Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Thr
Mitochondrial tRNA A15951G mutation may not be associated with Leber’s Hereditary Optic Neuropathy Xi Zhang, Shuaishuai Yu, Yunhai Tu & Wenjie Huang To cite this article: Xi Zhang, Shuaishuai Yu, Yunhai Tu & Wenjie Huang (2015): Mitochondrial Thr
tRNA A15951G mutation may not be associated with Leber’s Hereditary Optic Neuropathy, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1022763
Published online: 22 May 2015.
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Date: 19 September 2015, At: 08:08
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1022763
SHORT COMMUNICATION
Mitochondrial tRNAThr A15951G mutation may not be associated with Leber’s Hereditary Optic Neuropathy Xi Zhang1, Shuaishuai Yu2, Yunhai Tu1, and Wenjie Huang3 Department of Ophthalmic Endoscopic Surgery, the Eye Hospital of Wenzhou Medical University, Wenzhou, China, 2School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China, and 3Ward 3, The Eye Hospital of Wenzhou Medical University, Wenzhou, China
Downloaded by [University of Otago] at 08:08 19 September 2015
1
Abstract
Keywords
Mutation in mitochondrial DNA (mtDNA) has been found to play an important role in the pathogenesis of Leber’s Hereditary Optic Neuropathy (LHON). Three primary mutations, the ND4 G11778A, ND6 T14484C, and ND1 G3460A, have been found to account more than 90% of LHON patients in many families worldwide. In addition to the mutations in genes encoding the respiratory chain complex I, reports concerning the mt-tRNA gene mutations associated with LHON have increased, some pathogenic mutations caused the failure in mt-tRNA metabolism, thereby worsened the mitochondrial dysfunction that is responsible for LHON. Recently, the A15951G mutation in mt-tRNAThr gene has been reported to be a ‘‘modified’’ factor in increasing the penetrance and expressivity of LHON-associated ND4 G11778A mutation in three Chinese families. However, evolutionary conservation analysis of this mutation suggested a poor conservation index and the pathogenicity scoring system showed that this mutation was a neutral polymorphism.
A15951G mutation, LHON, mt-tRNAThr, pathogenic
Introduction Leber’s hereditary Optic Neuropathy (LHON) is a maternally inherited disorder leading to rapid, painless, bilateral vision loss (Howell, 1987; Newman, 1993). It is well known that LHON is a mitochondrial disorder caused by the mutations in mitochondrial genome. Since the landmark discovery of the association between the ND4 G11778A mutation and LHON (Wallace et al., 1988), approximately 25 LHON-associated mitochondrial DNA (mtDNA) mutations have been identified in various ethnic populations (Howell, 2003). Of these, the ND1 G3460A, ND4 G11778A, and ND6 T14484C mutations, which involved genes encoding the subunits of respiratory chain complex I, account for 80–95% of LHON pedigrees in different countries (Brown et al., 1995; Mashima, 1998). However, matrilineal intra-family or interfamily relatives, despite carrying the same LHON associated mtDNA mutations, exhibited the variable severity, age at onset, and progression in visual impairment. Therefore, other modified factors, such as environmental factors, nuclear genes, and mitochondrial genetic background, may contribute to the clinical expression of LHON. Due to the lack of histone protection and a poor DNA repair system, mtDNA has a much higher mutation rate than nuclear DNA (DiMauro & Schon 2001). Theoretically, mtDNA mutations may occur at any nucleotide of its 16.5 kb sequence, apart from the mutations in mitochondrial protein-coding genes, point mutations in mt-tRNA genes being the largest group among them (Brandon et al., 2005). Most recently, mutation at position 15,951 in mt-tRNAThr gene has been reported to be a ‘‘modifier’’ in
Correspondence: Wenjie Huang, Professor, Ward 3, The Eye Hospital of Wenzhou Medical University, Wenzhou, China. E-mail: [email protected]
History Received 22 January 2015 Revised 10 February 2015 Accepted 15 February 2015 Published online 22 May 2015
increasing the penetrance and expressivity of LHON-associated ND4 G11778A mutation (family 1) (Li et al., 2006); moreover, another two Chinese families carrying the A15951G mutation have been reported to be associated with LHON but lacking the three primary mutations (G11778A, T14484C, and G3460A) (families 2 and 3) (Zhang et al. 2011). In this study, we first performed a literature searching for the presence of the A15951G mutation; we further used the phylogenetic approach to see whether this mutation contributed to the penetrance and expressivity of ND4 G11778A mutation.
