Evolution of Plant MicroRNAs

Dalmay Tamas, University of East Anglia, Norwich, UK

Published online: April 2012

DOI: 10.1002/9780470015902.a0023756

Microribonucleic acids (miRNAs) are small noncoding regulatory molecules encoded in the genome and generated through several processing steps. They recognise specific messenger RNAs and regulate their expression by cleavage or by translational inhibition. MiRNAs were only discovered approximately 10 years ago but it quickly became evident that they play an important role in development and stress responses. Initially it was thought that all miRNAs are conserved in plants because the technology only allowed to sequence the most abundant miRNAs. However, the development of next generation sequencing technologies allowed researchers to generate millions of sequencing reads in a sample, which resulted in the identification of the less abundant miRNAs. Analysis of large‐scale sequencing data revealed that the number of nonconserved miRNAs is much larger than previously thought. This review focuses on the evolution of plant MIRNA genes from protein‐coding genes by describing the difference between conserved and nonconserved MIRNA families.

Key Concepts:

  • MicroRNAs are small noncoding regulatory molecules.
  • Primary miRNA transcripts are folded into a stem–loop secondary structure, which is cleaved twice by DICER‐LIKE1 releasing the microRNA duplex.
  • One strand of the microRNA duplex is incorporated into an ARGONAUTE complex and guides the complex to specific mRNAs.
  • The ARGONAUTE complex usually cleaves the target mRNA but it also suppresses the translation of noncleaved mRNAs.
  • Some MIRNA genes are ancient and conserved in all embryophytes but there are nonconserved MIRNA families that are only in angiosperms or specific to monocots or dicots. A large number of MIRNA families are even divergent between dicot families.
  • New MIRNA genes can potentially evolve from any inverted repeats but the most evidence exists for generation from inverse duplication of protein‐coding genes followed by deletions and mutations.
  • Indirect evidence suggests rapid birth and death of MIRNA genes: approximately 1–3 MIRNA genes per million years in the Arabidopsis lineage.
  • Nonconserved MIRNA genes are weakly expressed, imprecisely processed, show uniform nucleotide divergence and many lack targets, suggesting that they are evolving neutrally.
  • Nonconserved MIRNA genes could be a source of ‘regulatory diversity’, which can be selected for if they acquire target genes and that is advantageous for the plant, maybe in a new environment.

Keywords: microRNA; evolution; small noncoding RNA; gene expression regulation; siRNA

Figure 1. Biogenesis of miRNAs. MIRNA genes are transcribed by RNA polymerase II in the nucleus where the pri‐miRNA is capped and polyadenylated. DCL1, with the aid of the cap binding complex (CBP20 and ABH1/CBP80), HYL1, DDL and SE, recognises the characteristic hairpin structure and trims off the flanking regions. The resulting pre‐miRNA is cleaved again by DCL1 releasing the miRNA duplex. The 3′ end of the duplex is methylated by HEN1 and the duplex moves to the cytoplasm where one of the strands is taken up by RISC. MiRNA guides RISC to target mRNAs, which are cleaved by AGO1 (or other AGO family members).
Figure 2. Generation of new MIRNA genes. The ancestral protein‐coding gene is inverse duplicated to generate a long inverted repeat. Since the protein is expressed from the other copy, deletions and mutations can occur in the inverted repeat. The older the inverted duplication event, the more deletions/mutations can be accumulated. There are examples for the different stages, such as the MIR822 and MIR839 loci, which represent a transition between siRNA and miRNA producing loci, young MIRNA genes, where the stem sequences outside the miRNA α duplexes are still similar to the ancestral genes and finally the conserved MIRNA genes, where only the miRNA duplex resembles to the target gene. The promoter sequences may also drift. For example miR395 is expressed mainly in the phloem companion cells whereas one of its targets (SULTR2;1) is mainly expressed in the xylem parenchyma cells (Kawashima et al., 2009).
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Related Sub-Topics:

Molecular Evolution | RNA Structure and Function | Evolution of Coding and Functional Modules | Plant Evolution | Plant Genetics and Molecular Biology
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Article Title: Evolution of Plant MicroRNAs
 
How to Cite close
Tamas, Dalmay(Apr 2012) Evolution of Plant MicroRNAs. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023756]