Mitochondrial DNA rearrangements, including partial duplications, occur in young and old rat tissues

Effects of Ageing on the Mitochondrial Genome in Rat Vestibular Organs

Background:

Deterioration in vestibular function occurs with ageing and is linked to age-related falls. Sensory hair cells located in the inner ear vestibular labyrinth are critical to vestibular function. Vestibular hair cells rely predominantly on oxidative phosphorylation (OXPHOS) for ener-gy production and contain numerous mitochondria. Mitochondrial DNA (mtDNA) mutations and perturbed energy production are associated with the ageing process.

Objective:

We investigated the effects of ageing on mtDNA in vestibular hair and support cells, and vestibular organ gene expression, to better understand mechanisms of age-related vestibular deficits.

Methods:

Vestibular hair and supporting cell layers were microdissected from young and old rats, and mtDNA was quantified by qPCR. Additionally, vestibular organ gene expression was analysed by microarray and gene set enrichment analyses.

Results:

In contrast to most other studies, we found no evidence of age-related mtDNA deletion mu-tations. However, we found an increase in abundance of major arc genes near the mtDNA control re-gion. There was also a marked age-related reduction in mtDNA copy number in both cell types. Ves-tibular organ gene expression, gene set enrichment analysis showed the OXPHOS pathway was down regulated in old animals.

Conclusion:

Given the importance of mtDNA to mitochondrial OXPHOS and hair cell function, our findings suggest the vestibular organs are potentially on the brink of an energy crisis in old animals

Mitochondrial genome of Thais clavigera (Mollusca: Gastropoda): affirmation of the conserved, ancestral gene pattern within the mollusks

Class Gastropoda includes a large number of described species, many with extensively rearranged mitochondrial genomes. We sequenced the mitogenome of the rock shell, Thais clavigera (Gastropoda: Muricidae), an intertidal snail, using long PCR with primers designed on the basis of expressed sequence tags. The mitogenome of T. clavigera consists of 2 rRNAs, 22 tRNAs, and 13 protein-coding genes, but no control region. Structural comparisons revealed that the order Sorbeoconcha, including T. clavigera, have nearly identical mitochondrial gene patterns. However, they have an inversion between a tRNA(Phe)-tRNA(Glu) cluster that comprises 21 genes, but most of the remaining structure is similar to the putative mollusk ground pattern. These findings will provide a better insight into mitochondrial gene rearrangement over the course of gastropod evolution.

Detection of deletions flanked by short direct repeats in mitochondrial DNA of aging Drosophila

Cumulative damage due to reactive oxygen species (ROS) in mitochondria, especially in mitochondrial DNA (mtDNA), would result in a decrease in mitochondrial respiratory function and contributes to the age-related decline in the physiological functioning of organisms. Previously, we reported the tissue-specific accumulation of deleted mtDNA with age in Drosophila melanogaster. In the present study, to understand the mechanism by which mtDNA deletion is generated with age, nucleotide sequences of deleted mtDNA were determined. Consequently, 33 different sequences each containing a deletion were obtained from flies that were more than 55-day-old. Most of the deletions were found to be flanked by short direct repeats. The present results, together with those from other animals, suggest that there is a common mechanism generating mtDNA deletions through direct repeats.

Molecular Mechanisms of Extensive Mitochondrial Gene Rearrangement in Plethodontid Salamanders

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

Human mitochondrial DNA with large deletions repopulates organelles faster than full-length genomes under relaxed copy number control

Partially-deleted mitochondrial DNA (DeltamtDNA) accumulates during aging of postmitotic tissues. This accumulation has been linked to decreased metabolic activity, increased reactive oxygen species formation and the aging process. Taking advantage of cell lines with heteroplasmic mtDNA mutations, we showed that, after severe mtDNA depletion, organelles are quickly and predominantly repopulated with DeltamtDNA, whereas repopulation with the wild-type counterpart is slower. This behavior was not observed for full-length genomes with pathogenic point mutations. The faster repopulation of smaller molecules was supported by metabolic labeling of mtDNA with [3H]thymidine during relaxed copy number control conditions. We also showed that hybrid cells containing two defective mtDNA haplotypes tend to retain the smaller one as they adjust their normal mtDNA copy number. Taken together, our results indicate that, under relaxed copy number control, DeltamtDNAs repopulate mitochondria more efficiently than full-length genomes.

Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss

We determined the complete mitochondrial DNA (mtDNA) sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified, in both genomes, all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from others found in arthropod mtDNAs in the location of at least four genes or gene blocks. This novel gene arrangement is unusual for animal mtDNA in that genes with identical transcriptional polarities are clustered in the genome, and the two clusters are separated by two noncoding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.

Mitochondrial DNA deletion mutations are concomitant with ragged red regions of individual, aged muscle fibers: analysis by laser-capture microdissection

Laser-capture microdissection was coupled with PCR to define the mitochondrial genotype of aged muscle fibers exhibiting mitochondrial enzymatic abnormalities. These electron transport system (ETS) abnormalities accumulate with age, are localized segmentally along muscle fibers, are associated with fiber atrophy and may contribute to age-related fiber loss. DNA extracted from single, 10 microm thick, ETS abnormal muscle fibers, as well as sections from normal fibers, served as templates for PCR-based deletion analysis. Large mitochondrial (mt) DNA deletion mutations (4.4-9.7 kb) were detected in all 29 ETS abnormal fibers analyzed. Deleted mtDNA genomes were detected only in the regions of the fibers with ETS abnormalities; adjacent phenotypically normal portions of the same fiber contained wild-type mtDNA. In addition, identical mtDNA deletion mutations were found within different sections of the same abnormal region. These findings demonstrate that large deletion mutations are associated with ETS abnormalities in aged rat muscle and that, within a fiber, deletion mutations are clonal. The displacement of wild-type mtDNAs with mutant mtDNAs results in concomitant mitochondrial enzymatic abnormalities, fiber atrophy and fiber breakage.