| Literature DB >> 28594869 |
Michael Nafisinia1,2, Lisa G Riley1,2, Wendy A Gold1,2, Kaustuv Bhattacharya2,3,4, Carolyn R Broderick5,6, David R Thorburn7, Cas Simons8, John Christodoulou1,2,3,4,7.
Abstract
Glycyl-tRNA synthetase (GARS; OMIM 600287) is one of thirty-seven tRNA-synthetase genes that catalyses the synthesis of glycyl-tRNA, which is required to insert glycine into proteins within the cytosol and mitochondria. To date, eighteen mutations in GARS have been reported in patients with autosomal-dominant Charcot-Marie-Tooth disease type 2D (CMT2D; OMIM 601472), and/or distal spinal muscular atrophy type V (dSMA-V; OMIM 600794). In this study, we report a patient with clinical and biochemical features suggestive of a mitochondrial respiratory chain (MRC) disorder including mild left ventricular posterior wall hypertrophy, exercise intolerance, and lactic acidosis. Using whole exome sequencing we identified compound heterozygous novel variants, c.803C>T; p.(Thr268Ile) and c.1234C>T; p.(Arg412Cys), in GARS in the proband. Spectrophotometric evaluation of the MRC complexes showed reduced activity of Complex I, III and IV in patient skeletal muscle and reduced Complex I and IV activity in the patient liver, with Complex IV being the most severely affected in both tissues. Immunoblot analysis of GARS protein and subunits of the MRC enzyme complexes in patient fibroblast extracts showed significant reduction in GARS protein levels and Complex IV. Together these studies provide evidence that the identified compound heterozygous GARS variants may be the cause of the mitochondrial dysfunction in our patient.Entities:
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Year: 2017 PMID: 28594869 PMCID: PMC5464557 DOI: 10.1371/journal.pone.0178125
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Clinical phenotypes associated with GARS variants in human.
| Kawakami | Del Bo | Antonellis | Rohkamm | Sivakumar | Sivakumar | Lee | Lee | Liao | Liao | Sivakumar | Hamaguchi | James | James | James | Klein | Sivakumar | Dubourg | McMillan | This Study | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Inheritance | AD | AD | AD | AD | AD | AD | AD | AD | AD | ND | AD | AD | AD | AD | AD | AR | AR | |||
| Protein | CD | Ins III | CD | WD | CD | CD | Ins I | Ins III | Ins I | CD | CD | CD | CD | ACBD | ACBD | Ins II | CD | CD | ACBD | CD |
| Phenotype | CMT2 | CMT2D/ | dSMA-V | dHMN-V | CMT2D/ | dSMA-V | dHMN- V | dHMN- V | CMT2 | CMT2 | CMT2D | CMT2 | dHMN- V | Infantile SMA | CMT2 | CMT2 | dSMA-V | dHMN-V | MRCD | MRCD |
| Cohort | 1 affected | 4 affected | 2 affected | 1 affected | 17 affected | 5 affected | 1 affected | 1 affected | 1 affected | 1 affected | 14 affected | 1 affected | 1 affected | 1 affected | 1 affected | 1 affected | 1 affected | 16 affected | 1 affected | 1 affected |
| Age at | <2 Years | 10–35 Years | 13–26 Years | 12 Years | 18 Years (average) | 16.9 Years | 15Years | 13Years | <6 months | 2 Years | 23 Years | 10 Years | 11Years | <6 m | 27 Years | 24 Years | 26Years | 23.3Years | 7 Years | 6 Years |
| Consanguinity | NS | NS | NS | NS | NS | NS | NS | NS | NS | NS | NS | No | NS | NS | NS | NS | NS | No | No | No |
| Ethnicity | Japan | Italy | Sephardic | Ghana | Mongolia | Bulgaria | Korea | Korea | Taiwan | Taiwan | North America | Japan | UK | UK | UK | USA | UK/Australia | France | ND | UK/Australia |
| Clinical features | delayed onset of walking, slow running | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles | delayed milestones, severe generalised weakness | delayed onset of walking, unsteady gait | atrophy and weakness of the hand muscles | slow running | distal limb muscle atrophy and weakness | delayed milestones, severe generalised weakness | distal limb muscle weakness | progressive unsteadiness walking | atrophy and weakness of the hand muscles | atrophy and weakness of the hand muscles or distal four limbs | leukoencephalopathy, lactic acidosis and myalgia | fatigue, exercise-lactic acidosis, mild cardiomyopathy |
| Functional studies | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | MRC enzymology, immunoblotting for |
ND = not done; NS–not stated; CD: Catalytic domain, DI: dimer interface, WD: WHEP domain, Ins I: Insertion I domain, Ins II: Insertion II domain, Ins III: Insertion III domain, ACBD: anticodon binding domain; AD: autosomal dominant, AR: autosomal recessive; CMT2: Charcot-Marie-Tooth hereditary neuropathy type 2; CMT2D: upper limb predominant CMT2; SMA: Spinal muscular atrophy; dSMA: distal SMA, dHMN: distal hereditary motor neuropathy type V, MRC: Mitochondrial respiratory chain, MRCD: Mitochondrial respiratory chain disorder.
