DCL1

DCL1 is localized exclusively in the plant cell nucleus,^[3] together with the double-stranded RNA binding protein Hyponastic Leaves1 (HYL1), CTD-Phosphatase-Like1 (CPL1) and the zinc finger protein SERRATE (SE), form nuclear dicing bodies or D-bodies. In these membraneless organelles, pri-miRNAs are recognized and processes into pre-miRNAs and subsequently into mature miRNA duplexes, by the binding of additional proteins such as Constitutive Alterations in the Small RNAs Pathways9 (CARP9).^[3] In plants, DCL1 is responsible both for processing a primary miRNA to a pre-miRNA, and for then processing the pre-miRNA to a mature miRNA.^[4][5] In animals, the equivalents of these two steps are carried out by different proteins; First, pri-miRNA processing takes place in the nucleus by the ribonuclease Drosha as part of the Microprocessor complex. Second and finally processing to a mature miRNA takes place in the cytoplasm by Dicer to yield a mature miRNA.^[2]

In animals, hairpin-containing primary transcripts (pri-miRNAs) are cleaved by Drosha to generate precursor-miRNAs, a double strand palindromic structure typically call hairpin pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1), despite a similar domain architecture between both homologous enzymes.^[5] Recent single-particle cryo-electron microscopy structures of both complexes of dsRNA structures (pri-RNA and pre-miRNA) as ligand of Arabidopsis DCL1, in cleavage-competent state, suggest that PAZ domain plasticity allow its to get involved in pri-miRNA and pre-miRNA recognition, the possibility of an internal loop binding groove of this protein domain, which serves as an engine that transfers the substrate between two sequential cleavage events.^[5]

Although DCL1 is responsible for the majority of the miRNA processing in plants, most plants contain an additional set of DCLs proteins with related roles in RNA processing,^[6] the number of additional members of the same family depends on the plant family. For instance, in Brassicaceae there are 5 additional paralog genes to DLC1, DCL2, DCL3, DCL4 and two RNASE III-LIKE genes RTL1 and RTL2;^[7][8] Howeversome dicots such as Populus trichocarpa^[9] as well the majority of monocots plants have five to six DCLs, where DCL2 and DCL3 suffered an additional duplication into the genes DCL2a and DCL2. DCL3's duplication is monocot-specific, generating the genes DCL3a and DCL3b, also called DCL3 and DCL5 respectively.^[10][7]