3534–3548 Nucleic Acids Research, 2016, Vol. 44, No. 8 Published online 7 April 2016 doi: 10.1093/nar/gkw222 FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases Krzysztof Kuchta1,2,†, Anna Muszewska1,3,†, Lukasz Knizewski1, Kamil Steczkiewicz1, Lucjan S. Wyrwicz4, Krzysztof Pawlowski5, Leszek Rychlewski6 and Krzysztof Ginalski1,*
1Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02–089 Warsaw, Poland, 2College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02–097 Warsaw, Poland, 3Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02–106 Warsaw, Poland, 4Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02–781 Warsaw, Poland, 5Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Nowoursynowska 166, 02–787 Warsaw, Poland and 6BioInfoBank Institute, Limanowskiego 24A, 60–744 Poznan, Poland
Received December 16, 2015; Accepted March 22, 2016
ABSTRACT RNA metabolism in eukaryotes may guide their fur- ther functional studies. FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are INTRODUCTION thought to be involved in several diseases, with Proteins adopting the nucleotidyltransferase (NTase) fold FAM46C reported as a causal driver of multiple play crucial roles in various biological processes, such as myeloma; however, their exact functions remain un- RNA stabilization and degradation (e.g. RNA polyadenyla- known. By using a combination of various bioinfor- tion), RNA editing, DNA repair, intracellular signal trans- matics analyses (e.g. domain architecture, cellular duction, somatic recombination in B cells, regulation of localization) and exhaustive literature and database protein activity, antibiotic resistance and chromatin remod- searches (e.g. expression profiles, protein interac- elling (1). Almost all known members of this large and tors), we classified FAM46 proteins as active non- highly diverse superfamily transfer nucleoside monophos- canonical poly(A) polymerases, which modify cy- phate (NMP) from nucleoside triphosphate (NTP) to an ac- tosolic and/or nuclear RNA 3 ends. These pro- ceptor hydroxyl group belonging to protein, nucleic acid or teins may thus regulate gene expression and prob- small molecule. They are characterized by the presence of a common ␣/-fold structure composed of a three-stranded, ably play a critical role during cell differentiation. A mixed -sheet flanked by four ␣-helices. This common core detailed analysis of sequence and structure diver- corresponding to the minimal NTase fold is usually deco- / sity of known NTases possessing PAP OAS1 SBD rated by various additional structural elements and addi- domain, combined with state-of-the-art comparative tional domains, depending on the family. Sequence anal- modelling, allowed us to identify potential active ysis of distinct members of this superfamily revealed the site residues responsible for catalysis and substrate following common sequence patterns in NTase fold do- binding. We also explored the role of single point main: hG[GS], [DE]h[DE]h and h[DE]h (where h indicates mutations found in human cancers and propose that a hydrophobic amino acid) that include conserved active FAM46 genes may be involved in the development of site residues. Three conserved aspartates/glutamates are in- other major malignancies including lung, colorectal, volved in the coordination of divalent ions and activation of hepatocellular, head and neck, urothelial, endome- the acceptor hydroxyl group of the substrate. Two of them (from the [DE]h[DE]h motif) are located on the second core trial and renal papillary carcinomas and melanoma. -strand, while the third carboxylate (from the h[DE]h mo- Identification of these novel enzymes taking part in tif) is placed on the structurally adjacent third -strand. The hG[GS] pattern is placed at the beginning of a short, sec-
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