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RNAi Suppression and Its Application

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Book cover RNA Technologies and Their Applications

Part of the book series: RNA Technologies ((RNATECHN))

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Abstract

In eukaryotes, RNA interference (RNAi) is a gene silencing mechanism mediated by small RNAs (sRNAs), currently classified as small interfering RNA (siRNA), microRNA (miRNA), and piwi-interacting RNA (piRNA). These small RNAs are produced in Dicer (a ribonuclease III enzyme)-dependent (siRNA and miRNA) or Dicer-independent (piRNA) manner and are effected by a group of Argonaut (AGO) proteins. These small RNAs mediate silencing of target genes with complementary sequence at transcriptional or posttranscriptional level thereby to control a wide variety of biological functions. In worms and plants, RNA-dependent RNA polymerases (RdRPs) amplify RNAi by converting AGO cleavage products into dsRNAs for the generation of secondary siRNAs. One of the well characterized functions of RNAi is antiviral, which has been shown to serve as major viral innate immunity in fungi, plants, and invertebrates. Typically, RNAi-directed viral immunity (RDVI) is initiated with Dicer processing of viral dsRNAs, usually the replication intermediates, into siRNAs. These virus-derived siRNAs (viRNA) will then be used as sequence guide for target viral RNA destruction. Host-encoded miRNAs also contribute to viral control in mammal or bacterial control in plant. As a counterdefensive mechanism, many viruses and some bacteria are found to encode RNAi suppressors, previously known as pathogenicity factors. These RNAi antagonists target key components of RNAi for suppression, which eventually leads to defects in viRNA biogenesis or function. Since transgene expression in plants and invertebrates is often targeted by RNAi for suppression but can be reversed by various RNAi suppressors, codelivery of a VSR has been used to facilitate the isolation and biochemical characterization of a broad range of proteins of interests. RNAi suppressors can also be used as genetic tool for the study of biological functions controlled by certain class of endogenous sRNA (siRNA or miRNA). This is because, when expressed as transgenes, some RNAi suppressors can specifically target and interfere with the biogenesis or function of certain class of endogenous sRNA but not the other.

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Abbreviations

RNAi:

RNA interference

sRNA:

small RNA

siRNA:

small interfering RNA

miRNA:

microRNA

piRNA:

PIWI-interacting RNA

RdRP:

RNA-dependent RNA polymerase

AGO:

Argonaut

viRNA:

virus-derived siRNA

dsRNA:

double-stranded RNA

C. elegans :

Caenorhabditis elegans

PTGS:

posttranscriptional gene silencing

RISC:

RNA-induced silencing complex

S. pombe :

Schizosaccharomyces pombe

endo-siRNA:

endogenous siRNA

RDVI:

RNAi-directed viral immunity

TEV:

Tobacco etch virus

PVY:

Potato virus Y

CP:

coat protein

N. benthamiana :

Nicotiana benthamiana

PDS:

phytoene desaturase

N. clevelandii :

Nicotiana clevelandii

PVX:

Potato virus X

VSR:

viral suppressor of RNAi

HC-Pro:

Helper component-proteinase

CMV:

Cucumber mosaic virus

FHV:

Flock house virus

PFV:

Primate foamy virus

CTV:

Citrus tristeza virus

GFP:

green fluorescent protein

TYLCV:

Tomato yellow leaf curl geminivirus

TBSV:

Tomato bushy stunt virus

CNV:

Cucumber necrosis virus

CRV:

Cymbidium ringspot virus

SPCSV:

Sweet potato chlorotic stunt virus

ssRNA:

single-stranded RNA

SPFMV:

Sweet potato feathery mottle virus

TMV:

Tobacco mosaic virus

ORMV:

Oilseed rape mosaic tobamovirus

TCV:

Turnip crinkle virus

BWYV:

Beet western yellows virus

SKP1:

S-phase kinase-related protein 1

SCF:

Skp1-Cul1/Cdc53,-F-box protein

SYLV:

Sugarcane yellow leaf virus

shRNA:

short hairpin RNA

A. tumefaciens :

Agrobacterium tumefaciens

T-DNA:

transfer DNA

P. syringae :

Pseudomonas syringae

PAMP:

pathogen-associated molecular pattern

rgs-CaM:

regulator of gene silencing-calmodulin-like protein

SDN1:

small RNA degrading nuclease 1

eri-1 :

enhanced RNAi-1

CHS:

chalcone synthase

aa:

amino acids

nt:

nucleotide

bp:

base pair

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Authors and Affiliations

  1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA

    Xiaoping Yi & Rui Lu

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  1. Xiaoping Yi
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  2. Rui Lu
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Correspondence to Rui Lu .

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Editors and Affiliations

  1. Inst. Chemie und Biochemie, FU Berlin, Thielallee 63, Berlin, 14195, Germany

    Volker A. Erdmann

  2. Inst. Bioorganic Chemistry, PAN Poznan, ul. Z. Noskowskiego 12/14, Poznan, 61-704, Poland

    Jan Barciszewski

Appendix

Appendix

Table 1 Viral suppressors of RNAi
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Yi, X., Lu, R. (2010). RNAi Suppression and Its Application. In: Erdmann, V., Barciszewski, J. (eds) RNA Technologies and Their Applications. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-12168-5_3

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