Spectrophotometric MRC enzyme diagnostic data in skeletal muscle, liver and fibroblasts.
Patient liver and muscle samples. Data are expressed as activity relative to protein and as % CS ratio, which represents % of the normal control mean value when expressed relative to Citrate Synthase. Bold characters indicate clinically significant abnormal values (H–high, L–low). Complex I (CI), NADH-coenzyme Q1 oxidoreductase; Complex II (CII), succinate-coenzyme Q1 oxidoreductase; Complex III (CIII), decylbenzylquinol-cytochrome c oxidoreductase; Complex IV, cytochrome c oxidase (CIV).
| Enzyme Activity | % CS Ratio | |||
|---|---|---|---|---|
| Muscle | Patient | (Ref Range) | Patient | (Ref Range) |
| CI (nmol/min/mg) | 18 | 19–72 | 18 | 36–269 |
| CII (nmol/min/mg) | 142 | 26–63 | 126 | 52–156 |
| CIII (/min/mg) | 13.1 | 12.8–50.9 | 17 | 62–185 |
| CIV (/min/mg) | 0.21 | 3.3–9.1 | 1 | 36–192 |
| CS (nmol/min/mg) | 320 | 85–179 | - | - |
| CI (nmol/min/mg) | 6 | 8–11 | 53 | 65–137 |
| CII (nmol/min/mg) | 116 | 54–73 | 158 | 59–127 |
| CIII (/min/mg) | 11.7 | 5.2–10.3 | 127 | 77–127 |
| CIV (/min/mg) | 0.05 | 0.5–0.9 | 6 | 75–134 |
| CS (nmol/min/mg) | 33 | 26–31 | - | - |
Dipstick MRC enzyme data from cultured fibroblasts.
Enzyme activity data are expressed as % residual activity relative to protein (% protein).
| Enzyme Activity % | ||
|---|---|---|
| Skin fibroblasts | Patient | Control |
| Complex I | 75% (p = 0.0004) | 100% |
| Complex IV | 45% (p < 0.0001) | 100% |
Fig 1A) Sanger sequencing profile of GARS from the proband and parents showing c.803C>T; p.(Thr268Ile) variant is heterozygous in the proband and the father. B) Sanger sequencing profile of GARS from the proband and parents showing c.1234C>T; p.(Arg412Cys) variant is heterozygous in the proband and the mother. C) Evolutionary sequence conservations of the altered amino acid residues p.Thr268 and p. Arg412 are denoted in bold red in boxes.
In silico analyses of the GARS variants identified in this study.
| Position | Pathogenicity prediction | Grade of conservation | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Patient | Gene | Exon | cDNA | Protein | Sift | GVGD | Polyphen-2 | Mutationtster | PhyloP | PhastCons | MAF (ExAC) | Genotype | Inheritance |
N/A: not applicable; MAF: minor allele frequency; PhyloP: values vary between -14 and +6 (Sites predicted to be conserved are assigned positive scores); PhastCons: values vary between 0 and 1. The closer the value is to 1, the more probable the nucleotide is conserve.
Fig 2Relative position and conservation of GARS mutations.
Model of GARS protein structure showing catalytic domain (blue) and anticodon binding domain (grey). Residues mutated in the proband are displayed as red (Thr268) and green (Arg412) spheres. ATP (sticks) and glycine (orange spheres) are seen in the active site pocket. Pink and purple residues indicate previously reported pathogenic mutations in CMT2D and dSMA-V respectively [6,27,28]. Model based on PDB structure 2ZT7.
Fig 3A) Immunoblot analysis of cultured fibroblasts lysates indicated reduction in expression of GARS protein in patient (P) compared to control (C). Samples containing 20 μg of total protein per lane were loaded in duplicate. Porin was used as a loading control. B) Each data point is immunoblot showing OXPHOS expression in cultured fibroblasts from the proband (P) compared to controls (C) in duplicate with a total of 30 μg of protein in each lane. Porin was used as a loading control.