Pseudouridylation is the most common post-transcriptional modification, wherein uridine is isomerized into 5-ribosyluracil (pseudouridine, Ψ). The resulting increase in base stacking and creation of additional hydrogen bonds are thought to enhance RNA stability. Pseudouridine synthases are encoded in humans by 13 genes, two of which are linked to Mendelian diseases: PUS1 and PUS3. Very recently, PUS7 mutations were reported to cause intellectual disability with growth retardation. We describe two families in which two different homozygous PUS7 mutations (missense and frameshift deletion) segregate with a phenotype comprising intellectual disability and progressive microcephaly. Short stature and hearing loss were variable in these patients. Functional characterization of the two mutations confirmed that both result in decreased levels of Ψ13 in tRNAs. Furthermore, the missense variant of the S. cerevisiae ortholog failed to complement the growth defect of S. cerevisiae pus7Δ trm8Δ mutants. Our results confirm that PUS7 is a bona fide Mendelian disease gene and expand the list of human diseases caused by impaired pseudouridylation.
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Alazami AM, Hijazi H, Al-Dosari MS, Shaheen R, Hashem A, Aldahmesh MA, Mohamed JY, Kentab A, Salih MA, Awaji A, Masoodi TA, Alkuraya FS (2013) Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus. J Med Genet 50(7):425–430
Alkuraya FS (2013) The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. Hum Genet 132:1197–1211
Andrew TY, Ge J, Yu Y-T (2011) Pseudouridines in spliceosomal snRNAs. Protein Cell 2:712–725
Bakin A, Ofengand J (1993) Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique. Biochemistry 32:9754–9762
Behm-Ansmant I, Urban A, Ma X, Yu Y-T, Motorin Y, Branlant C (2003) The Saccharomyces cerevisiae U2 snRNA: pseudouridine-synthase Pus7p is a novel multisite–multisubstrate RNA: Ψ-synthase also acting on tRNAs. RNA 9:1371–1382
Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Holter SM, Garrett L, Wurst W, Becker L, Klopstock T, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Karadottir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M (2014) Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J 33(18):2020–2039
Boccaletto P, Machnicka MA, Purta E, Piątkowski P, Bagiński B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A (2017) MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res 46:D303–D307
Branlant C, Krol A, Machatt MA, Pouyet J, Ebel J-P, Edwards K, Kössel H (1981) Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs. Nucleic Acids Res 9:4303–4324
Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, Vendeix FA, Fabris D, Agris PF (2011) The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res 39:D195–D201
Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515:143
Charette M, Gray MW (2000) Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49:341–351
Chernyakov I, Whipple JM, Kotelawala L, Grayhack EJ, Phizicky EM (2008) Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′–3′ exonucleases Rat1 and Xrn1. Genes Dev 22:1369–1380
Cohn WE (1959) 5-Ribosyl uracil, a carbon-carbon ribofuranosyl nucleoside in ribonucleic acids. Biochim Biophys Acta 32:569–571
Cohn WE, Volkin E (1951) Nucleoside-5′-phosphates from ribonucleic acid. Nature 167:483
Davis DR (1995) Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res 23:5020–5026
de Brouwer APM, Abou Jamra R, Kortel N, Soyris C, Polla DL, Safra M, Zisso A, Powell CA, Rebelo-Guiomar P, Dinges N, Morin V, Stock M, Hussain M, Shahzad M, Riazuddin S, Ahmed ZM, Pfundt R, Schwarz F, de Boer L, Reis A, Grozeva D, Raymond FL, Riazuddin S, Koolen DA, Minczuk M, Roignant JY, van Bokhoven H, Schwartz S (2018) Variants in PUS7 cause intellectual disability with speech delay, microcephaly, short stature, and aggressive behavior. Am J Hum Genet 103:1045–1052
Endres L, Dedon PC, Begley TJ (2015) Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses. RNA Biol 12:603–614
Fahiminiya S, Almuriekhi M, Nawaz Z, Staffa A, Lepage P, Ali R, Hashim L, Schwartzentruber J, Abu Khadija K, Zaineddin S, Gamal H, Majewski J, Ben-Omran T (2013) Whole exome sequencing unravels disease-causing genes in consanguineous families in Qatar. Clin Genet 86(2):134–141