Materials and methods To accentuate the need for reassessment of the dataset, we took the clinical, genetic, and molecular datasets from Li et al.’s work (2006). For comparison, we incorporated the previous studies concerning the A15951G mutation (Zhang et al., 2011) to evaluate the potential association between this mutation and clinical phenotype. In addition, a phylogenetic approach was used to analyze A15951G mutation between different species. The conservation index (CI) was then calculated by comparing the human nucleotide substitutions with the other vertebrates. We also used the pathogenicity scoring system to predict the A15951G mutation (Yarham et al., 2010, 2011).
Results Complete mitochondrial sequence analysis for LHON families carrying the A15951G mutation Sequence analysis for the mitochondrial genome of the proband in family 1 showed the occurrence of the ND4 G11778A mutation and a distinct set of polymorphisms belonging to Asia haplogroup D4 (Li et al., 2006; Yao et al., 2002). Nevertheless, mtDNA
Downloaded by [University of Otago] at 08:08 19 September 2015
2
X. Zhang et al.
Mitochondrial DNA, Early Online: 1–3
mutations in this Chinese family with LHON showed many of the following reading errors: the C5178A mutation was associated with longevity (Kokaze et al., 2010), the ND3 G10398A mutation was associated with breast cancer (Darvishi et al., 2007), while the CO2/tRNALys intergenic 9-bp deletion corresponding to mtDNA positions 8271–8279 was regarded as a risk factor for hearing loss, and encephalomyopathy in Caucasian population (Borgione et al., 2013); also, this deletion had been found to be a marker for hepatocellular carcinoma (HCC) in the Chinese population (Jin et al., 2012), and polycystic ovary syndrome (Zhuo et al., 2010). Notably, a high prevalence of this deletion has been found in Taiwanese patients with MELAS or MERRF syndrome (Liu et al., 2005), suggested that this deletion may play an important role in the pathogenesis of mitochondrial diseases. On the contrary, a carefully check for the complete mtDNA sequences presented in families 2 and 3 also showed many problems (Zhang et al., 2011): the C8414T mutation was localized at A8 gene but not in A4 gene. Thus, it seemed that other SNPs or mutations in mitochondrial protein-coding genes may play significant roles in clinical manifestation of LHON-associated ND4 G11778A mutation in various ethnic families.
different species (Florentz et al,. 2003). However, Li et al. (2006) regarded this mutation as a candidate pathogenic mutation because this mutation (i) disrupted the A–U base-pairing on the 50 side of the acceptor stem of this tRNA; (ii) 35% reduction of mt-tRNAThr steady-state level was observed from the lymphoblastic cells carrying the A15951G mutation. However, the A15951G mutation was in a homoplasmic form, not heteroplasmic, strongly indicated that this mutation may not be deleterious, as most of the pathogenic mutations were in the heteroplasmic form (Schon et al., 2012). Moreover, pathogenic mutations should be absent from health controls and the mutant mtDNA should segregate with biochemical defect. Thus, the A15951G mutation in mt-tRNAThr gene may not be pathogenic. Pathogenicity scoring system for the A15951G mutation According to the revised pathogenicity scoring system for mt-tRNA mutations (Yarham et al., 2011), we classified the A15951G mutation as ‘‘Neutral polymorphism’’ with a total score of 3 points (Table 1).
Discussion Molecular features of the A15951G mutation The identified homoplasmic A15951G mutation occurred at position 71 in the acceptor arm of mt-tRNAThr gene, as shown in Figure 1, mutation at this 15,951 was not very conserved between
In the current study, we reassessed the possible role of the A15951G mutation in clinical expression of LHON-associated ND4 G11778A mutation by using phylogenetic approach. In fact, the maternal transmission of visual dysfunction in families with
Figure 1. Alignment of mitochondrial tRNAThr gene from different species, arrow indicated the position 71, corresponding to the A15951G mutation.
