Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans

Abstract

The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX₂CX₄HX₄C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX₂CX₄HX₄C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.

Keywords: Arabidopsis; Human; RNA metabolism; Yeast; ZCCHC; Zinc-knuckle.

Fig. 1

Partial three-dimensional structure of the lentiviral EIAV nucleocapsid protein NCp11. The three-dimensional structure of a peptide of 37 amino acids (QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS) corresponding to residues 22–58 from the lentiviral EIAV nucleocapsid protein NCp11 (Protein Data Bank identification code for the partial structure: 2BL6) is shown. This peptide contains two ZCCHCs of the CX₂CX₃GHX₄C type, which are underlined in the sequence above, and is complexed with zinc (red spheres). Only the relevant C and H residues of the ZCCHCs are highlighted. The structure shown in this figure was determined by two-dimensional hydrogen isotope nuclear magnetic resonance spectroscopy, as previously described [10]. We obtained this image using the Visual Molecular Dynamics molecular visualization program (https://www.ks.uiuc.edu/Research/vmd/) [11]

Fig. 2

Schematic representation of the structures of yeast ZCCHC-containing factors, with indication of their putative Arabidopsis and human orthologs. Schemes have been drawn to scale. Motifs, domains, and low-complexity regions are represented by symbols, and were obtained from the UniProtKB database and publications. The Arabidopsis Genome Initiative [19] gene code is shown for Arabidopsis proteins. In cases of several paralogs, the asterisk indicates which protein is represented

Fig. 3

Schematic representation of the structure of human ZCCHC-containing factors with indication of their putative Arabidopsis orthologs. Other details are as described in the legend of Fig. 2

Fig. 4

Schematic representation of the structure of Arabidopsis ZCCHC-containing factors. Other details are as described in the legend of Fig. 2

Fig. 5

Logos representing normalized amino acid frequencies obtained from the multiple alignment of the 18 amino acids that constitute the ZCCHCs of yeast, human, and Arabidopsis proteins. Sequences were taken grouped by species (a–c) or all together (d) to generate the corresponding logos from multiple alignments, using the WebLogo version 3 software (https://weblogo.threeplusone.com/create.cgi). Uncertain and retrotransposon-related factors were not taken into account, and the resulting 198 sequences were aligned, all together or grouped by species

Fig. 6

Phylogeny of the ZCCHCs of yeast, Arabidopsis, and human proteins. The unrooted tree was obtained with the MEGA X software (https://www.megasoftware.net/) from the alignment of the 18 amino acids of the 198 ZCCHCs found in yeast, human, and Arabidopsis proteins. The Neighbor-Joining algorithm was used, with bootstrap values from 1000 replicates. The position of a given ZCCHC in proteins with more than one of these motifs is indicated in brackets (1, 2, and 3 indicate first, second, and third, respectively, within the protein sequence, from its N- to its C-terminus). Clades highlighted in yellow or blue include ZCCHCs from proteins with a single ZCCHC that are known to be orthologs, or without a known functional relationship, respectively