Protein universe containing a PUA RNA-binding domain

Authors

  • Carolina S. Cerrudo,

    1. Laboratory of Genetic Engineering and Cellular and Molecular Biology, Quilmes National University, Bernal, Buenos Aires, Argentina
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  • Pablo D. Ghiringhelli,

    Corresponding author
    1. Laboratory of Genetic Engineering and Cellular and Molecular Biology, Quilmes National University, Bernal, Buenos Aires, Argentina
    • Correspondence

      P. D. Ghiringhelli, Laboratory of Genetic Engineering and Cellular and Molecular Biology, Department of Science and Technology, Quilmes National University, Roque Saenz Peña 352, Bernal 1876, Buenos Aires, Argentina

      Fax: +54 11 4365 7132

      Tel: +54 11 4365 7100 (ext. 4152)

      E-mail: pdg@unq.edu.ar

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  • Daniel E. Gomez

    1. Laboratory of Molecular Oncology, Quilmes National University, Bernal, Buenos Aires, Argentina
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  • Pablo D. Ghiringhelli and Daniel E. Gomez contributed equally to this work.

Abstract

Here, we review current knowledge about pseudouridine synthase and archaeosine transglycosylase (PUA)-domain-containing proteins to illustrate progress in this field. A methodological analysis of the literature about the topic was carried out, together with a ‘qualitative comparative analysis’ to give a more comprehensive review. Bioinformatics methods for whole-protein or protein-domain identification are commonly based on pairwise protein sequence comparisons; we added comparison of structures to detect the whole universe of proteins containing the PUA domain. We present an update of proteins having this domain, focusing on the specific proteins present in Homo sapiens (dyskerin, MCT1, Nip7, eIF2D and Nsun6), and explore the existence of these in other species. We also analyze the phylogenetic distribution of the PUA domain in different species and proteins. Finally, we performed a structural comparison of the PUA domain through data mining of structural databases, determining a conserved structural motif, despite the differences in the sequence, even among eukaryotes, archaea and bacteria. All data discussed in this review, both bibliographic and analytical, corroborate the functional importance of the PUA domain in RNA-binding proteins.

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