Table 1. The pathogenicity scoring system for the A15951G mutation. Scoring criteria
A15951G mutation
Score/20
More than one independent report Evolutionary conservation of the base pair Variant heteroplasmy Segregation of the mutation with disease Histochemical evidence of mitochondrial disease Biochemical defect in complex I, III or IV Evidence of mutation segregation with biochemical defect from single-fiber studies Mutant mt-tRNA steady-state level or evidence of pathogenicity in trans-mitochondrial cybrid studies Maximum score
No multiple changes No No No evidence No No
0 0 0 0 0 0 0
Yes
3 3
Classification
6 points: neutral polymorphisms 7–10 points: possibly pathogenic 11 points: definitely pathogenic
Neutral polymorphisms
Downloaded by [University of Otago] at 08:08 19 September 2015
DOI: 10.3109/19401736.2015.1022763
LHON indicates that mutations in mtDNA were the molecular basis for this disorder. Three primary mutations, the G11778A, T14484C, and G3460A mutations, were the most commonly LHON-associated mtDNA mutations, accounting for 80–95% of LHON pedigrees in different ethnic backgrounds (Zhou et al., 2006). In addition, a group called ‘‘secondary’’ LHON-associated mtDNA mutations, including the T4216C, A4917G, and G13708A mutations, were implicated as acting in synergy with primary mtDNA mutation (Johns & Berman, 1991). Moreover, mitochondrial haplogroup J can influence the phenotypic manifestation of the primary LHON G11778A and T14484C mutations in a very large cohort of families of European ancestry (Brown et al., 2002; Howell et al., 2003). The homoplasmic A15951G mutation was localized at adjacent to 30 end of tRNAThr (Florentz et al., 2003). The adenine at this position of tRNA was not conserved from bacteria to human mitochondria (Helm et al., 2000). The conservation index of this mutation was only 56% (Figure 1), an extremely low level of conservation may rule out its involvement in clinical manifestation of LHON-associated ND4 G11778A mutation; moreover, the pathogenicity scoring system showed that the total score of this mutation was only 3 points and belonging to ‘‘neutral polymorphism’’. Apparently, the A15951G mutation should not be regarded as a mutation associated with LHON. Functional analysis of this mutation should be performed to confirm its pathogenicity.
Declaration of interest The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Borgione E, Lo Giudice M, Castello F, Musumeci SA, Di Blasi FD, Savio M, Elia M, et al. (2013). The 9-bp deletion in region V of mtDNA: A risk factor of hearing loss and encephalomyopathy in Caucasian populations? Neurol Sci 34:1223–6. Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, Wallace DC. (2005). MITOMAP: A human mitochondrial genome database – 2004 update. Nucleic Acids Res 33:611–13. Brown MD, Starikovskaya E, Derbeneva O, Hosseini S, Allen JC, Mikhailovskaya IE, Sukernik RI, Wallace DC. (2002). The role of mtDNA background in disease expression: A new primary LHON mutation associated with Western Eurasian haplogroup. J Hum Genet 110:130–8. Brown MD, Torroni A, Reckord CL, Wallace DC. (1995). Phylogenetic analysis of Leber’s hereditary optic neuropathy mitochondrial DNA’s indicates multiple independent occurrences of the common mutations. Hum Mutat 6:311–25. Darvishi K, Sharma S, Bhat AK, Rai E, Bamezai RN. (2007). Mitochondrial DNA G10398A polymorphism imparts maternal Haplogroup N a risk for breast and esophageal cancer. Cancer Lett 249:249–55. DiMauro S, Schon EA. (2001). Mitochondrial DNA mutations in human disease. Am J Med Genet 106:18–26. Florentz C, Sohm B, Tryoen-To´th P, Pu¨tz J, Sissler M. (2003). Human mitochondrial tRNAs in health and disease. Cell Mol Life Sci 60: 1356–75. Helm M, Brule´ H, Friede D, Giege´ R, Pu¨tz D, Florentz C. (2000). Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 6:1356–79.
