Mutation in WDR4 impairs tRNA m7G46 methylation and causes a distinct form of microcephalic primordial dwarfism

BackgroundPrimordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity.ResultsTwo presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m7G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m7G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m7G46 modification causes a growth deficiency phenotype in yeast.ConclusionOur study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification.

[1]  F. Alkuraya,et al.  Genomic analysis of primordial dwarfism reveals novel disease genes , 2014, Genome research.

[2]  H. Mandel,et al.  Acute infantile liver failure due to mutations in the TRMU gene. , 2009, American journal of human genetics.

[3]  Sandya Liyanarachchi,et al.  Mutations in U4atac snRNA, a Component of the Minor Spliceosome, in the Developmental Disorder MOPD I , 2011, Science.

[4]  Graham R Taylor,et al.  Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families , 2006, Human mutation.

[5]  F. Alkuraya Primordial dwarfism: an update , 2015, Current opinion in endocrinology, diabetes, and obesity.

[6]  Mohamed Abouelhoda,et al.  Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. , 2015, Cell reports.

[7]  Xiang-Dong Fu,et al.  CLP1 Founder Mutation Links tRNA Splicing and Maturation to Cerebellar Development and Neurodegeneration , 2014, Cell.

[8]  K. Devriendt,et al.  Mutations in the Pericentrin (PCNT) Gene Cause Primordial Dwarfism , 2008, Science.

[9]  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.

[10]  E. Phizicky,et al.  Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. , 2002, RNA.

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

[12]  Sebastian A. Leidel,et al.  Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity , 2015, Cell.

[13]  Y. Goto,et al.  A loss‐of‐function mutation in the FTSJ1 gene causes nonsyndromic X‐linked mental retardation in a japanese family , 2008, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[14]  E. Phizicky,et al.  tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. , 2005, RNA.

[15]  Hans Christian Pedersen,et al.  Mammostrat® as a tool to stratify breast cancer patients at risk of recurrence during endocrine therapy , 2010, Breast Cancer Research.

[16]  T. Begley,et al.  Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: activities, predications, and potential roles in human health. , 2012, DNA and cell biology.

[17]  J. Gécz,et al.  Loss of SLC38A5 and FTSJ1 at Xp11.23 in three brothers with non-syndromic mental retardation due to a microdeletion in an unstable genomic region , 2007, Human Genetics.

[18]  Haiyan Jiang,et al.  Mutations in origin recognition complex gene ORC4 cause Meier-Gorlin syndrome , 2011, Nature Genetics.

[19]  A. Jackson,et al.  Mechanisms and pathways of growth failure in primordial dwarfism. , 2011, Genes & development.

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

[21]  E. Phizicky,et al.  Do all modifications benefit all tRNAs? , 2010, FEBS letters.

[22]  Judith A. Goodship,et al.  A splicing mutation affecting expression of ataxia–telangiectasia and Rad3–related protein (ATR) results in Seckel syndrome , 2003, Nature Genetics.

[23]  C. Schwartz,et al.  A splice site mutation in the methyltransferase gene FTSJ1 in Xp11.23 is associated with non-syndromic mental retardation in a large Belgian family (MRX9) , 2004, Journal of Medical Genetics.

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

[25]  B. Rubin,et al.  Familial dysautonomia is caused by mutations of the IKAP gene. , 2001, American journal of human genetics.

[26]  Yusuke Nakamura,et al.  Amino-acid substitutions in the IKAP gene product significantly increase risk for bronchial asthma in children , 2001, Journal of Human Genetics.

[27]  O. Uhlenbeck,et al.  Structure of an unmodified tRNA molecule. , 1989, Biochemistry.

[28]  Jingyue Ju,et al.  Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELP4) , 2009, European Journal of Human Genetics.

[29]  Paul F Agris,et al.  tRNA's wobble decoding of the genome: 40 years of modification. , 2007, Journal of molecular biology.

[30]  J. Gécz,et al.  Mutations in the FTSJ1 gene coding for a novel S-adenosylmethionine-binding protein cause nonsyndromic X-linked mental retardation. , 2004, American journal of human genetics.

