Nuclear mitochondrial DNA segment
Nuclear mitochondrial DNA segments or genetic loci describe a transposition of any type of cytoplasmic mitochondrial DNA into the nuclear genome of eukaryotic organisms.
More NUMT sequences of different sizes and lengths in the diverse number of eukaryotes have been detected as whole genome sequencing of different organisms accumulates. They have often been unintentionally discovered by researchers who were looking for mitochondrial DNA. NUMTs have been reported in all studied eukaryotes, and nearly all mitochondrial genome regions can be integrated into the nuclear genome. However, NUMTs differ in number and size across different species. Such differences may be accounted for by interspecific variation in such factors as germline stability and mitochondria number. After the release of the mtDNA into the cytoplasm, due to the mitochondrial alteration and morphological changes, it is transferred into the nucleus and inserted by double-stranded break repair processes into the nuclear DNA. A correlation has been found between the fraction of noncoding DNA and NUMT abundance in the genome, and NUMTs are observed to have non-random distribution and a higher likelihood of being inserted in certain genomic regions. Depending on the location of the insertion, NUMTs might disrupt gene function. In addition, de novo integration of NUMT pseudogenes into the nuclear genome can have adverse effects.
In the domestic cat, mitochondrial gene number and content were amplified 38 to 76 times in the cat's nuclear genome besides being transposed from the cytoplasm. Cat NUMT sequences did not appear to be functional due to the discovery of multiple mutations, differences in mitochondrial and nuclear genetic codes, and the apparent insertion within typically inert centromere regions. The presence of NUMT fragments in the genome is not problematic in all species; for instance, it is shown that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. Although the extended translocation of mtDNA fragments and their co-amplification with free mitochondrial DNA has been problematic in the diagnosis of mitochondrial disorders, in the study of population genetics and phylogenetic analyses, scientists have used NUMTs as genetic markers to determine the relative rate of nuclear and mitochondrial mutation and recreating the evolutionary tree.
In 2022, scientists reported the discovery of ongoing transfer of mitochondrial DNA into DNA in the cell nucleus. Previously, NUMTs were thought to have arisen before the existence of humans. 66,000 whole-genome sequences indicate this occurs as frequently as approximately once every 4,000 human births.
History
According to the endosymbiosis theory, which gained acceptance around the 1970s, the mitochondrion, as a major energy producer in the cell, was previously a free-living prokaryote that invaded a eukaryotic cell. Under this theory, symbiotic organelles gradually transferred their genes to the eukaryotic genome, implying that mitochondrial DNA was gradually integrated into the nuclear genome. Despite the metabolic alterations and functional adaptations in the host eukaryotes, circular mitochondrial DNA is contained within the organelles. mtDNA has an essential role in the production of necessary compounds, such as required enzymes for the proper function of mitochondria. Specifically, it has been suggested that certain genes within the organelle are necessary to regulate redox balance throughout membrane-associated electron transport chains. These parts of the mitochondrial genome have been reported to be the most frequently employed. Mitochondria are not the only locations within which mtDNA can be found; sometimes mtDNA can be transferred from organelles to the nucleus; the evidence of such translocation has been seen by comparing mtDNA sequences with the genome sequence in the nucleus. The integration and recombination of cytoplasmic mtDNA into the nuclear DNA is called nuclear mitochondrial DNA.The possible presence of organelle DNA inside the nuclear genome was suggested after discovering homologous structures to the mitochondrial DNA in the nucleus, which was shortly after the discovery of independent DNA within the organelles in 1967. This topic stayed untouched until the 1980s. Initial evidence that DNA could move among cell compartments came when fragments of chloroplast DNA were found in the maize mitochondrial genome with the help of cross-hybridization, chloroplast and mitochondrial DNA, and physical mapping of homologous regions. After this initial observation, John Ellis coined the term promiscuous DNA to signify the transfer of DNA intracellularly from one organelle to the other and denote the presence of organelle DNA in multiple cellular compartments. The search for mtDNA in nuclear DNA continued until 1994, when the transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat was reported by evolutionary geneticist, Jose V. Lopez, who coined the term NUMT to designate the large stretches of mitochondrial DNA in the nuclear genome.