Mitochondrial A15951G mutation
3
Howell N. (1987). Leber hereditary optic neuropathy: Mitochondrial mutations and degeneration of the optic nerve. Vision Res 37: 3495–507. Howell N. (2003). LHON and other optic nerve atrophies: The mitochondrial connection. Dev Ophthalmol 37:94–108. Howell N, Oostra RJ, Bolhuis PA, Spruijt L, Clarke LA, Mackey DA, Preston G, Herrnstadt C. (2003). Sequence analysis of the mitochondrial genomes from Dutch pedigrees with Leber hereditary optic neuropathy. Am J Hum Genet 72:1460–9. Jin Y, Yu Q, Zhou D, Chen L, Huang X, Xu G, Huang J, et al. (2012). The mitochondrial DNA 9-bp deletion polymorphism is a risk factor for hepatocellular carcinoma in the Chinese population. Genet Test Mol Biomarkers 16:330–4. Johns DR, Berman J. (1991). Alternative, simultaneous complex I mitochondrial DNA mutations in Leber’s hereditary optic neuropathy. Biochem Biophys Res Commun 174:1324–30. Kokaze A, Ishikawa M, Matsunaga N, Karita K, Yoshida M, Ohtsu T, Ochiai H, et al. (2010). Combined effect of longevity-associated mitochondrial DNA 5178 C/A polymorphism and coffee consumption on the risk of hyper-LDL cholesterolemia in middle-aged Japanese men. J Hum Genet 55:577–81. Li R, Qu J, Zhou X, Tong Y, Hu Y, Qian Y, Lu F, et al. (2006). The mitochondrial tRNA(Thr) A15951G mutation may influence the phenotypic expression of the LHON-associated ND4 G11778A mutation in a Chinese family. Gene 376:79–86. Liu CS, Cheng WL, Chen YY, Ma YS, Pang CY, Wei YH. (2005). High prevalence of the COII/tRNA(Lys) intergenic 9-bp deletion in mitochondrial DNA of Taiwanese patients with MELAS or MERRF syndrome. Ann N Y Acad Sci 1042:82–7. Mashima Y, Yamada K, Wakakura M, Kigasawa K, Kudoh J, Shimizu N, Oguchi Y. (1998). Spectrum of pathogenic mitochondrial DNA mutations and clinical features in Japanese families with Leber’s hereditary optic neuropathy. Curr Eye Res 17:403–8. Newman NJ. (1993). Leber’s hereditary optic neuropathy. Ophthalmol Clin North Am 4:431–47. Schon EA, DiMauro S, Hirano M. (2012). Human mitochondrial DNA: Roles of inherited and somatic mutations. Nat Rev Genet 13:878–90. Wallace DC, Singh G, Lott MT, Hodge JA, Schurr TG, Lezza AM, Elsas II LJ, Nikoskelainen EK. (1988). Mitochondrial DNA mutation associated with Leber’s hereditary optic neuropathy. Science 242: 1427–30. Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP. (2002). Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70:635–51. Yarham JW, Al-Dosary M, Blakely EL, Alston CL, Taylor RW, Elson JL, McFarland R. (2011). A comparative analysis approach to determining the pathogenicity of mitochondrial tRNA mutations. Hum Mutat 32: 1319–25. Yarham JW, Elson JL, Blakely EL, McFarland R, Taylor RW. (2010). Mitochondrial tRNA mutations and disease. Wiley Interdiscip Rev RNA 1:304–24. Zhang Y, Zhang JJ, Ji YC, Zhang ML, Tong Y, Zhao FX, Qu J, et al. (2011). The mitochondrial tRNA(Thr) A15951G mutation may be associated with Leber’s hereditary optic neuropathy in two Chinese families. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 28:501–6 (in Chinese). Zhou X, Wei Q, Yang L, Tong Y, Zhao F, Lu C, Qian Y, et al. (2006). Leber’s hereditary optic neuropathy is associated with the mitochondrial ND4 G11696A mutation in five Chinese families. Biochem Biophys Res Commun 340:69–75. Zhuo G, Feng G, Leng J, Yu L, Jiang Y. (2010). A 9-bp deletion homoplasmy in women with polycystic ovary syndrome revealed by mitochondrial genome-mutation screen. Biochem Genet 48:157–63.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Thr
Mitochondrial tRNA A15951G mutation may not be associated with Leber’s Hereditary Optic Neuropathy Xi Zhang, Shuaishuai Yu, Yunhai Tu & Wenjie Huang To cite this article: Xi Zhang, Shuaishuai Yu, Yunhai Tu & Wenjie Huang (2015): Mitochondrial Thr
tRNA A15951G mutation may not be associated with Leber’s Hereditary Optic Neuropathy, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1022763
Published online: 22 May 2015.
