Ubiquitous RNA-dependent RNA polymerase and gene silencing

Birchler, James A.

doi:10.1186/gb-2009-10-11-243

Cited by 13 publications

(8 citation statements)

References 21 publications

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“…The absence of clear RdRP homologues in the Neocallimastigomycota and related basal fungal phyla despite their presence in other fungi could suggest that either an RdRP is not involved in dsRNA-mediated mRNA silencing as shown before in mammals ( Stein et al, 2003 ). Alternatively, RNA-dependent RNA polymerase activity could be mediated through a non-canonical RdRP in basal fungi, e.g., the RNA polymerase II core elongator complex subunit Elp1 shown to have RdRP activity in Drosophila, as well as Caenorhabditis elegans, Schizosaccharomyces pombe, and human ( Birchler, 2009 ; Lipardi & Paterson, 2009 ).…”

Section: Discussionmentioning

confidence: 99%

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A

Calkins

Elledge

Mueller

et al. 2018

PeerJ

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Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.

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Section: Discussionmentioning

confidence: 99%

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A

Calkins

Elledge

Mueller

et al. 2018

PeerJ

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show abstract

“…RNA-dependent RNA polymerases (RdRPs) catalyze the formation of phosphodiester bonds between ribonucleotides in an RNA template-dependent fashion (Kenneth et al, 2008). More than 40 years ago, RdRP activity was detected in the tissue of numerous plants (Birchler et al, 2009;Hunter et al, 2016). RdRp is involved in the regeneration of dsRNA which is the key component in the gene silencing (Dalmay et al, 2000;Smith et al, 2004).…”

Section: Argonaute Proteinmentioning

confidence: 99%

Gene Silencing: The Mechanism to Down Regulate the Target Gene

Shreya¹,

Pandey²,

Bhandari³

2018

IJBSM

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Gene silencing is one of the most efficient and promising functional genomics tools which down regulates the expression of a gene in a very precise manner and has significant impact on crop improvement. Silencing of a target gene can be achieved at two levels; transcriptional and post-transcriptional stages. In broader sense, transcriptional gene silencing occurs through the repression of the process of transcription while the post transcriptional gene silencing can occur through the degradation of the mRNA. Small RNA molecules like siRNAs & miRNAs are key players which mediate the mechanism of gene silencing. These small RNA molecules are generated through Dicer digestion of the endogenous or exogenous dsRNA by which RISC (RNA induced gene silencing complex) is activated which inhibits expression of a gene. Apart from these small RNA molecules, viruses can also accomplish gene silencing which is known as VIGS (Virus induced gene silencing). VIGS consists of cloning and inserting plant endogenous gene sequences in recombinant viral vectors, which are then inoculated in plants, triggering RNA interference. Gene silencing as reverse genetic tool, has been exploited successfully to build up the resistant against biotic (insect/pest, nematodes, viruses etc.) and abiotic stresses (drought, salinity, frost etc.), and for the enhancement of yield and quality parameters. With the development of cutting edge biotechnological tools and techniques, it is now affordable to knock down/down regulate the expression of any undesirable gene. Ultimately this kind of technology can be important to global food security and sustainability.

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“…This would be particularly useful in eukaryotes since enzymes such as RNA-dependent RNA transcriptases are restricted to virions of RNA viruses and supposedly do not exist in the DNA world. This strong conventional wisdom, based on the lack of genes coding for RNAdependent RNA transcriptase in eukaryotes, however, does not exclude the possibility that insect tissues such as the moth pheromone gland retain some RNA-dependent RNA transcription activities via specific mechanisms similar to those described in vertebrates [63][64][65]. It could also well be that specific infectious viruses and/or symbiotic bacteria take control of RNA editing not only in invertebrate but also in vertebrate host-cells [66,67].…”

Section: Biotechnological Applications In Biomedicine and Transgenesismentioning

confidence: 99%

RNA Mutations: Source of Life

Picimbon¹

2014

Gene Technology

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In a recent study published in PLoS ONE, our group showed that the genes coding for the chemosensory proteins in silkworm moth Bombyx mori were subjected to RNA editing. This post-transcriptional process, described from bacteria to complex organisms as plants and humans, by changing nucleotide sequence enables to increase a repertoire of proteins from a single RNA. After a short introduction in which I remind the dogma initially established with the discovery of the double helix of DNA where a single gene encodes for a single protein, I present processes, RNA editing and alternative splicing, as two complementary modes for generating different proteins with different functions and regulation. Then, using intronless genes as example, I stress the role of RNA editing over alternative splicing. In the second part of the commentary, I discuss about RNA editing and alternative splicing in the course of evolution and I provide arguments supporting RNA editing as an early mechanism on earth that could have generated various proteins from few RNA. RNA mutations are proposed to be fuel for evolution of pheromone systems and even perhaps the mechanism that brought the original dormant RNA molecule to life. I propose RNA editing contributes source of life in an original RNA world. In the last part, I raise questions for new biotechnological prospects about cell molecular biology, RNA editing, genetic mutation, pathology, therapy, cloning and transgenesis.

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Ubiquitous RNA-dependent RNA polymerase and gene silencing

Abstract: The discovery of a ubiquitous RNA-dependent RNA polymerase raises new questions about small RNA silencing mechanisms.

Cited by 13 publications

References 21 publications

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A

Gene Silencing: The Mechanism to Down Regulate the Target Gene

RNA Mutations: Source of Life

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