Currently, the whole genomes of many eukaryotes, both vertebrate and invertebrate, have been sequenced and NUMTs have been observed in the nuclear genome of various organisms, including yeast, Podospora, sea urchin, locust, honey bee, Tribolium, rat, maize, rice, and primates. In Plasmodium, Anopheles gambiae and Aedes aegypti, NUMTs can barely be detected. In contrast, conserved fragments of NUMT were identified in genome data for Ciona intestinalis, Neurospora crassa, Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, and Rattus norvegicus. Agostinho Antunes and Maria João Ramos discovered the presence of NUMTs in the fish genome in 2005 by using BLAST, MAFFT, genome mapping, and phylogenic analysis. The western honey bee and Hydra magnipapillata are, respectively, the first and second animals with the highest ratio of NUMTs to the total size of the nuclear genome while the gray short-tailed opossum is the record holder for NUMT frequency among vertebrates. Like animals, NUMTs are abundant in plants, and the longest NUMT fragment known so far is a 620 kb partially-duplicated insertion of the 367 kb mtDNA of Arabidopsis thaliana.
Mechanism of NUMT insertion
NUMT insertion into the nuclear genome and its persistence in the nuclear genome is initiated by the physical delivery of mitochondrial DNA to the nucleus. This step follows by the mtDNA integration into the genome through a non-homologous end joining mechanism during the double-strand break repair process as envisioned by studying Saccharomyces cerevisiae, and terminates by intragenomic dynamics of amplification, mutation, or deletion, collectively known as post-insertion modifications. The mechanism of mtDNA transfer into nucleus is not yet fully understood.Transfer of the released mtDNA into the nucleus
The first step in the transfer process is the release of mtDNA into the cytoplasm. Peter Thorsness and Thomas Fox demonstrated the rate of relocation of mtDNA from mitochondria into the nucleus using ura3- yeast strain with an engineered URA3 plasmid, a required gene for uracil biosynthesis, in the mitochondria. During the propagation of such yeast strains carrying a nuclear ura3 mutation, plasmid DNA that escapes from the mitochondrion to the nucleus complements the uracil biosynthetic defect, restoring growth in the absence of uracil, and easily scored phenotype. The rate of DNA transfer from the mitochondria to the nucleus was estimated as 2 x 10−5 per cell per generation, while in the case of the cox2 mutant the rate of transfer of the plasmid from the nucleus to the mitochondria is approximately at least 100,000 times less. Many factors control the rate of mtDNA escapes from mitochondria to the nucleus. The higher rate of mutation in mtDNA in comparison with nDNA in the cells of many organisms is an important factor promoting the transfer of mitochondrial genes into the nuclear genome. One of the intergenic factors that results in more frequent destruction of mitochondrial macromolecules, including mtDNA, is the presence of high level of reactive oxygen species generated in mitochondria as the by-products in ATP synthesis. Some other factors influencing the escape of mtDNA from mitochondria include the action of mutagenic agents and other forms of cellular stress that can damage mitochondria or their membranes, which makes assuming that exogenous damaging agents increase the rate of mtDNA escape into the cytoplasm possible. Thorsness and Fox continued their research to find the endogenous factors effecting mtDNA escape into the nucleus. They isolated and studied 21 nuclear mutants with different combinations of mutations in at least 12 nuclear loci called the yme mutations, in different environmental conditions since some of these mutations cause temperature sensitivity. They discover that these mutations which perturb mitochondrial functions affect mitochondrial integrity and led to mtDNA escaping into the cytoplasm. Additionally, defects in the proteins change the rate of mtDNA transfer into the nucleus; for instance, in the case of the yme1 mutant, abnormal mitochondria are targeted for degradation by the vacuole with the help of pep4, a major proteinase, and degradation increases mtDNA escape into the nucleus through mitophagy. Thorsness and Corey Campbell found that by disrupting pep4, the frequency of mtDNA escape in yme1 strains decreases. Similarly, the disruption of PRC1, which encodes carboxypeptidase Y, lowers the rate of mtDNA escape in yme1 yeast.Evidence shows that mitophagy is one of the possible ways for mtDNA transfer into the nucleus and determined to be the most supported pathway up to now. The first pathway is a yme1 mutant that results in inactivation of YMe1p protein, a mitochondrial-localized ATP-dependent metalloproteinase, leading to high escape rate of mtDNA to the nucleus. Mitochondria of the yme1 strain are taken up for degradation by the vacuole more frequently than the wild-type strain. Moreover, cytological investigations have suggested several other possible pathways in the diverse number of species, including a lysis of the mitochondrial compartment, direct physical connection and membrane fusion between mitochondria and nucleus, and the encapsulation of mitochondrial compartments inside the nucleus.