Submit your article to this journal
Article views: 12
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Otago]
Date: 19 September 2015, At: 08:08
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1022763
SHORT COMMUNICATION
Mitochondrial tRNAThr A15951G mutation may not be associated with Leber’s Hereditary Optic Neuropathy Xi Zhang1, Shuaishuai Yu2, Yunhai Tu1, and Wenjie Huang3 Department of Ophthalmic Endoscopic Surgery, the Eye Hospital of Wenzhou Medical University, Wenzhou, China, 2School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China, and 3Ward 3, The Eye Hospital of Wenzhou Medical University, Wenzhou, China
Downloaded by [University of Otago] at 08:08 19 September 2015
1
Abstract
Keywords
Mutation in mitochondrial DNA (mtDNA) has been found to play an important role in the pathogenesis of Leber’s Hereditary Optic Neuropathy (LHON). Three primary mutations, the ND4 G11778A, ND6 T14484C, and ND1 G3460A, have been found to account more than 90% of LHON patients in many families worldwide. In addition to the mutations in genes encoding the respiratory chain complex I, reports concerning the mt-tRNA gene mutations associated with LHON have increased, some pathogenic mutations caused the failure in mt-tRNA metabolism, thereby worsened the mitochondrial dysfunction that is responsible for LHON. Recently, the A15951G mutation in mt-tRNAThr gene has been reported to be a ‘‘modified’’ factor in increasing the penetrance and expressivity of LHON-associated ND4 G11778A mutation in three Chinese families. However, evolutionary conservation analysis of this mutation suggested a poor conservation index and the pathogenicity scoring system showed that this mutation was a neutral polymorphism.
A15951G mutation, LHON, mt-tRNAThr, pathogenic
Introduction Leber’s hereditary Optic Neuropathy (LHON) is a maternally inherited disorder leading to rapid, painless, bilateral vision loss (Howell, 1987; Newman, 1993). It is well known that LHON is a mitochondrial disorder caused by the mutations in mitochondrial genome. Since the landmark discovery of the association between the ND4 G11778A mutation and LHON (Wallace et al., 1988), approximately 25 LHON-associated mitochondrial DNA (mtDNA) mutations have been identified in various ethnic populations (Howell, 2003). Of these, the ND1 G3460A, ND4 G11778A, and ND6 T14484C mutations, which involved genes encoding the subunits of respiratory chain complex I, account for 80–95% of LHON pedigrees in different countries (Brown et al., 1995; Mashima, 1998). However, matrilineal intra-family or interfamily relatives, despite carrying the same LHON associated mtDNA mutations, exhibited the variable severity, age at onset, and progression in visual impairment. Therefore, other modified factors, such as environmental factors, nuclear genes, and mitochondrial genetic background, may contribute to the clinical expression of LHON. Due to the lack of histone protection and a poor DNA repair system, mtDNA has a much higher mutation rate than nuclear DNA (DiMauro & Schon 2001). Theoretically, mtDNA mutations may occur at any nucleotide of its 16.5 kb sequence, apart from the mutations in mitochondrial protein-coding genes, point mutations in mt-tRNA genes being the largest group among them (Brandon et al., 2005). Most recently, mutation at position 15,951 in mt-tRNAThr gene has been reported to be a ‘‘modifier’’ in
Correspondence: Wenjie Huang, Professor, Ward 3, The Eye Hospital of Wenzhou Medical University, Wenzhou, China. E-mail: [email protected]
History Received 22 January 2015 Revised 10 February 2015 Accepted 15 February 2015 Published online 22 May 2015
increasing the penetrance and expressivity of LHON-associated ND4 G11778A mutation (family 1) (Li et al., 2006); moreover, another two Chinese families carrying the A15951G mutation have been reported to be associated with LHON but lacking the three primary mutations (G11778A, T14484C, and G3460A) (families 2 and 3) (Zhang et al. 2011). In this study, we first performed a literature searching for the presence of the A15951G mutation; we further used the phylogenetic approach to see whether this mutation contributed to the penetrance and expressivity of ND4 G11778A mutation.
