Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome

Abstract

Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by cysteines and histidines. The zinc finger domain defines one of the largest protein superfamilies in mammalian genomes;46 different conserved zinc finger domains are listed in InterPro (http://www.ebi.ac.uk/InterPro). Zinc finger proteins can bind to DNA, RNA, other proteins, or lipids as a modular domain in combination with other conserved structures. Owing to this combinatorial diversity, different members of zinc finger superfamilies contribute to many distinct cellular processes, including transcriptional regulation, mRNA stability and processing, and protein turnover. Accordingly, mutations of zinc finger genes lead to aberrations in a broad spectrum of biological processes such as development, differentiation, apoptosis, and immunological responses. This study provides the first comprehensive classification of zinc finger proteins in a mammalian transcriptome. Specific detailed analysis of the SP/Krüppel-like factors and the E3 ubiquitin-ligase RING-H2 families illustrates the importance of such an analysis for a more comprehensive functional classification of large protein families. We describe the characterization of a new family of C2H2 zinc-finger-containing proteins and a new conserved domain characteristic of this family, the identification and characterization of Sp8, a new member of the Sp family of transcriptional regulators, and the identification of five new RING-H2 proteins.

Figure 1

(A) Unrootedphylogeny among the Fzf family. The entire mouse and human protein sequences of the Fzf family (Table 3) were aligned and subjected to Neighbor Joining with 1000 bootstrap analysis. (B) Protein sequence alignment of the six C2H2 core zinc finger domains of the FZF proteins. The secondary structure of the six fingers is shown above the alignment; the domain consensus is shown below the alignment, the FFAB domain is indicated by the black bar. (C) Domain architecture of the mouse and human Fzf proteins. Protein structural representation was generated using Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de).

Figure 2

(A) Unrootedphylogeny among the Sp/Krüppel-like factors. The entire mouse and human protein sequences of the Sp/Krüppel-like factors (Table 4) were aligned and subjected to Neighbor Joining with 1000 bootstrap analysis. (B) Magnification of the Sp branch of the phylogeny tree and alignment of the zinc finger region of the Sp proteins. The secondary structure of the six fingers is shown above the alignment; the domain consensus is shown below the alignment. (C) Mouse and human Sp protein domain architecture. Those highlighted in red are the newly described proteins.

Figure 3

(A) Unrootedphylogeny of the cluster 7. The entire mouse and human protein sequences of the RING-H2 proteins (Table 5) were aligned and subjected to Neighbor Joining with 1000 bootstrap analysis. Domain architecture of the RING-H2 proteins is also shown in the picture. (B) RING-H2 zinc finger alignment of the C2H2 zinc finger consensus sequence is shown below the alignment. In red are highlighted the proteins described for the first time in this study.