Phylogenetic Distribution and Evolution of the Linked RNA-Binding and NOT1-Binding Domains in the Tristetraprolin Family of Tandem CCCH Zinc Finger Proteins

Abstract

In humans, the tristetraprolin or TTP family of CCCH tandem zinc finger (TZF) proteins comprises 3 members, encoded by the genes ZFP36, ZFP36L1, and ZFP36L2. These proteins have direct orthologues in essentially all vertebrates studied, with the exception of birds, which appear to lack a version of ZFP36. Additional family members are found in rodents, amphibians, and fish. In general, the encoded proteins contain 2 critical macromolecular interaction domains: the CCCH TZF domain, which is necessary for high-affinity binding to AUrich elements in mRNA; and an extreme C-terminal domain that, in the case of TTP, interacts with NOT1, the scaffold of a large multi-protein complex that contains deadenylases. TTP and its related proteins act by first binding to AU-rich elements in mRNA, and then recruiting deadenylases to the mRNA, where they can processively remove the adenosine residues from the poly(A) tail. Highly conserved TZF domains have been found in unicellular eukaryotes such as yeasts, and these domains can bind AU-rich elements that resemble those bound by the mammalian proteins. However, certain fungi appear to lack proteins with intact TZF domains, and the TTP family proteins that are expressed in other fungi often lack the characteristic C-terminal NOT1 binding domain found in the mammalian proteins. For these reasons, we investigated the phylogenetic distribution of the relevant sequences in available databases. Both domains are present in family member proteins from most lineages of eukaryotes, suggesting their mutual presence in a common ancestor. However, the vertebrate type of NOT1-binding domain is missing in most fungi, and the TZF domain itself has disappeared or degenerated in recently evolved fungi. Nonetheless, both domains are present together in the proteins from several unicellular eukaryotes, including at least 1 fungus, and they seem to have remained together during the evolution of metazoans.

The Drosophila Tis11 Protein and Its Effects on mRNA Expression in Flies

“…Whether this is the optimum binding sequence for the fly protein remains to be determined. The Tis11 protein also caused the deadenylation and destabilization of target transcripts co-expressed in 293 cells in a manner similar to its mammalian counterparts, an effect that was at least partially abrogated by removal of a C-terminal, highly conserved sequence that, in human TTP, forms a binding site for the NOT1 protein and presumably its associated multiprotein complexes (19,33), which include multiple deadenylases. Importantly, the same C-terminal sequence does not appear to contain the Drosophila nuclear export sequence (48), in contrast to what has been seen with some TTP family members in mammals (7,47), thus allowing these two functional domains of the protein to be experimentally separable.…”

“…Proteins with similar TZF domains have been identified in other eukaryotes, including plants, protists, nematodes, yeasts, and insects (19). At least one of the two such proteins expressed in Saccharomyces cerevisiae affects the stability of a collection of transcripts involved in regulating iron metabolism, apparently also by binding to ARE elements that are similar to their mammalian counterparts (20,21).…”

Functional Equivalence of an Evolutionarily Conserved RNA Binding Module

“…2 is a well characterized CCCH tandem zinc finger (TZF) domain RNA binding protein that can promote the decay of target mRNAs after binding to AU-rich elements (AREs) found in their 3ЈUTRs (1)(2)(3). TTP family members contain two highly conserved CCCH zinc fingers of the CX 8 CX 5 CX 3 H type that are separated by an 18-amino acid linker.…”

Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe–2S cluster

“…1). As a class, these proteins are predicted to be involved in RNA regulation; however, the function(s) of most of these proteins have not yet been established (1,2,10,11).…”