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Comparative Study
. 2002 Sep 3;12(17):1484-95.
doi: 10.1016/s0960-9822(02)01017-5.

CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana

Wonkeun Park  1 , Junjie Li, Rentao Song, Joachim Messing, Xuemei Chen
Affiliations
Comparative Study

CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana

Wonkeun Park et al. Curr Biol. .

Abstract

Background: In metazoans, microRNAs, or miRNAs, constitute a growing family of small regulatory RNAs that are usually 19-25 nucleotides in length. They are processed from longer precursor RNAs that fold into stem-loop structures by the ribonuclease Dicer and are thought to regulate gene expression by base pairing with RNAs of protein-coding genes. In Arabidopsis thaliana, mutations in CARPEL FACTORY (CAF), a Dicer homolog, and those in a novel gene, HEN1, result in similar, multifaceted developmental defects, suggesting a similar function of the two genes, possibly in miRNA metabolism.

Results: To investigate the potential functions of CAF and HEN1 in miRNA metabolism, we aimed to isolate miRNAs from Arabidopsis and examine their accumulation during plant development in wild-type plants and in hen1-1 and caf-1 mutant plants. We have isolated 11 miRNAs, some of which have potential homologs in tobacco, rice, and maize. The putative precursors of these miRNAs have the capacity to form stable stem-loop structures. The accumulation of these miRNAs appears to be spatially or temporally controlled in plant development, and their abundance is greatly reduced in caf-1 and hen1-1 mutants. HEN1 homologs are found in bacterial, fungal, and metazoan genomes.

Conclusions: miRNAs are present in both plant and animal kingdoms. An evolutionarily conserved mechanism involving a protein, known as Dicer in animals and CAF in Arabidopsis, operates in miRNA metabolism. HEN1 is a new player in miRNA accumulation in Arabidopsis, and HEN1 homologs in metazoans may have a similar function. The developmental defects associated with caf-1 and hen1-1 mutations and the patterns of miRNA accumulation suggest that miRNAs play fundamental roles in plant development.

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Figures

Figure 1
Figure 1. miRNA Precursors and Complementarity of miRNAs to mRNAs
(A) Stem-loop structures of putative miRNA precursors. Genomic sequences (62–102 nt) containing the miRNAs were used for RNA secondary structure prediction with the m-fold program (see the Experimental Procedures). The structures shown are the outputs from m-fold without manual modification. The miRNA sequences are underlined. Two miRNA sequences in the same precursors are differentiated by colors (one in black and the other in gray). A hyphen indicates the absence of nucleotides. For MIR167, MIR172, MIR175, MIR176, MIR177, and MIR179, identical miRNA sequences were found at multiple genomic loci (as indicated by numbers after dashes; MIR167a-2 not shown). For MIR167, MIR172, MIR175, and MIR179, the putative precursors of the different identical miRNA copies were related but were not identical in sequence, but they were able to form stem-loop structures. For MIR176 and MIR177, which were found in the same precursor, the precursor sequences of the identical miRNA copies at different genomic loci were identical with one exception (MIR176-4 and MIR177-4). (B) Complementarity of selected miRNAs to their putative target mRNAs.
Figure 2
Figure 2. Spatial and Temporal Patterns of miRNA Accumulation as Revealed by RNA-Filter Hybridization with Antisense Oligonucleotide Probes Complementary to MIR Sequences
MIR163 and MIR167 showed distinct temporal patterns of expression during development (RNAs from aerial portions of plants were used). The numbers of days were calculated from the time stratified seeds were transferred to growth chambers. MIR172, MIR173, MIR167, and MIR178 were expressed preferentially in some organs. The MIR172 transcript was present in inflorescences, leaves, and stems at similar levels but was barely detectable in siliques and was not detectable in roots. The MIR173 transcript was present in inflorescences and leaves but was barely detectable in roots. The MIR167 transcript was most abundant in inflorescences. The mature MIR178 transcript (20 nt) was only present in inflorescences, although the probe also detected two bands at 80–100 nt in all three tissues. In, inflorescences; L, leaves; R, roots; St, stems; and Si, siliques. The sense probe for MIR173 did not detect any signals. 5S rRNA was used as an internal control.
Figure 3
Figure 3. Requirement for CAF and HEN1 in miRNA Accumulation
The accumulation of mature transcripts corresponding to MIR173, 163, 167, 159, 177, and 176 was undetectable in hen1-1 and caf-1 or was greatly reduced compared to wild-type. Note that MIR177 and MIR176 antisense probes detected an approximately 70-nt signal in all genotypes but detected a 27-nt signal only in wild-type. Lower exposures of the precursor-sized transcripts are shown on the right. The MIR178 panel is meant to show that the two transcripts of intermediate size (arrowheads) are not present in either hen1-1 or caf-1. The mature 20-nt transcript was not visible at this exposure. However, it was visibly present in wild-type but was absent from hen1-1 or caf-1 upon longer exposure. RNAs from the entire aerial portions of 1 month-old plants were used for the MIR173, 163, 167, and 159 hybridization, whereas RNAs from inflorescences were used for the MIR177, MIR176, and MIR178 hybridization. MW, molecular weight standards. Vertical arrows in MIR167 and MIR159 panels indicate signals from maize seedlings.
Figure 4
Figure 4. Potential HEN1 Homologs
(A) A Clustal W alignment of a conserved domain shared among HEN1 homologs (predicted proteins from cDNAs or from genome annotation) from a few species. The overall amino acid similarity within this domain among these proteins is 40%–50%. Positions at which at least five amino acids are identical are shown in a darker gray color, whereas positions at which at least five amino acids are similar are shown in a lighter gray color. Hs, Homo sapiens; Mm, Mus musculus; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans; Sp, Schizosaccharomyces pombe; and Sc, Streptomyces coelicolor. Nostoc, Nostoc sp. PCC 7120, a cyanobacterium. GenBank accession numbers of the proteins are shown after the species abbreviation. (B) Diagrams of HEN1 and potential HEN1 homologs, showing the positions of the conserved domain (hatched boxes) in these proteins.
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