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Bi-allelic CLPB mutations cause cataract, renal cysts, nephrocalcinosis and 3-methylglutaconic aciduria, a novel disorder of mitochondrial protein disaggregation

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Journal of Inherited Metabolic Disease

Abstract

Whole exome sequencing was used to investigate the genetic cause of mitochondrial disease in two siblings with a syndrome of congenital lamellar cataracts associated with nephrocalcinosis, medullary cysts and 3-methylglutaconic aciduria. Autosomal recessive inheritance in a gene encoding a mitochondrially targeted protein was assumed; the only variants which satisfied these criteria were c.1882C>T (p.Arg628Cys) and c.1915G>A (p.Glu639Lys) in the CLPB gene, encoding a heat shock protein/chaperonin responsible for disaggregating mitochondrial and cytosolic proteins. Functional studies, including quantitative PCR (qPCR) and Western blot, support pathogenicity of these mutations. Furthermore, molecular modelling suggests that the mutations disrupt interactions between subunits so that the CLPB hexamer cannot form or is unstable, thus impairing its role as a protein disaggregase. We conclude that accumulation of protein aggregates underlies the development of cataracts and nephrocalcinosis in CLPB deficiency, which is a novel genetic cause of 3-methylglutaconic aciduria. A common mitochondrial cause for 3-methylglutaconic aciduria appears to be disruption of the architecture of the mitochondrial membranes, as in Barth syndrome (tafazzin deficiency), Sengers syndrome (acylglycerol kinase deficiency) and MEGDEL syndrome (impaired remodelling of the mitochondrial membrane lipids because of SERAC1 mutations). We now propose that perturbation of the mitochondrial membranes by abnormal protein aggregates leads to 3-methylglutaconic aciduria in CLPB deficiency.

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References

  • Anikster Y, Kleta R, Shaag A, Gahl WA, Elpeleg O (2001) Type III 3-methylglutaconic aciduria (optic atrophy plus syndrome, or Costeff optic atrophy syndrome): identification of the OPA3 gene and its founder mutation in Iraqi Jews. Am J Hum Genet 69:1218–1224

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Aya-Bonilla C, Green MR, Camilleri E et al (2013) High-resolution loss of heterozygosity screening implicates PTPRJ as a potential tumor suppressor gene that affects susceptibility to non-Hodgkin’s lymphoma. Genes Chromosom Cancer 52:467–479

    Article  CAS  PubMed  Google Scholar 

  • Carroni M, Kummer E, Oguchi Y et al (2014) Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation. Elife 3:e02481

    Article  PubMed Central  PubMed  Google Scholar 

  • Caspers GJ, Leunissen JA, de Jong WW (1995) The expanding small heat-shock protein family, and structure predictions of the conserved “alpha-crystallin domain”. J Mol Evol 40:238–248

    Article  CAS  PubMed  Google Scholar 

  • Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75:333–366

    Article  CAS  PubMed  Google Scholar 

  • Davey KM, Parboosingh JS, McLeod DR et al (2006) Mutation of DNAJC19, a human homologue of yeast inner mitochondrial membrane co-chaperones, causes DCMA syndrome, a novel autosomal recessive Barth syndrome-like condition. J Med Genet 43:385–393

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Di Fonzo A, Ronchi D, Lodi T et al (2009) The mitochondrial disulfide relay system protein GFER is mutated in autosomal-recessive myopathy with cataract and combined respiratory-chain deficiency. Am J Hum Genet 84:594–604

    Article  PubMed Central  PubMed  Google Scholar 

  • Doyle SM, Genest O, Wickner S (2013) Protein rescue from aggregates by powerful molecular chaperone machines. Nat Rev Mol Cell Biol 14:617–629

    Article  CAS  PubMed  Google Scholar 

  • Haargaard B, Wohlfahrt J, Fledelius HC, Rosenberg T, Melbye M (2004) Incidence and cumulative risk of childhood cataract in a cohort of 2.6 million Danish children. Invest Ophthalmol Vis Sci 45:1316–1320

    Article  PubMed  Google Scholar 

  • Hargreaves P, Rahman S, Guthrie P et al (2002) Diagnostic value of succinate ubiquinone reductase activity in the identification of patients with mitochondrial DNA depletion. J Inherit Metab Dis 25:7–16

    Article  CAS  PubMed  Google Scholar 

  • Hejtmancik JF (2008) Congenital cataracts and their molecular genetics. Semin Cell Dev Biol 19:134–149

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Holcakova J, Hernychova L, Bouchal P et al (2008) Identification of alphaB-crystallin, a biomarker of renal cell carcinoma by SELDI-TOF MS. Int J Biol Markers 23:48–53

    CAS  PubMed  Google Scholar 

  • Ijlst L, Loupatty FJ, Ruiter JP, Duran M, Lehnert W, Wanders RJ (2002) 3-Methylglutaconic aciduria type I is caused by mutations in AUH. Am J Hum Genet 71:1463–1466

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Iwaki T, Iwaki A, Liem RK, Goldman JE (1991) Expression of alpha B-crystallin in the developing rat kidney. Kidney Int 40:52–56

    Article  CAS  PubMed  Google Scholar 

  • Laube GF, Leonard JV, van’t Hoff WG (2003) Nephrocalcinosis and medullary cysts in 3-methylglutaconic aciduria. Pediatr Nephrol 18:712–713

    PubMed  Google Scholar 

  • Lee S, Sowa ME, Watanabe YH et al (2003) The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell 115:229–240

