Alfano, C. et al. Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. Nat. Struct. Mol. Biol. 11, 323-329

Biophysics Laboratories, University of Portsmouth, Portsmouth, England, United Kingdom
Nature Structural & Molecular Biology (Impact Factor: 13.31). 05/2004; 11(4):323-9. DOI: 10.1038/nsmb747
Source: PubMed


The La protein is a conserved component of eukaryotic ribonucleoprotein complexes that binds the 3' poly(U)-rich elements of nascent RNA polymerase III (pol III) transcripts to assist folding and maturation. This specific recognition is mediated by the N-terminal domain (NTD) of La, which comprises a La motif and an RNA recognition motif (RRM). We have determined the solution structures of both domains and show that the La motif adopts an alpha/beta fold that comprises a winged-helix motif elaborated by the insertion of three helices. Chemical shift mapping experiments show that these insertions are involved in RNA interactions. They further delineate a distinct surface patch on each domain-containing both basic and aromatic residues-that interacts with RNA and accounts for the cooperative binding of short oligonucleotides exhibited by the La NTD.

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Available from: Domenico Sanfelice, Aug 05, 2014
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    • "Although the La module is conserved across the LARP superfamily, the recognised RNA targets are not, and this RNA binding versatility is thought, at least in part, to account for the different cellular processes in which LARPs are involved (Bayfield et al. 2010). Contrary to the archetype La protein, for which high resolution structures of several domains in the apo and bound form, as well as biophysical insights into its RNA binding properties, have been reported (Jacks et al. 2003; Alfano et al. 2004; Teplova et al. 2006; Kotik-Kogan et al. 2008; Martino et al. 2012), the LARPs are much less well understood and the mechanism by which La modules of LARPs can recognise a great variety of RNA molecules, with different shapes and sequences, is still elusive. "
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    ABSTRACT: We report here the nearly complete (1)H, (15)N and (13)C resonance assignment of the La motif and RNA recognition motif 1 of human LARP6, an RNA binding protein involved in regulating collagen synthesis.
    Full-text · Article · Apr 2015 · Biomolecular NMR Assignments
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    • "Thus the structure of the p65 C-terminal domain-TER complex reveals a new mode for RNA recognition combining ssRNA and dsRNA binding by a new class of RRM that appears to be unique to genuine La and LARP7 proteins. This mode of binding may be general to the chaperone function of genuine La and LARP7 proteins, potentially explaining how xRRM2 would function in the biogenesis of various RNAs (Alfano et al., 2004; Dong et al., 2004; Jacks et al., 2003; Kucera et al., 2011; Martino et al., 2012). "
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    ABSTRACT: Telomerase is a ribonucleoprotein complex essential for maintenance of telomere DNA at linear chromosome ends. The catalytic core of Tetrahymena telomerase comprises a ternary complex of telomerase RNA (TER), telomerase reverse transcriptase (TERT), and the essential La family protein p65. NMR and crystal structures of p65 C-terminal domain and its complex with stem IV of TER reveal that RNA recognition is achieved by a combination of single- and double-stranded RNA binding, which induces a 105° bend in TER. The domain is a cryptic, atypical RNA recognition motif with a disordered C-terminal extension that forms an α helix in the complex necessary for hierarchical assembly of TERT with p65-TER. This work provides the first structural insight into biogenesis and assembly of TER with a telomerase-specific protein. Additionally, our studies define a structurally homologous domain (xRRM) in genuine La and LARP7 proteins and suggest a general mode of RNA binding for biogenesis of their diverse RNA targets.
    Full-text · Article · Jun 2012 · Molecular cell
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    • "In genuine La proteins or LARPs, RNA-binding activity is mediated by the LAM and an adjacent RRM (Goodier et al. 1997; Ohndorf et al. 2001; Alfano et al. 2004; Dong et al. 2004; Horke et al. 2004). Therefore, seven residues within the LAM mediate high-affinity binding to terminal Us, but only one residue within the juxtapositioned RRM (Fig. 1B; Dong et al. 2004; Teplova et al. 2006; Kotik-Kogan et al. 2008). "
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    ABSTRACT: The La-motif (LAM) is an ancient and ubiquitous RNA-binding domain defining a superfamily of proteins, which comprises the genuine La proteins and La-related proteins (LARPs). In contrast to La, which binds and stabilizes pre-tRNAs and other RNA polymerase III transcripts, data on function and RNA targets of the LARPs have remained scarce. We have undertaken a global approach to elucidate the previously suggested role of the yeast LARP Slf1p in copper homeostasis. By applying RNA-binding protein immunopurification-microarray (RIP-Chip) analysis, we show that Slf1p and its paralog Sro9p copurify with overlapping sets of hundreds of functionally related mRNAs, including many transcripts coding for ribosomal proteins and histones. Interestingly, among these potential RNA targets were also mRNAs coding for proteins critical for protection of cells against elevated copper concentrations. Mutations introduced in the conserved aromatic patch of the LAM in Slf1p drastically impaired both association with its targets and Slf1-mediated protection of cells against toxic copper concentrations. Furthermore, we show that Slf1p stabilizes copper-related mRNA targets in a LAM-dependent manner. These results provide the first evidence for post-transcriptional regulation of factors/pathways implicated in copper homeostasis by a cytoplasmic RBP.
    Full-text · Article · Mar 2012 · RNA
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