Conserved Structures and Diversity of Functions of RNA-Binding Proteins

Abstract

In eukaryotic cells, a multitude of RNA-binding proteins play key roles in the posttranscriptional regulation of gene expression. Characterization of these proteins has led to the identification of several RNA-binding motifs, and recent experiments have begun to illustrate how several of them bind RNA. The significance of these interactions is reflected in the recent discoveries that several human and other vertebrate genetic disorders are caused by aberrant expression of RNA-binding proteins. The major RNA-binding motifs are described and examples of how they may function are given.

Sequence Analysis of LRPPRC and Its SEC1 Domain Interaction Partners Suggests Roles in Cytoskeletal Organization, Vesicular Trafficking, Nucleocytosolic Shuttling, and Chromosome Activity

“…An arginine-rich sequence in MAP1 light chain 3 has been proposed to underlie its interaction with fibronectin mRNA [24]. We noted a similar arginine-rich, potential RNA-binding motif [25] at the N-terminus of the MAP homology in C19ORF5 (Fig. 6B).…”

1H‐NMR and photo‐CIDNP spectroscopies show a possible role for Trp23 and Phe31 in nucleic acid binding by P2 ribonuclease from the archaeon Sulfolobus solfataricus

“…These proteins belong to a large family of molecules involved in RNA processing, in which a RNA recognition motif of about 80 amino acids represents the core of their RNA-binding domains [14,27,28]. Although the RNA-binding domains in these proteins have very low homology at the amino acid level, two consensus sequences, RNP1 and RNP2, have been identified.…”

“…Although the RNA-binding domains in these proteins have very low homology at the amino acid level, two consensus sequences, RNP1 and RNP2, have been identified. They are juxtaposed in adjacent fl-strands and contain residues which are thought to be involved in nucleic acid binding; particularly, conserved aromatic side chains, critical for RNA binding, are clustered on the surface of the protein, close to the variable loop that determines recognition of specific RNA sequences [14,27,28]. In these proteins, involvement of theft-sheet region in RNA binding has been clearly established.…”

An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element

“…The PSI protein was identified as a component that interacts with the IVS3 59 exon and is required for the inhibition of IVS3 splicing in vitro+ PSI is highly expressed in the soma and is thought to be the determinant of the tissue-specific expression of the transposase protein (Siebel et al+, 1995)+ Ectopic expression of PSI in the female germ line is sufficient to repress splicing of an IVS3 reporter transgene (Adams et al+, 1997)+ PSI contains a N-terminal domain consisting of four hnRNP K homology (KH) RNA-binding motifs and a C-terminal region with two glutamine-rich repeats (A and B; Siebel et al+, 1995)+ An N-terminal fragment of PSI containing only the four KH motifs (KH0-3) can specifically bind to the IVS3 59 exon RNA (R+ MacDiarmid and D+C+ Rio, unpubl+; see below)+ PSI is known to interact directly with U1 snRNP through the A and B motifs (Labourier et al+, 2001)+ KH domains have been identified in over 100 RNAbinding proteins with diverse cellular functions from a wide variety of organisms (Burd & Dreyfuss, 1994)+ In Drosophila, it is predicted that the genome sequence encodes 27 KH domain proteins (Lasko, 2000)+ The KH motif is about 70 amino acids in length and can be present in single or multiple copies within a given protein+ The KH domain was first identified as a region in hnRNP K (the K-homology region) that binds to singlestranded RNA nonspecifically (Siomi et al+, 1993)+ The hnRNP K protein has three KH motifs and binds poly r(C) (Matunis et al+, 1992)+ The RNA-binding properties of several KH domain proteins have been studied, including Nova-1, Nova-2, and vigilin (Buckanovich & Darnell, 1997;Kanamori et al+, 1998)+ These proteins have been shown to bind to specific target RNA sequences+ The Nova-1 protein recognizes RNA stem loops containing the (UCAUY) 3 , and the Nova-2 protein binds to a high affinity consensus site, GAGUCAU, in RNA stem loops (Yang et al+, 1998)+ These studies show that these KH domain proteins can recognize short pyrimidine-rich RNA sequences+ A recent crystal structure of the Nova-2 protein KH domain bound to RNA shows that a single KH motif interacts with as few as 4-5 nt of single-stranded RNA (Lewis et al+, 2000)+ These studies also showed that other regions of the RNA-bound KH domain are accessible to carry out protein-protein interactions+ Studies on vigilin, a multi-KH domain protein containing 14 KH motifs, showed that it recognizes sequences with conserved (A) n CU and UC(A) n motifs (Kanamori et al+, 1998)+ The Sam68 protein, a specific target of the src tyrosine kinase in mitosis, is another KH domaincontaining protein that recognizes specific target RNAs+ Sam68 was shown to recognize RNA sequences with a UAAA motif (Lin et al+, 1997)+ Thus, KH domains appear to recognize short motifs in RNA+ Although the PSI protein is known to bind the P element IVS3 59 exon RNA, its exact RNA-binding site has not been identified+ Using an in vitro genetic selection approach (SELEX), we have identified high affinity RNA-binding sequences for PSI+ The deduced consensus sequence suggests that ...…”