    Article  CAS  PubMed  Google Scholar 

  • Litt M, Kramer P, LaMorticella DM, Murphey W, Lovrien EW, Weleber RG (1998) Autosomal dominant congenital cataract associated with a missense mutation in the human alpha crystallin gene CRYAA. Hum Mol Genet 7:471–474

    Article  CAS  PubMed  Google Scholar 

  • Magner M, Dvorakova V, Tesarova M et al. (2014) TMEM70 deficiency: long-term outcome of 48 patients. J Inherit Metab Dis

  • Mayr JA, Haack TB, Graf E et al (2012) Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome. Am J Hum Genet 90:314–320

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Molecular Operating Environment (MOE), 2012.10; Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2012

  • Nakazaki Y, Watanabe YH (2014) ClpB chaperone passively threads soluble denatured proteins through its central pore. Genes Cells 19:891–900

    Article  CAS  PubMed  Google Scholar 

  • Nian R, Tan L, Choe W-S (2008) Folding-like-refolding of heat-denatured MDH using unpurified ClpB and DnaKJE. Biochem Eng J 40:35–43

    Article  CAS  Google Scholar 

  • Pagliarini DJ, Calvo SE, Chang B et al (2008) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134:112–123

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Parsell DA, Kowal AS, Lindquist S (1994) Saccharomyces cerevisiae Hsp104 protein. Purification and characterization of ATP-induced structural changes. J Biol Chem 269:4480–4487

    CAS  PubMed  Google Scholar 

  • Pras E, Frydman M, Levy-Nissenbaum E et al (2000) A nonsense mutation (W9X) in CRYAA causes autosomal recessive cataract in an inbred Jewish Persian family. Invest Ophthalmol Vis Sci 41:3511–3515

    CAS  PubMed  Google Scholar 

  • Rahman S, Hall AM (2013) Mitochondrial disease—an important cause of end-stage renal failure. Pediatr Nephrol 28:357–361

    Article  CAS  PubMed  Google Scholar 

  • Razi M, Chan EY, Tooze SA (2009) Early endosomes and endosomal coatomer are required for autophagy. J Cell Biol 185:305–321

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sanchez Y, Lindquist SL (1990) HSP104 required for induced thermotolerance. Science 248:1112–1115

    Article  CAS  PubMed  Google Scholar 

  • Schirmer EC, Glover JR, Singer MA, Lindquist S (1996) HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem Sci 21:289–296

    Article  CAS  PubMed  Google Scholar 

  • Schlame M, Ren M (2006) Barth syndrome, a human disorder of cardiolipin metabolism. FEBS Lett 580:5450–5455

    Article  CAS  PubMed  Google Scholar 

  • Schlieker C, Tews I, Bukau B, Mogk A (2004) Solubilization of aggregated proteins by ClpB/DnaK relies on the continuous extraction of unfolded polypeptides. FEBS Lett 578:351–356

    Article  CAS  PubMed  Google Scholar 

  • Thomas JG, Baneyx F (2000) ClpB and HtpG facilitate de novo protein folding in stressed Escherichia coli cells. Mol Microbiol 36:1360–1370

    Article  CAS  PubMed  Google Scholar 

  • Venkatachalam R, Ligtenberg MJ, Hoogerbrugge N et al (2010) Germline epigenetic silencing of the tumor suppressor gene PTPRJ in early-onset familial colorectal cancer. Gastroenterology 139:2221–2224

    Article  PubMed  Google Scholar 

  • Vorobieva AA, Khan MS, Soumillion P (2014) Escherichia coli d-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway. J Biol Chem 289:29086–29096

    Article  CAS  PubMed  Google Scholar 

  • Wong CW, Wong TY, Cheng CY, Sabanayagam C (2014) Kidney and eye diseases: common risk factors, etiological mechanisms, and pathways. Kidney Int 85:1290–1302

    Article  PubMed  Google Scholar 

  • Wortmann SB, Vaz FM, Gardeitchik T et al (2012) Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness. Nat Genet 44:797–802

    Article  CAS  PubMed  Google Scholar 

  • Wortmann SB, Kluijtmans LA, Rodenburg RJ et al (2013) 3-Methylglutaconic aciduria—lessons from 50 genes and 977 patients. J Inherit Metab Dis 36:913–921

    Article  CAS  PubMed  Google Scholar 

  • Zeymer C, Barends TR, Werbeck ND, Schlichting I, Reinstein J (2014) Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor. Acta Crystallogr D Biol Crystallogr 70:582–595

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank the Lily Foundation for grant funding for this study. SR is supported by Great Ormond Street Hospital Children’s Charity, and MK received a PhD studentship from Vitaflo International Ltd. The researchers were independent of the funders. The organisations responsible for funding had no role in the design or conduct of the study or in collection, analysis and interpretation of data or preparation, review or approval of this manuscript. The authors had full access to all data and had final responsibility for the decision to submit for publication.

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None declared.

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Correspondence to Shamima Rahman.

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Communicated by: John Christodoulou

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Kanabus, M., Shahni, R., Saldanha, J.W. et al. Bi-allelic CLPB mutations cause cataract, renal cysts, nephrocalcinosis and 3-methylglutaconic aciduria, a novel disorder of mitochondrial protein disaggregation. J Inherit Metab Dis 38, 211–219 (2015). https://doi.org/10.1007/s10545-015-9813-0

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  • DOI: https://doi.org/10.1007/s10545-015-9813-0

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