Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability

Abstract

Background: The emergence of eukaryotes was characterized by the expansion and diversification of several ancient RNA-binding domains and the apparent de novo innovation of new RNA-binding domains. The identification of these RNA-binding domains may throw light on the emergence of eukaryote-specific systems of RNA metabolism.

Results: Using sensitive sequence profile searches, homology-based fold recognition and sequence-structure superpositions, we identified novel, divergent versions of the Sm domain in the Scd6p family of proteins. This family of Sm-related domains shares certain features of conventional Sm domains, which are required for binding RNA, in addition to possessing some unique conserved features. We also show that these proteins contain a second previously uncharacterized C-terminal domain, termed the FDF domain (after a conserved sequence motif in this domain). The FDF domain is also found in the fungal Dcp3p-like and the animal FLJ22128-like proteins, where it fused to a C-terminal domain of the YjeF-N domain family. In addition to the FDF domains, the FLJ22128-like proteins contain yet another divergent version of the Sm domain at their extreme N-terminus. We show that the YjeF-N domains represent a novel version of the Rossmann fold that has acquired a set of catalytic residues and structural features that distinguish them from the conventional dehydrogenases.

Conclusions: Several lines of contextual information suggest that the Scd6p family and the Dcp3p-like proteins are conserved components of the eukaryotic RNA metabolism system. We propose that the novel domains reported here, namely the divergent versions of the Sm domain and the FDF domain may mediate specific RNA-protein and protein-protein interactions in cytoplasmic ribonucleoprotein complexes. More specifically, the protein complexes containing Sm-like domains of the Scd6p family are predicted to regulate the stability of mRNA encoding proteins involved in cell cycle progression and vesicular assembly. The Dcp3p and FLJ22128 proteins may localize to the cytoplasmic processing bodies and possibly catalyze a specific processing step in the decapping pathway. The explosive diversification of Sm domains appears to have played a role in the emergence of several uniquely eukaryotic ribonucleoprotein complexes, including those involved in decapping and mRNA stability.

Figure 1

Multiple alignment of the Scd6p family with representatives of other Sm domains. Multiple sequence alignment of the Sm domain of the Scd6p family was constructed using T-Coffee after parsing high-scoring pairs from PSI-BLAST search results. The secondary structure from the crystal structures is shown above the alignment with E representing a strand. The 90% consensus shown below the alignment was derived using the following amino acid classes: hydrophobic (h: ALICVMYFW, yellow shading) and its aliphatic subset (l: ALIV, yellow shading); small (s: ACDGNPSTV, green); and polar (p: CDEHKNQRST, blue). The limits of the domains are indicated by the residue positions, on each end of the sequence. A '*' denotes the end of the protein sequence. The numbers within the alignment are non-conserved inserts that have not been shown. The conserved GTEx+ motif of the scd6p family is shaded red. The residues involved in RNA binding are denoted by '#'s on the top of the aligment. The conserved C-terminal extension of the Scd6p family is shown in a box. The sequences are denoted by their gene name followed by the species abbreviation and GenBank Identifier (gi). The species abbreviations are: Af – Archaeoglobus fulgidus; Ec – Escherichia coli; Sau – Staphylococcus aureus; Afum – Aspergillus fumigatus; At – Arabidopsis thaliana; Cbr – Caenorhabditis briggsae; Ce – Caenorhabditis elegans; Dm – Drosophila melanogaster; Hs – Homo sapiens; Nc – Neurospora crassa; Pf-Plasmodium falciparum; Pwal – Pleurodeles waltl; Sc – Saccharomyces cerevisiae; and Sp – Schizosaccharomyces pombe.

Figure 2

Domain architectures of Scd6p and FDF domain proteins. The domain architectures of the proteins containing the Scd6p, FDF and Yjef-N domains are shown. The representative protein name, organism and the phyletic pattern are given below the protein. The globular domains are drawn approximately to scale.

Figure 3

A multiple alignment of the FDF domain. Multiple sequence alignment of the FDF domain was constructed as described in Figure 1. In the secondary structure H represents a helix. The species abbreviations are as given in Figure 1 and additionally Ani – Aspergillus nidulans; Gze – Gibberella zeae; Mgr – Magnaporthe grisea.

Figure 4

A Cartoon representation of the YjeF-N type Rossmann fold and its conserved features. The cartoon representation of the YjeF-N-type Rossmann fold domain was constructed using the crystal structure of the yeast YjeF-N domain containing protein (PDB: 1JZT). The N terminal helices are named N1 and N2, and the core helices and strands are named H1 to H7 and S1 to S8 respectively. The conserved residues of this fold corresponding to D16, E33, N69, N70, R79, H80, D138, D173 and T176 in this fold are shown in ball and stick representation. The salt bridges (E33 and R79 and H80) and hydrogen bonds (D138 and T176) between these conserved residues that are critical for the stabilization of the fold are shown as magenta dotted lines. The region between the strand 1 and helix 1 of the α/β core that corresponds to the glycine-rich nucleotide binding loop in the classic Rossmann fold (residues 66 and 72) is shown in red. Note the curvature of the central sheet and the packing of helix 1 of the α/β core and the second N-terminal additional helix.