5 Small RNAs in Fungi
FRANCISCO E. NICOLA ´ S
1
, LAURA MURCIA
1
, EUSEBIO NAVARRO
1
, JOSE ´ T. CA ´ NOVAS-MA ´ RQUEZ
1
, VICTORIANO
GARRE
1
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
II. Protective Small RNAs . . . . . . . . . . . . . . . . . . . . . . . 109
A. Small RNAs in Genome Defense . . . . . . . . . . . 109
B. Small-Interfering RNAs in Chromosome
Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
III. Small RNAs in the Regulation of Gene
Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
A. MicroRNA-Like Small RNAs . . . . . . . . . . . . . . . 113
B. Exon-Derived Regulatory Endogenous Small
RNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
C. Phenotypic Plasticity . . . . . . . . . . . . . . . . . . . . . . . 115
D. Small RNAs Associated with Antisense
Transcripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
E. Cross-Kingdom Regulation . . . . . . . . . . . . . . . . . 116
IV. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
I. Introduction
Fungi are one of the oldest groups of organisms
on the Earth, where they play pivotal roles in
maintaining life by participating in nutrient
recycling and symbiosis with plants. Despite
their benefits to the planet, they also put in
risk the survival of other species, including
humans, when they are genuine or opportunistic pathogens. Besides, we use several fungi for
our own benefit in different aspects from food
to the treatment of diseases. Thereby, understanding the biology of fungi at different levels
ranging from ecology to molecular details is
essential, although this kingdom received little
attention in the past apart from some classical
models such as yeasts, Neurospora crassa, and
Aspergillus nidulans. Fortunately, the study of
fungi is living now an exciting period with
spectacular advances in our knowledge about
the molecular mechanisms underlying the
fascinating responses of these organisms to
their faced environmental challenges. Several
examples are showing how fungi can adapt
rapidly to stressful situations that can put
their lives at risk, such as the presence of antifungal drugs and high temperature (Calo et al.
2014; Chang et al. 2019; Kronholm et al. 2016;
Noble et al. 2016; Slepecky and Starmer 2009).
In this context, non-coding small RNAs
(sRNAs) play essential roles in genome integrity preservation, gene expression, phenotypic
plasticity, and the ability to interact with other
organisms via the conserved eukaryotic RNA
interference (RNAi) pathway, known also as
the RNA-mediated gene silencing mechanism,
which mainly represses the expression of
target genes at the transcriptional or posttranscriptional level (Torres-Martı ´nez and
Ruiz-Va ´zquez 2017).
The phenomenon of RNAi was initially discovered in plants when the introduction of the
chalcone synthase gene in petunia suppressed
the expression of both the transgene and the
endogenous gene, a phenomenon called cosuppression (Napoli et al. 1990). Several RNAi
pathways have been described in fungi (Chang
et al. 2012; Torres-Martı ´nez and Ruiz-Va ´zquez
2017; Villalobos-Escobedo et al. 2016) and
other species, but the basic conserved machinery (Fig. 5.1) comprises an RNase III protein,
called Dicer, which produces the sRNA molecules from a double-stranded RNA (dsRNA)
precursor. These sRNAs, which receive differ1 Departamento de Gene ´tica y Microbiologı ´a, Facultad de Biologı ´a, Universidad de Murcia, Murcia, Spain; e-mail: fnicolas@um.es;
lauramur@um.es;
sebi@um.es;
josetomas.
canovas@um.es; vgarre@um.es
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020
FRANCISCO E. NICOLA ´ S
1
, LAURA MURCIA
1
, EUSEBIO NAVARRO
1
, JOSE ´ T. CA ´ NOVAS-MA ´ RQUEZ
1
, VICTORIANO
GARRE
1
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
II. Protective Small RNAs . . . . . . . . . . . . . . . . . . . . . . . 109
A. Small RNAs in Genome Defense . . . . . . . . . . . 109
B. Small-Interfering RNAs in Chromosome
Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
III. Small RNAs in the Regulation of Gene
Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
A. MicroRNA-Like Small RNAs . . . . . . . . . . . . . . . 113
B. Exon-Derived Regulatory Endogenous Small
RNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
C. Phenotypic Plasticity . . . . . . . . . . . . . . . . . . . . . . . 115
D. Small RNAs Associated with Antisense
Transcripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
E. Cross-Kingdom Regulation . . . . . . . . . . . . . . . . . 116
IV. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
I. Introduction
Fungi are one of the oldest groups of organisms
on the Earth, where they play pivotal roles in
maintaining life by participating in nutrient
recycling and symbiosis with plants. Despite
their benefits to the planet, they also put in
risk the survival of other species, including
humans, when they are genuine or opportunistic pathogens. Besides, we use several fungi for
our own benefit in different aspects from food
to the treatment of diseases. Thereby, understanding the biology of fungi at different levels
ranging from ecology to molecular details is
essential, although this kingdom received little
attention in the past apart from some classical
models such as yeasts, Neurospora crassa, and
Aspergillus nidulans. Fortunately, the study of
fungi is living now an exciting period with
spectacular advances in our knowledge about
the molecular mechanisms underlying the
fascinating responses of these organisms to
their faced environmental challenges. Several
examples are showing how fungi can adapt
rapidly to stressful situations that can put
their lives at risk, such as the presence of antifungal drugs and high temperature (Calo et al.
2014; Chang et al. 2019; Kronholm et al. 2016;
Noble et al. 2016; Slepecky and Starmer 2009).
In this context, non-coding small RNAs
(sRNAs) play essential roles in genome integrity preservation, gene expression, phenotypic
plasticity, and the ability to interact with other
organisms via the conserved eukaryotic RNA
interference (RNAi) pathway, known also as
the RNA-mediated gene silencing mechanism,
which mainly represses the expression of
target genes at the transcriptional or posttranscriptional level (Torres-Martı ´nez and
Ruiz-Va ´zquez 2017).
The phenomenon of RNAi was initially discovered in plants when the introduction of the
chalcone synthase gene in petunia suppressed
the expression of both the transgene and the
endogenous gene, a phenomenon called cosuppression (Napoli et al. 1990). Several RNAi
pathways have been described in fungi (Chang
et al. 2012; Torres-Martı ´nez and Ruiz-Va ´zquez
2017; Villalobos-Escobedo et al. 2016) and
other species, but the basic conserved machinery (Fig. 5.1) comprises an RNase III protein,
called Dicer, which produces the sRNA molecules from a double-stranded RNA (dsRNA)
precursor. These sRNAs, which receive differ1 Departamento de Gene ´tica y Microbiologı ´a, Facultad de Biologı ´a, Universidad de Murcia, Murcia, Spain; e-mail: fnicolas@um.es;
lauramur@um.es;
sebi@um.es;
josetomas.
canovas@um.es; vgarre@um.es
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020