Cleavage of RNA Hairpins Mediated by a Developmentally Regulated CCCH Zinc Finger Protein

Abstract

Control of RNA turnover is a major, but poorly understood, aspect of gene regulation. In multicellular organisms, progress toward dissecting RNA turnover pathways has been made by defining some cis-acting sequences that function as either regulatory or cleavage targets (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993). However, the identification of genes encoding proteins that regulate or cleave target RNAs has been elusive (C. A. Beelman and R. Parker, Cell 81:79-183, 1995); this gap in knowledge has made it difficult to identify additional components of RNA turnover pathways. We have utilized a modified expression cloning strategy to identify a developmentally regulated gene from Drosophila melanogaster that encodes a RNase that we refer to as Clipper (CLP). Significant sequence matches to open reading frames encoding unknown functions identified from the Caenorhabditis elegans and Saccharomyces cerevisiae genome sequencing projects suggest that all three proteins are members of a new protein family conserved from lower eukaryotes to invertebrates. We demonstrate that a member of this new protein family specifically cleaves RNA hairpins and that this activity resides in a region containing five copies of a previously uncharacterized CCCH zinc finger motif. CLP's endoribonucleolytic activity is distinct from that associated with RNase A (P. Blackburn and S. Moore, p. 317-433, in P. D. Boyer, ed., The Enzymes, vol. XV, part B, 1982) and is unrelated to RNase III processing of rRNAs and tRNAs (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993, and S. A. Elela, H. Igel, and M. Ares, Cell 85:115-124, 1995). Our results suggest that CLP may function directly in RNA metabolism.

Protein factors in pre-mRNA 3′-end processing

“…Clipper contains five CCCH zinc finger motifs and two zinc knuckle motifs, and the high sequence conservation covers the five zinc finger motifs. This region of clipper has endoribonuclease activity and cleaves RNA hairpins [130]. Consequently, it has been suggested that CPSF-30 might be the endoribonuclease responsible for the cleavage reaction [131].…”

C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival

“…This domain is found in a subset of zinc-finger family proteins; its consensus sequence corresponds to C-X 8-10 -C-X 5 -C-X 3 -H, where X refers to any amino acid (Varnum et al 1989). CCCH zinc fingers were first described in the mouse TIS11 protein, where they are responsible for nucleic-acid binding (Varnum et al 1989;DuBois et al 1990;Bai and Tolias 1996). Mammalian TIS11-like zinc-finger-containing proteins have been shown to function either as transcription factors or RNA-binding proteins (Taylor et al 1996;Worthington et al 2002).…”

Overexpression of AtSZF2 from Arabidopsis Showed Enhanced Tolerance to Salt Stress in Soybean

“…The goal of our study was to investigate the potential of the salt stress tolerant candidate gene in major crop such as soybean. Among many candidate genes, CCCH-type zinc finger protein which has shown to be associated with RNA metabolism (Bai and Tolias 1996;Carballo et al 1998;Lai et al 2006;Hurt et al 2009) and known to be involved in abiotic and biotic stresses could be a good gene source for salt stress tolerance. In previous report, GHZFP1, a CCCH-type zinc finger protein from cotton, was found to enhance the tolerance of salt stress ).…”

“…CCCH-type zinc finger proteins role as DNA-binding transcription factors. However, most of CCCH-type zinc finger proteins have shown to be associated with RNA metabolism by directly binding to RNA targets (Bai and Tolias 1996;Carballo et al 1998;Lai et al 2006;Hurt et al 2009). In addition, some CCCH zinc finger proteins are involved in abiotic and biotic stresses.…”