The Maintenance of Mitochondrial DNA Integrity and Dynamics by Mitochondrial Membranes

Abstract

Mitochondria are complex organelles that harbour their own genome. Mitochondrial DNA (mtDNA) exists in the form of a circular double-stranded DNA molecule that must be replicated, segregated and distributed around the mitochondrial network. Human cells typically possess between a few hundred and several thousand copies of the mitochondrial genome, located within the mitochondrial matrix in close association with the cristae ultrastructure. The organisation of mtDNA around the mitochondrial network requires mitochondria to be dynamic and undergo both fission and fusion events in coordination with the modulation of cristae architecture. The dysregulation of these processes has profound effects upon mtDNA replication, manifesting as a loss of mtDNA integrity and copy number, and upon the subsequent distribution of mtDNA around the mitochondrial network. Mutations within genes involved in mitochondrial dynamics or cristae modulation cause a wide range of neurological disorders frequently associated with defects in mtDNA maintenance. This review aims to provide an understanding of the biological mechanisms that link mitochondrial dynamics and mtDNA integrity, as well as examine the interplay that occurs between mtDNA, mitochondrial dynamics and cristae structure.

Keywords: cristae; mitochondria; mitochondrial diseas; mitochondrial fission; mitochondrial fusion; mtDNA.

Figure 1

Schematic overview of the human mtDNA genome, its replication and the formation of deletions. (a) The structure of mtDNA highlighting the arrangement of protein coding genes, rRNAs (orange) and tRNAs (yellow). The replication origins of the heavy and light strand (OriH and OriL, respectively) are highlighted. (b) Enlargement of the mtDNA non-coding region (NCR) depicting the arrangement of the heavy strand promoter (HSP) and light strand promoter (LSP), the three conserved sequence boxes (CSB), OriH and the termination-associated sequence (TAS). The premature termination of the DNA synthesis of the H-strand at TAS results in the formation of a triple-stranded displacement-loop structure termed the D-loop. The short double stranded product formed within the D-loop is termed 7S DNA. (c) mtDNA replication is initiated at OriH and proceeds unidirectionally until OriL is reached. At this point, DNA synthesis of the light strand is initiated, and both strands are synthesised simultaneously until two completely replicated genomes are produced. The two replicated genomes are physically interlinked by a single-stranded overlap structure, termed a hemicatenane. This structure is resolved by topoisomerase 3α (TOP3α) to produce two separate mtDNA molecules. (d) Copy choice recombination model for the formation of mtDNA deletions. mtDNA deletions generally occur in the major arc. The replication of a repeat sequence in the template heavy strand (yellow boxes) can lead to stalling of POLγ which results in its dissociation from the newly synthesised DNA-end. When Polγ reanneals, it may associate at another repeat sequence further along the template. Following the completion of replication, this slippage event produces two mtDNA genomes; one full length molecule and a second heteroduplex molecule (which has a full-length heavy strand alongside a deletion-containing light strand). The subsequent replication of the heteroduplex molecule culminates in the formation of mtDNA harbouring the deletion.

Figure 2

Mitochondrial dynamics and its role in mtDNA distribution. (a) Schematic overview of mitochondrial fission. Constriction of the mitochondrion occurs by the endoplasmic reticulum (ER) and dynamin related protein 1 (DRP1). The final scission step is performed by DRP1 to produce multiple independent mitochondria. (b) Mitochondrial fusion outline. The mitofusins (MFNs) are responsible for tethering neighbouring mitochondria and fusing the outer membranes together. Fusion of the inner mitochondrial membrane is mediated by optic atrophy 1 (OPA1). (c) Summary of mtDNA segregation and distribution. First, newly replicated mtDNA molecules that are joined by a hemicatenane must be physically separated by topoisomerase 3α. Failure of this process results in the formation of multiple physically joined mtDNA genomes, termed mtDNA catenanes. Following separation, mitochondrial fission is required to distribute the replicated nucleoids into separate mitochondria and facilitate distribution of the genomes around the mitochondrial network. An impairment of fission results in a clustered phenotype whereby many replicated nucleoids are observed in close proximity to each other but are not physically linked together. (d) A lack of mitochondrial fusion is associated with mtDNA instability as observed by the progressive onset of mtDNA deletions and point mutations. In addition, the lack of fusion leads to a depletion in mtDNA copy number.

Figure 3

The relationship between cristae modulators and mtDNA organisation. (a) Schematic overview of a normal mitochondrion. (b) Enlarged cristae region depicting the spatial arrangement of key proteins that are necessary for dictating cristae structure and shape, as well as the organisation of the respiratory chain complexes. Proteins that are potentially responsible for the tethering of mtDNA to the IBM are also highlighted. (c) Loss of the fission factor DRP1 has been associated with the formation of mito-bulb structures. These are regions of dense cristae structure which harbour a number of clustered mtDNA molecules. (d) The loss of IMM fusion and cristae shaping protein OPA1 results in mitochondria that display enlarged cristae junctions and a perturbed cristae structure. In addition, mtDNA copy number is reduced. (e) The loss of MICOS components (MIC60, MIC10 and MIC19) has been associated with a complete loss of cristae junctions and the formation of cristae in concentric circles. Nucleoid clustering is evident following the loss of MICOS components.