Small
RNAs
in Plants
Authors: Vazquez Franck 
Published: March 2009

Abstract

Small
ribonucleic acids
(smRNAs), 20–40 nucleotides in length, are the core components of basic eukaryotic regulatory processes collectively termed as RNA silencing. smRNAs afford sequence specificity to these processes, guiding effector proteins to
deoxyribonucleic acid
(DNA) or RNA targets through complementary base pairing. These effectors act either by cleaving cognate RNAs, blocking their productive translation or inducing the methylation of specific DNA targets. Plant smRNAs are produced from longer double‐stranded RNAs by a family of RNase III enzymes called DICER‐LIKE proteins and guide effector proteins of the ARGONAUTE family. Several endogenous smRNA classes are produced by distinct biosynthetic pathways and have critical functions in development, stress responses or genome stability. Moreover, the plant smRNA machinery contributes to defence against viruses. The proteins involved in these pathways are members of conserved protein families; thus, redundancy and compensation between family members create a complex network of smRNA regulation.

Key Concepts

Features of smRNAs: Plant smRNAs are 20–40‐nt long RNAs produced from longer double‐stranded (ds) RNA precursors. The smRNA duplex intermediates have 2‐nt overhangs at their 3′ ends. These products of DICER‐LIKE proteins also have hydroxyl groups at 3′ ends and phosphate groups at 5′ ends. The smRNA methyltransferase HEN1 subsequently modifies the 2′ hydroxyl group of the 3′ most distal ribose of each strand to make stable smRNA duplexes with 2′
O
‐methyl groups at 3′ ends.

Two smRNA categories in plants: Although all plant smRNAs have similar chemical attributes, they are grouped in two categories based on their origin. smRNAs produced from dsRNAs composed of two distinct RNA strands are called small interfering RNAs (siRNAs), whereas smRNAs produced from the foldback dsRNA regions of a single RNA strand are called microRNAs (miRNAs).

smRNAs guide effector proteins to cognate targets: smRNAs guide ARGONAUTE (AGO) effector proteins to cognate DNA or RNA targets. In plants, smRNAs are loaded into different AGO proteins depending, at least in part, on the identity of the first 5′ nucleotide of each smRNA. The 5′ nucleotide of the selected guide strand interacts with the MID domain of the protein and the 3′ nucleotide is incorporated into a binding pocket of the PAZ domain. As in animals, the passenger strand of plant smRNA duplexes is certainly removed by cleavage in the centre of the paired smRNA by the catalytic, RNase H activity located in the PIWI domain. The selected smRNA strand guides an AGO effector protein to cognate DNA or RNA targets through antiparallel complementary base pairing.

AGO effector proteins exert various functions: ARGONAUTE effector proteins act on nucleic acid targets in different ways: (i) by cleaving mRNAs, (ii) by blocking the productive translation of mRNAs or (iii) by inducing DNA methylation of specific targets.

Trans
‐acting siRNAs are a class of plant‐specific siRNAs: Biogenesis of
trans
‐acting siRNAs (ta‐siRNAs), a class of endogenous, plant‐specific siRNAs, is initiated by smRNA‐guided cleavage or recognition of precursor transcripts at one or two distinct sites. Truncated RNA precursors serve as a template for the RNA‐dependent RNA polymerase RDR6, which synthesizes a complementary RNA strand. The resulting long dsRNA is processed by DCL4 in 21‐nt increments. Each 21‐nt siRNA regulates the expression of specific genes by guiding cleavage of complementary mRNAs. This can initiate production of additional ta‐siRNAs from the cleaved mRNA target; amplification cascade of ta‐siRNAs can regulate expression of genes with sequences unrelated to the initial smRNA trigger.

smRNAs versus viruses: The smRNA machinery of plants, which has dedicated functions in development, is also central to the co‐evolutionary race between plants and viruses. smRNA machinery contributes to plant defence against viruses by producing virus‐derived siRNAs that block virus proliferation. As a counter defence, viruses have evolved suppressor proteins that block smRNA machinery at specific steps.