Complete mitochondrial DNA genome sequence variation of Chinese families with mutation m.3635G>A and Leber hereditary optic neuropathy

Abstract

Purpose: The majority of Leber hereditary optic neuropathy (LHON) cases are caused by one of three mitochondrial DNA (mtDNA) primary mutations (m.3460G>A, m.11778G>A, and m.14484T>C). In recent studies, we and others have shown that mutation m.3635G>A is a primary LHON mutation, particularly in Chinese. The purpose of this study was to perform a thorough analysis for the complete mtDNA genome sequence variation in Chinese patients with m.3635G>A and to identify potentially functional variants cosegregated with m.3635G>A.

Methods: The complete mtDNA genomes of five Chinese patients with LHON carrying m.3635G>A were determined. A phylogenetic tree was constructed to distinguish the private and ancestral mtDNA variants in each lineage. Previously unreported variants in each mtDNA were defined with a web-based and database search. mtDNA variants that changed the structure of the membrane-spanning region of the protein were also evaluated, together with evolutionary conservation analysis, to predict their potential pathogenicity.

Results: The five patients with LHON sequenced in this study belonged to haplogroups M7b4 (Le131), F1a (Le329 and Le337), B5b (Le569), and M7b6 (Le834), which suggested multiple origins of m.3635G>A. Private variants m.12811T>C, m.14063T>C, m.15237T>C, and m.9071C>T in these patients were predicted to change the structure of the membrane-spanning region of the respective proteins.

Conclusions: Mutation m.3635G>A had multiple origins in Chinese patients with LHON. We also identified several potentially functional variants cosegregated with m.3635G>A.

Figure 1

Haplogroup classification tree of nine complete mtDNA sequences with m.3635G>A. The revised Cambridge Reference Sequence (rCRS) [18] was included in the tree to show the phylogenetic position of each lineage. Deletions and insertions are denoted with a “d” and “+”, respectively; “r” indicates the variant occurs in the rRNA genes; “t” indicates the variant occurs in the tRNA genes; “nc” indicates the variant occurs in the non-coding region; synonymous and non-synonymous variants are labeled “s” and “ns”, respectively; suffixes A, C, and G mean transversions; recurrent mutations are underlined; back mutations are underlined and marked “@”.

Figure 2

Membrane-spanning region prediction plot produced by the TMpred program. The protein membrane-spanning regions and their orientation were predicted by the TMPRED program. A: Variants m.12811T>C (p.Y159H) and m.14063T>C (p.I576T) changed the structure of the membrane-spanning region of the MT-ND5 protein. B: Variant m.15237T>C (p.I164T) changed the structure of the membrane-spanning region of the MT-CYB protein. C: Variant m.9071C>T (p.S182L) changed the structure of the membrane-spanning region of the MT-ATP6 protein.