Materials and methods To accentuate the need for reassessment of the dataset, we took the clinical, genetic, and molecular datasets from Li et al.’s work (2006). For comparison, we incorporated the previous studies concerning the A15951G mutation (Zhang et al., 2011) to evaluate the potential association between this mutation and clinical phenotype. In addition, a phylogenetic approach was used to analyze A15951G mutation between different species. The conservation index (CI) was then calculated by comparing the human nucleotide substitutions with the other vertebrates. We also used the pathogenicity scoring system to predict the A15951G mutation (Yarham et al., 2010, 2011).
Results Complete mitochondrial sequence analysis for LHON families carrying the A15951G mutation Sequence analysis for the mitochondrial genome of the proband in family 1 showed the occurrence of the ND4 G11778A mutation and a distinct set of polymorphisms belonging to Asia haplogroup D4 (Li et al., 2006; Yao et al., 2002). Nevertheless, mtDNA
Downloaded by [University of Otago] at 08:08 19 September 2015
2
X. Zhang et al.
Mitochondrial DNA, Early Online: 1–3
mutations in this Chinese family with LHON showed many of the following reading errors: the C5178A mutation was associated with longevity (Kokaze et al., 2010), the ND3 G10398A mutation was associated with breast cancer (Darvishi et al., 2007), while the CO2/tRNALys intergenic 9-bp deletion corresponding to mtDNA positions 8271–8279 was regarded as a risk factor for hearing loss, and encephalomyopathy in Caucasian population (Borgione et al., 2013); also, this deletion had been found to be a marker for hepatocellular carcinoma (HCC) in the Chinese population (Jin et al., 2012), and polycystic ovary syndrome (Zhuo et al., 2010). Notably, a high prevalence of this deletion has been found in Taiwanese patients with MELAS or MERRF syndrome (Liu et al., 2005), suggested that this deletion may play an important role in the pathogenesis of mitochondrial diseases. On the contrary, a carefully check for the complete mtDNA sequences presented in families 2 and 3 also showed many problems (Zhang et al., 2011): the C8414T mutation was localized at A8 gene but not in A4 gene. Thus, it seemed that other SNPs or mutations in mitochondrial protein-coding genes may play significant roles in clinical manifestation of LHON-associated ND4 G11778A mutation in various ethnic families.
different species (Florentz et al,. 2003). However, Li et al. (2006) regarded this mutation as a candidate pathogenic mutation because this mutation (i) disrupted the A–U base-pairing on the 50 side of the acceptor stem of this tRNA; (ii) 35% reduction of mt-tRNAThr steady-state level was observed from the lymphoblastic cells carrying the A15951G mutation. However, the A15951G mutation was in a homoplasmic form, not heteroplasmic, strongly indicated that this mutation may not be deleterious, as most of the pathogenic mutations were in the heteroplasmic form (Schon et al., 2012). Moreover, pathogenic mutations should be absent from health controls and the mutant mtDNA should segregate with biochemical defect. Thus, the A15951G mutation in mt-tRNAThr gene may not be pathogenic. Pathogenicity scoring system for the A15951G mutation According to the revised pathogenicity scoring system for mt-tRNA mutations (Yarham et al., 2011), we classified the A15951G mutation as ‘‘Neutral polymorphism’’ with a total score of 3 points (Table 1).
Discussion Molecular features of the A15951G mutation The identified homoplasmic A15951G mutation occurred at position 71 in the acceptor arm of mt-tRNAThr gene, as shown in Figure 1, mutation at this 15,951 was not very conserved between
In the current study, we reassessed the possible role of the A15951G mutation in clinical expression of LHON-associated ND4 G11778A mutation by using phylogenetic approach. In fact, the maternal transmission of visual dysfunction in families with
Figure 1. Alignment of mitochondrial tRNAThr gene from different species, arrow indicated the position 71, corresponding to the A15951G mutation.
