Diversification of Polynucleotide Kinase Clp1 Family Proteins and Their Possible Origins in Eukaryotic Evolution

The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5' end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species and identified a group of protist proteins that we consider to be the evolutionary origin of Clp1 family proteins. First, we detected an average of 4.2 Clp1 family genes in members of in the protist phylum Euglenozoa, arising from gene duplication. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. In a phylogenetic analysis of the PNK domain, Tb-Clp1-t2 mapped to the earliest position on the tree. Interestingly, Tb-Clp1-t1, for which no PNK activity was detected, was located on the phylogenetic tree near fungal Saccharomyces cerevisiae Clp1, which also lacks PNK activity. The analysis also revealed that in the higher eukaryotes, such as humans and plants, the Clp1 proteins diversified with the creation of isoforms by alternative splicing.