food
et al. 2007) and antitumor activities (Ghoneum et al. 2007). fermentations is unparalled by other organisms of biotech-
Further studies are needed in this area to evaluate health nological relevance. The utility of yeasts in biotechnological
promotion by yeast cell wall polysaccharides. processes is accelerating due to a number of properties and
developments. Most yeast species are nonpathogenic to
Genetically modified and recombinant yeast for use in food humans and animals, and thus are anticipated to see more
utility in a variety of disciplines of importance to human
Because of its long history of safe use and consumption, S. activities. It is likely that yeasts will be increasingly used as
cerevisiae was among the first organisms to be designated GMOs in traditional processes as their safety is more exten-
“generally recognized as safe” (GRAS) and was the first sively established. S. cerevisiae and certain other species are
genetically modified (micro)organism (GMO) used for re- being developed for the production of biofuels from cellu-
combinant production of food and feed additives. In 1990, a losic materials and potentially other substrates and will have
genetically modified strain of S. cerevisiae became one of the importance in the generation of new sources of energy.
first GMOs to be approved for food use in the UK (Aldhous During the past decade, yeast systems have been developed
2000). It has been used in bakery products for enhanced for the production of heterologous proteins in high yields
production of carbon dioxide. Many genes encoding desirable and with post-translational modifications equivalent or sim-
traits mentioned above have been cloned in S. cerevisiae, ilar to modifications performed in humans. Yeasts have
Saccharommyces pastorianus, and Saccharomyces bayunus increasing importance as sources of biocatalysts for the
that have primary roles in food fermentations (Bisson 2004; production of high-value fine chemicals and protein phar-
Pretorius 2003; Schuller and Casal 2005). However, most of maceuticals. Due to their metabolic capabilities, they have
these strains have not been used commercially because of important roles in environmental bioremediation. S. cerevi-
regulatory and public hurdles. siae has become the premier model eukaryotic organism for
Concerns have been raised that certain yeast species and the understanding of human physiology, including disease
strains may be opportunistically pathogenic or toxigenic to processes, and will increase in importance for the under-
immunocompromised humans (Klein and Favreau 1995; standing and treatment of disease. Tremendous advances
Fenn 2007; Lin and Heitman 2006). In addition to the have been made in the development of S. cerevisiae as the
well-known pathogens, Candida albicans, Cryptococcus premier eukaryotic organism for the development of
Appl Microbiol Biotechnol (2013) 97:503–517 513

functional genomics and systems biology. Other species of heterologous genes in the yeast Pichia pastoris—comparative
view of 79 human genes. J Biotechnol 130:1–10
ascomycetous yeast also have tremendous utility and poten-
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Acknowledgments I would like to acknowledge Professor Herman yeast with biotechnological potential. Yeast 23:415–437
Jan Phaff (deceased) and Professor Michael J. Lewis and their post- Buckholz RG, Gleeson MAG (1991) Yeast systems for the commercial
odoctoral fellows for encouragment and guidance in working on Phaf- production of heterologous proteins. Nature Biotechnol 9:1067–
fia/Xanthopyllomyces over the years. I also thank the students and 1072
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