Phylogenetic analysis of the endoribonuclease Dicer family

Abstract

Dicers are proteins of the ribonuclease III family with the ability to process dsRNA, involved in regulation of gene expression at the post-transcriptional level. Dicers are conserved from basal metazoans to higher metazoans and contain a number of functional domains that interact with dsRNA. The completed genome sequences of over 34 invertebrate species allowed us to systematically investigate Dicer genes over a diverse range of phyla. The majority of invertebrate Dicers clearly fell into the Dicer1 or Dicer2 subfamilies. Most nematodes possessed only one Dicer gene, a member of the Dicer1 subfamily, whereas two Dicer genes (Dicer1 and Dicer2) were present in all platyhelminths surveyed. Analysis of the key domains showed that a 5' pocket was conserved across members of the Dicer1 subfamily, with the exception of the nematode Bursaphelenchus xylophilus. Interestingly, Nematostella vectensis DicerB grouped into Dicer2 subfamily harbored a 5' pocket, which is commonly present in Dicer1. Similarly, the 3' pocket was also found to be conserved in all Dicer proteins with the exceptions of Schmidtea mediterranea Dicer2 and Trichoplax adherens Dicer A. The loss of catalytic residues in the RNase III domain was noted in platyhelminths and cnidarians, and the 'ball' and 'socket' junction between two RNase III domains in platyhelminth Dicers was different from the canonical junction, suggesting the possibility of different conformations. The present data suggest that Dicers might have duplicated and diversified independently, and have evolved for various functions in invertebrates.

Figure 1. A maximum likelihood tree of invertebrate Dicers.

The tree was constructed using maximum likelihood method. Two number sets, 1.00/1.00/0.99 and 0.87/0.96/0.28, at the nodes were SH-like approximate likelihood ratio, Bayes likelihood and bootstrap values, respectively.

Figure 2. The key residues critical for recognition of 3′ and 5′ pockets.

The key residues involved in 3′ pocket (a) and 5′ pocket recognition (b) were indicated using asterisks in red. The Dicers in which a PAZ domain was not identified using Pfam and SMART are highlighted in grey (a). Gaps are filled using question marks (?).

Figure 3. The key residues of RNase III domains.

Catalytic residues are marked by red asterisks and gaps filled using question marks (?).

Figure 4. The residues of “ball and socket” junction.

The ‘Ball’ residue within RNaseIII a domain is marked by a black asterisk, and the ‘socket’ residues within RNase III b domain are marked by red asterisks. Gaps are filled using question marks (?).