Table 1. The pathogenicity scoring system for the A15951G mutation. Scoring criteria
A15951G mutation
Score/20
More than one independent report Evolutionary conservation of the base pair Variant heteroplasmy Segregation of the mutation with disease Histochemical evidence of mitochondrial disease Biochemical defect in complex I, III or IV Evidence of mutation segregation with biochemical defect from single-fiber studies Mutant mt-tRNA steady-state level or evidence of pathogenicity in trans-mitochondrial cybrid studies Maximum score
No multiple changes No No No evidence No No
0 0 0 0 0 0 0
Yes
3 3
Classification
6 points: neutral polymorphisms 7–10 points: possibly pathogenic 11 points: definitely pathogenic
Neutral polymorphisms
Downloaded by [University of Otago] at 08:08 19 September 2015
DOI: 10.3109/19401736.2015.1022763
LHON indicates that mutations in mtDNA were the molecular basis for this disorder. Three primary mutations, the G11778A, T14484C, and G3460A mutations, were the most commonly LHON-associated mtDNA mutations, accounting for 80–95% of LHON pedigrees in different ethnic backgrounds (Zhou et al., 2006). In addition, a group called ‘‘secondary’’ LHON-associated mtDNA mutations, including the T4216C, A4917G, and G13708A mutations, were implicated as acting in synergy with primary mtDNA mutation (Johns & Berman, 1991). Moreover, mitochondrial haplogroup J can influence the phenotypic manifestation of the primary LHON G11778A and T14484C mutations in a very large cohort of families of European ancestry (Brown et al., 2002; Howell et al., 2003). The homoplasmic A15951G mutation was localized at adjacent to 30 end of tRNAThr (Florentz et al., 2003). The adenine at this position of tRNA was not conserved from bacteria to human mitochondria (Helm et al., 2000). The conservation index of this mutation was only 56% (Figure 1), an extremely low level of conservation may rule out its involvement in clinical manifestation of LHON-associated ND4 G11778A mutation; moreover, the pathogenicity scoring system showed that the total score of this mutation was only 3 points and belonging to ‘‘neutral polymorphism’’. Apparently, the A15951G mutation should not be regarded as a mutation associated with LHON. Functional analysis of this mutation should be performed to confirm its pathogenicity.
Declaration of interest The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Borgione E, Lo Giudice M, Castello F, Musumeci SA, Di Blasi FD, Savio M, Elia M, et al. (2013). The 9-bp deletion in region V of mtDNA: A risk factor of hearing loss and encephalomyopathy in Caucasian populations? Neurol Sci 34:1223–6. Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, Wallace DC. (2005). MITOMAP: A human mitochondrial genome database – 2004 update. Nucleic Acids Res 33:611–13. Brown MD, Starikovskaya E, Derbeneva O, Hosseini S, Allen JC, Mikhailovskaya IE, Sukernik RI, Wallace DC. (2002). The role of mtDNA background in disease expression: A new primary LHON mutation associated with Western Eurasian haplogroup. J Hum Genet 110:130–8. Brown MD, Torroni A, Reckord CL, Wallace DC. (1995). Phylogenetic analysis of Leber’s hereditary optic neuropathy mitochondrial DNA’s indicates multiple independent occurrences of the common mutations. Hum Mutat 6:311–25. Darvishi K, Sharma S, Bhat AK, Rai E, Bamezai RN. (2007). Mitochondrial DNA G10398A polymorphism imparts maternal Haplogroup N a risk for breast and esophageal cancer. Cancer Lett 249:249–55. DiMauro S, Schon EA. (2001). Mitochondrial DNA mutations in human disease. Am J Med Genet 106:18–26. Florentz C, Sohm B, Tryoen-To´th P, Pu¨tz J, Sissler M. (2003). Human mitochondrial tRNAs in health and disease. Cell Mol Life Sci 60: 1356–75. Helm M, Brule´ H, Friede D, Giege´ R, Pu¨tz D, Florentz C. (2000). Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 6:1356–79.
Mitochondrial A15951G mutation
3
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