et al. AMB Expr (2018) 8:39
Transcriptome proﬁling of Issatchenkia
orientalis under ethanol stress
, Guotong Xiong
, Ruoyun Li, Zufang Wu
, Xin Zhang and Peifang Weng
Issatchenkia orientalis, a non-Saccharomyces yeast that can resist a wide variety of environmental stresses, has potential
use in winemaking and bioethanol production. Little is known about gene expression or the physiology of I. orien-
talis under ethanol stress. In this study, high-throughput RNA sequencing was used to investigate the transcriptome
proﬁle of I. orientalis in response to ethanol. 502 gene transcripts were diﬀerentially expressed, of which 451 were
more abundant, and 51 less abundant, in cells subjected to 4 h of ethanol stress (10% v/v). Annotation and statistical
analyses suggest that multiple genes involved in ergosterol biosynthesis, trehalose metabolism, and stress response
are diﬀerentially expressed under these conditions. The up-regulation of molecular chaperones HSP90 and HSP70,
and also genes associated with the ubiquitin–proteasome proteolytic pathway suggests that ethanol stress may
cause aggregation of misfolded proteins. Finally, ethanol stress in I. orientalis appears to have a nitrogen starvation
eﬀect, and many genes involved in nutrient uptake were up-regulated.
Keywords: Issatchenkia orientalis, RNA-Seq, Transcriptome, Ethanol stress, Wine fermentation
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Fruit wines are fermented alcoholic beverages that derive
their ﬂavors from raw materials (fruits, and often ﬂowers
and herbs) as well as from the fermentation process. Two
distinct yeasts are usually involved in the production of
a savory and pleasant fruit wine. e wine yeast Saccha
romyces cerevisiae is primarily responsible for alcoholic
fermentation and the synthesis of secondary metabolites,
while non-Saccharomyces yeasts or non-conventional
wine yeasts contribute additional ﬂavor, texture, and
nutritional qualities (Archana et al. 2015). e role of
non-Saccharomyces wine yeasts in fruit wine fermenta
tion has attracted increasing interest (Ciani et al. 2010).
Several studies have focused on multi-strain fermenta
tion and mixed yeast culture (Fleet 2003; Giovani et al.
2012; Sadoudi et al. 2012), and some non-Saccharomyces
yeasts have been suggested for use in mixed starter cul
tures with S. cerevisiae (Masneufpomarede et al. 2015).
e non-conventional wine yeast Issatchenkia orien
talis was ﬁrst described in 1960 but was reclassiﬁed to
P. kudriavzevii in 1965 (Kurtzman et al. 2008). Several
I. orientalis strains produce ethanol and have higher
thermotolerance, salt tolerance, and acid tolerance than
S. cerevisiae (Isono et al. 2012; Koutinas et al. 2016).
Because of its resistance to multiple stress factors, I. ori
entalis has potential application in bioethanol production
and succinic acid production (Kitagawa et al. 2010; Kwon
et al. 2011; Xiao et al. 2014).
High-throughput RNA sequencing (RNA-Seq) is now
routinely used to generate global transcription proﬁles,
often to compare gene expression under diﬀerent con
ditions. Many studies have used RNA-Seq to examine
transcription in S. cerevisiae and the ﬁssion yeast Schizos
accharomyces pombe in response to environmental shifts
(Kasavi et al. 2016; Lackner et al. 2012; Lewis et al. 2014).
However, gene expression in I. orientalis has not yet
been studied. In particular, the underlying mechanisms
that allow I. orientalis to tolerate ethanol have not been
explored, nor have they been compared with those in S.
In this study we used RNA-Seq to investigate changes
in the gene expression proﬁle of I. orientalis under
Yingjie Miao and Guotong Xiong contributed equally to this work
Department of Food Science and Engineering, School of Marine Sciences,
Ningbo University, Ningbo 315211, People’s Republic of China