Fernandez-Vizarra E, Berardinelli A, Valente L, Tiranti V, Zeviani M (2007) Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA). J Med Genet 44:173–180
Gerber AP, Keller W (1999) An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286:1146–1149
Gillis D, Krishnamohan A, Yaacov B, Shaag A, Jackman JE, Elpeleg O (2014) TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. J Med Genet 51:581–586
Grosjean H, Sprinzl M, Steinberg S (1995) Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77:139–141
Hoernes TP, Hüttenhofer A, Erlacher MD (2016) mRNA modifications: Dynamic regulators of gene expression? RNA Biol 13:760–765
Huang C, Karijolich J, Yu Y-T (2016) Detection and quantification of RNA 2′-O-methylation and pseudouridylation. Methods 103:68–76
Igoillo-Esteve M, Genin A, Lambert N, Desir J, Pirson I, Abdulkarim B, Simonis N, Drielsma A, Marselli L, Marchetti P, Vanderhaeghen P, Eizirik DL, Wuyts W, Julier C, Chakera AJ, Ellard S, Hattersley AT, Abramowicz M, Cnop M (2013) tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans. PLoS Genet 9:e1003888
Jackman JE, Alfonzo JD (2013) Transfer RNA modifications: nature’s combinatorial chemistry playground. Wiley Interdiscip Rev RNA 4:35–48
Jackman JE, Montange RK, Malik HS, Phizicky EM (2003) Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA 9:574–585
Kapur M, Ackerman SL (2018) mRNA translation gone awry: translation fidelity and neurological disease. Trends Genet 34:218–231
Kaya Y, Del Campo M, Ofengand J, Malhotra A (2004) Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold. J Biol Chem 279:18107–18110
Kirchner S, Ignatova Z (2015) Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet 16:98
Li X, Zhu P, Ma S, Song J, Bai J, Sun F, Yi C (2015) Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat Chem Biol 11:592
Lovejoy AF, Riordan DP, Brown PO (2014) Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 9:e110799
Martinez FJ, Lee JH, Lee JE, Blanco S, Nickerson E, Gabriel S, Frye M, Al-Gazali L, Gleeson JG (2012) Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome. J Med Genet 49:380–385
Motorin Y, Helm M (2010) tRNA stabilization by modified nucleotides. Biochemistry 49:4934–4944
Ramos J, Fu D (2018) The emerging impact of tRNA modifications in the brain and nervous system. Biochim Biophys Acta Gene Regul Mech. https://doi.org/10.1016/j.bbagrm.2018.11.007
Schattner P, Barberan-Soler S, Lowe TM (2006) A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA 12:15–25
Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES (2014) Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159:148–162
Shaheen R, Abdel-Salam GM, Guy MP, Alomar R, Abdel-Hamid MS, Afifi HH, Ismail SI, Emam BA, Phizicky EM, Alkuraya FS (2015) Mutation in WDR4 impairs tRNA m 7 G 46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome Biol 16:210
Shaheen R, Han L, Faqeih E, Ewida N, Alobeid E, Phizicky EM, Alkuraya FS (2016) A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Hum Genet 135:707–713
Sherman F (1991) Getting started with yeast. Methods Enzymol 194:3–21
Spenkuch F, Motorin Y, Helm M (2014) Pseudouridine: still mysterious, but never a fake (uridine)! RNA Biol 11:1540–1554
Tahmasebi S, Khoutorsky A, Mathews MB, Sonenberg N (2018) Translation deregulation in human disease. Nat Rev Mol Cell Biol 19:791–807
Torres AG, Batlle E, de Pouplana LR (2014) Role of tRNA modifications in human diseases. Trends Mol Med 20:306–314
Zhao BS, Roundtree IA, He C (2017) Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol 18:31
We thank the study family for their enthusiastic participation. We also thank Mais Hashem, Niema Ibrahim and Firdous Abdulwahab for their help in coordinating the recruitment of the families and the Sequencing and Genotyping Core Facilities at KFSHRC for their technical help. This work was supported by the King Salman Center for Disability Research (F.S.A.), the Saudi Human Genome Program (F.S.A.), and by National Institutes of Health grant GM052347 (E.M.P.). M.T. was partially supported by NIH Training Grant in Cellular, Biochemical, and Molecular Sciences GM068411.
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Shaheen, R., Tasak, M., Maddirevula, S. et al. PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly. Hum Genet 138, 231–239 (2019). https://doi.org/10.1007/s00439-019-01980-3