Molecular cloning of a RNA binding protein, S1-1

Abstract

S1 proteins A-D constitute a nuclear protein family that are liberated rapidly in a set from chromatin by mild digestion with a DNA or RNA hydrolyzing enzyme. With an anti-S1-protein B antiserum that reacted with B2, C1 and D1, a cDNA clone, pS1-1, was obtained, which encoded a protein of 852 amino acids. The S1-1 protein, encoded within the cells by a mRNA of 3480 nt, was a novel protein and could be distinguished from the S1 proteins B, C and D by their amino acid sequences. The S1-1 protein synthesized by in vitro translation bound to RNA homopolymers, with a preference for G and U polyribonucleotides and little for poly(A). The protein contained two tandem RNP motifs and several intriguing sequences, such as a novel repeat of five octamers with a consensus sequence DP-S(Q/G)YYY and a potentially perfect amphipathic α-helix of five turns with basic and acidic amino acids positioned in an ordered way. The two RNP motif sequences were similar, although homologies were low, to the RNP motif sequences of yeast NSR1 protein, animal nucleolins, Drosophila hnRNP A1 and tobacco chloroplast RNP precursor protein, suggesting a functional uniqueness of the S1-1 protein in RNA metabolism and also the evolution of its RNP motif structure before plants and animals diverged. These results indicate that the S1-1 protein encoded by the cDNA is a new class of RNA binding protein.

DEF-3(g16/NY-LU-12), an RNA binding protein from the 3p21.3 homozygous deletion region in SCLC

“…Preferential binding was observed by the DEF-3(g16/NY-LU-12) and LUCA15 RRM domains to poly(G) RNA (lanes 14, 16 and 20, respectively) at near physiologic salt concentration (0.1 M NaCl, pH 7.5). Of note, the DEF-3(g16/NY-LU-12)/LUCA15 family member S1-1 (rat homologue of human KIA0122) was previously shown to bind G and U polyribonucleotides (Inoue et al, 1996). In contrast, HuD was found to bind poly(A) RNA (lane 6) in agreement with its reported binding to speci®c A+U-rich substrates (Okano and Darnell, 1997;Gao et al, 1994).…”

A comparison of genomic structures and expression patterns of two closely related flanking genes in a critical lung cancer region at 3p21.3

“…Functionality tests of S1-1 revealed that its protein product, synthesised by in vitro translation, binds to RNA homopolymers, with a preference for G and U polyribonucleotides and little affinity to poly(A). 19 The amino acid sequences derived from the genes belonging to the RBM5 family (RBM5, DXS8237E and S1-1) show two RNA-binding motifs, two potential zinc finger domains and a bipartite nuclear signal (Figure 2), suggesting that the protein products are located in the nucleus and have a RNA/ DNA binding function.…”

“…16 RBM5 also shows a similarity to DXS8237E 17 /KIAA0122 18 on Xp11.23 of 51% at the amino acid level and a comparable similarity to the rat equivalent S1-1. 19 A homology search for RBM6 revealed that this gene is identical (differing by only 3 bp) to the cDNA sequence NY-LU-12, 20 (differing by only 4 bp) to the cDNA sequence DEF-3 (accession no. AF069517) and to the cDNA sequence g16 (accession no.…”

Association of hnRNP S1 Proteins C2 and D2 with Vimentin Intermediate Filaments.

“…Withthis antiserum, the SI proteins were detected in the extranucleolar nucleoplasm, localizing in the euchromatin bordering the heterochromatic areas (14), where most of the RNApolymerase II transcription takes place (3). In a molecular cloning from a rat liver CDNA expression library using the polyclonal antibody, a clone was isolated that encoded a new class of RNA-binding protein, Sl-1, of 852 amino acid residues (10). Although the Sl-1 protein did not coincide with the SI proteins, the Sl-1 and B2, Cl, and Dl were similar in that they possess the same or similar epitope structures as well as the RNA-bindingactivities.…”