PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly

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.

[1]  V. Tiranti,et al.  Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA) , 2006, Journal of Medical Genetics.

[2]  E. Phizicky,et al.  Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. , 2003, RNA.

[3]  R. Pfundt,et al.  Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior. , 2018, American journal of human genetics.

[4]  A. Shaag,et al.  TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly , 2014, Journal of Medical Genetics.

[5]  Jernej Ule,et al.  Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders , 2014, The EMBO journal.

[6]  Fowzan S. Alkuraya,et al.  Mutation in WDR4 impairs tRNA m7G46 methylation and causes a distinct form of microcephalic primordial dwarfism , 2015, Genome Biology.

[7]  F. Alkuraya.  The application of next-generation sequencing in the autozygosity mapping of human recessive diseases , 2013, Human Genetics.

[8]  D. Davis.  Stabilization of RNA stacking by pseudouridine. , 1995, Nucleic acids research.

[9]  S. Gabriel,et al.  Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome , 2012, Journal of Medical Genetics.

[10]  W. Gilbert,et al.  Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells , 2014, Nature.

[11]  Jef Rozenski,et al.  The RNA modification database, RNAMDB: 2011 update , 2010, Nucleic Acids Res..

[12]  J. Ebel,et al.  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. , 1981, Nucleic acids research.

[13]  Thomas J. Begley,et al.  Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses , 2015, RNA biology.

[14]  A. Hüttenhofer,et al.  mRNA modifications: Dynamic regulators of gene expression? , 2016, RNA biology.

[15]  Maxwell R. Mumbach,et al.  Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA , 2014, Cell.

[16]  A. Hattersley,et al.  tRNA Methyltransferase Homolog Gene TRMT10A Mutation in Young Onset Diabetes and Primary Microcephaly in Humans , 2013, PLoS genetics.

[17]  V. Tiranti,et al.  Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA) , 2009, BMJ Case Reports.

[18]  D. H. Gauss,et al.  Compilation of sequences of tRNA genes. , 1982, Nucleic acids research.

[19]  M. W. Gray,et al.  Pseudouridine in RNA: What, Where, How, and Why , 2000, IUBMB life.

[20]  Christiane Branlant,et al.  The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs. , 2003, RNA.

[21]  J Ofengand,et al.  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. , 1993, Biochemistry.

[22]  W. Keller,et al.  An adenosine deaminase that generates inosine at the wobble position of tRNAs. , 1999, Science.

[23]  Z. Ignatova,et al.  Emerging roles of tRNA in adaptive translation, signalling dynamics and disease , 2014, Nature Reviews Genetics.

[24]  John Karijolich,et al.  Detection and quantification of RNA 2'-O-methylation and pseudouridylation. , 2016, Methods.

[25]  M. Helm,et al.  Pseudouridine: Still mysterious, but never a fake (uridine)! , 2014, RNA biology.

[26]  J. Ofengand,et al.  Crystal Structure of TruD, a Novel Pseudouridine Synthase with a New Protein Fold* , 2004, Journal of Biological Chemistry.

[27]  Chuan He,et al.  Post-transcriptional gene regulation by mRNA modifications , 2016, Nature Reviews Molecular Cell Biology.

[28]  E. Phizicky,et al.  Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. , 2008, Genes & development.

[29]  WALDO E. COHN,et al.  Nucleoside-5′-Phosphates from Ribonucleic Acid , 1951, Nature.

[30]  Tariq Ahmad Masoodi,et al.  Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus , 2013, Journal of Medical Genetics.

[31]  N. Sonenberg,et al.  Translation deregulation in human disease , 2018, Nature Reviews Molecular Cell Biology.

[32]  W. Cohn,et al.  5-Ribosyl uracil, a carbon-carbon ribofuranosyl nucleoside in ribonucleic acids. , 1959, Biochimica et biophysica acta.

[33]  S. Ackerman,et al.  mRNA Translation Gone Awry: Translation Fidelity and Neurological Disease. , 2018, Trends in genetics : TIG.

[34]  J. Alfonzo,et al.  Transfer RNA modifications: nature's combinatorial chemistry playground , 2013, Wiley interdisciplinary reviews. RNA.

[35]  S. Steinberg,et al.  Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. , 1995, Biochimie.

[36]  Dragony Fu,et al.  The emerging impact of tRNA modifications in the brain and nervous system. , 2019, Biochimica et biophysica acta. Gene regulatory mechanisms.

[37]  F. Sherman.  Getting started with yeast. , 1991, Methods in enzymology.

[38]  A. Yu,et al.  Pseudouridines in spliceosomal snRNAs , 2011, Protein & Cell.

[39]  Todd M Lowe,et al.  A computational screen for mammalian pseudouridylation guide H/ACA RNAs. , 2006, RNA.

[40]  F. Sherman.  Getting started with yeast. , 2002, Methods in enzymology.

[41]  M. Helm,et al.  tRNA stabilization by modified nucleotides. , 2010, Biochemistry.

[42]  Fowzan S. Alkuraya,et al.  A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition , 2016, Human Genetics.

[43]  Z. Nawaz,et al.  Whole exome sequencing unravels disease‐causing genes in consanguineous families in Qatar , 2014, Clinical genetics.

[44]  Eduard Batlle,et al.  Role of tRNA modifications in human diseases. , 2014, Trends in molecular medicine.

[45]  Shiqing Ma,et al.  Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. , 2015, Nature chemical biology.

[46]  P. Brown,et al.  Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae , 2014, PloS one.