[31]  E. Phizicky,et al.  The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA. , 2011, Genes & development.

[32]  Martin S. Taylor,et al.  CEP152 is a genome maintenance protein disrupted in Seckel syndrome , 2011, Nature Genetics.

[33]  A. Hopper,et al.  Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. , 2012, RNA.

[34]  Clement T Y Chan,et al.  A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress , 2010, PLoS genetics.

[35]  F. Alkuraya Discovery of Rare Homozygous Mutations from Studies of Consanguineous Pedigrees , 2012, Current protocols in human genetics.

[36]  Nicolas Leulliot,et al.  Structure of the yeast tRNA m7G methylation complex. , 2008, Structure.

[37]  Clement T Y Chan,et al.  Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins , 2012, Nature Communications.

[38]  A. Hopper Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the Yeast Saccharomyces cerevisiae , 2013, Genetics.

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

[40]  Wei Chen,et al.  Deep sequencing reveals 50 novel genes for recessive cognitive disorders , 2011, Nature.

[41]  Dagmar Wieczorek,et al.  Mutations in NSUN2 cause autosomal-recessive intellectual disability. , 2012, American journal of human genetics.

[42]  R Giegé,et al.  A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys. , 1999, Biochemistry.

[43]  F. Alkuraya,et al.  Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. , 2014, American journal of human genetics.

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

[45]  J. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways—2013 update , 2012, Nucleic Acids Res..

[46]  Nine V.A.M. Knoers,et al.  Mutations in the Pre-Replication Complex cause Meier-Gorlin syndrome , 2011, Nature Genetics.

[47]  F. Alkuraya,et al.  Mutation in PLK4, encoding a master regulator of centriole formation, defines a novel locus for primordial dwarfism , 2014, Journal of Medical Genetics.

[48]  A. Noor,et al.  Mutation in NSUN2, which encodes an RNA methyltransferase, causes autosomal-recessive intellectual disability. , 2012, American journal of human genetics.

[49]  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.

[50]  A. Hopper,et al.  tRNA biology charges to the front. , 2010, Genes & development.

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

[52]  E. Phizicky,et al.  The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications. , 2012, RNA.

[53]  C Maayan,et al.  Tissue-specific expression of a splicing mutation in the IKBKAP gene causes familial dysautonomia. , 2001, American journal of human genetics.

[54]  angesichts der Corona-Pandemie,et al.  UPDATE , 1973, The Lancet.

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

[56]  J. Gusella,et al.  Tissue-specific reduction in splicing efficiency of IKBKAP due to the major mutation associated with familial dysautonomia. , 2003, American journal of human genetics.

[57]  Robert W. Taylor,et al.  Defective i6A37 Modification of Mitochondrial and Cytosolic tRNAs Results from Pathogenic Mutations in TRIT1 and Its Substrate tRNA , 2014, PLoS genetics.

[58]  Weifeng Gu,et al.  Rapid tRNA decay can result from lack of nonessential modifications. , 2006, Molecular cell.

[59]  A. Kintanar,et al.  Nucleoside modifications stabilize Mg2+ binding in Escherichia coli tRNA(Val): an imino proton NMR investigation. , 1994, Biochemistry.

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

[61]  E. Phizicky,et al.  tRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae. , 2013, RNA.

[62]  F. Alkuraya,et al.  POC1A truncation mutation causes a ciliopathy in humans characterized by primordial dwarfism. , 2012, American journal of human genetics.

[63]  M. Tatsuka,et al.  tRNA Modifying Enzymes, NSUN2 and METTL1, Determine Sensitivity to 5-Fluorouracil in HeLa Cells , 2014, PLoS Genetics.

[64]  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.

[65]  P. Jeggo,et al.  Identification of the First ATRIP–Deficient Patient and Novel Mutations in ATR Define a Clinical Spectrum for ATR–ATRIP Seckel Syndrome , 2012, PLoS genetics.

[66]  Marcin Feder,et al.  MODOMICS: a database of RNA modification pathways , 2005, Nucleic Acids Res..