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Title: The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides

Journal Article · · BMC Genomics
 [1];  [1];  [2];  [1];  [1];  [1];  [1]
  1. Univ. of Murcia, Murcia (Spain)
  2. The Genome Analysis Centre, Norwich (United Kingdom)
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Here, RNA interference (RNAi) is a conserved mechanism of genome defence that can also have a role in the regulation of endogenous functions through endogenous small RNAs (esRNAs). In fungi, knowledge of the functions regulated by esRNAs has been hampered by lack of clear phenotypes in most mutants affected in the RNAi machinery. Mutants of Mucor circinelloides affected in RNAi genes show defects in physiological and developmental processes, thus making Mucor an outstanding fungal model for studying endogenous functions regulated by RNAi. Some classes of Mucor esRNAs map to exons (ex-siRNAs) and regulate expression of the genes from which they derive. To have a broad picture of genes regulated by the silencing machinery during vegetative growth, we have sequenced and compared the mRNA profiles of mutants in the main RNAi genes by using RNA-seq. In addition, we have achieved a more complete phenotypic characterization of silencing mutants Deletion of any main RNAi gene provoked a deep impact in mRNA accumulation at exponential and stationary growth. Genes showing increased mRNA levels, as expected for direct ex-siRNAs targets, but also genes with decreased expression were detected, suggesting that, most probably, the initial ex-siRNA targets regulate the expression of other genes, which can be up- or down-regulated. Expression of 50% of the genes was dependent on more than one RNAi gene in agreement with the existence of several classes of ex-siRNAs produced by different combinations of RNAi proteins. These combinations of proteins have also been involved in the regulation of different cellular processes. Besides genes regulated by the canonical RNAi pathway, this analysis identified processes, such as growth at low pH and sexual interaction that are regulated by a dicer-independent non-canonical RNAi pathway. In conclusion, this work shows that the RNAi pathways play a relevant role in the regulation of a significant number of endogenous genes in M. circinelloides during exponential and stationary growth phases and opens up an important avenue for in-depth study of genes involved in the regulation of physiological and developmental processes in this fungal model.

Research Organization:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1345508
Journal Information:
BMC Genomics, Vol. 16, Issue 1; ISSN 1471-2164
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 37 works
Citation information provided by
Web of Science

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Cited By (8)

Mucor circinelloides : Growth, Maintenance, and Genetic Manipulation journal April 2018
RNAi-Based Functional Genomics Identifies New Virulence Determinants in Mucormycosis journal January 2017
A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi journal April 2015
The interaction of fungi with the environment orchestrated by RNAi
  • Villalobos-Escobedo, José Manuel; Herrera-Estrella, Alfredo; Carreras-Villaseñor, Nohemí
  • Mycologia, Vol. 108, Issue 3 https://doi.org/10.3852/15-246
journal May 2016
An Adult Zebrafish Model Reveals that Mucormycosis Induces Apoptosis of Infected Macrophages journal August 2018
Functional characterization of three trehalase genes regulating the chitin metabolism pathway in rice brown planthopper using RNA interference journal June 2016
A non-canonical RNAi pathway controls virulence and genome stability in Mucorales journal July 2020
Corrigendum: Dicer-Like Genes Are Required for H2O2 and KCl Stress Responses, Pathogenicity and Small RNA Generation in Valsa mali journal July 2017

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
asexual sporulation
sexual interaction
pH regulation
non-canonical RNAi pathway
esRNAs
mRNA profiling