Mitochondrial Genome

The mitochondria are organelles present in the vast majority of cell eukaryotes that are derived from the endosymbiosis of an alpha-proteobacterium about two billion years ( endosymbiotic theory ). The mitochondria retained their own genomes. The latter, although very small compared to that of a bacterium, is essential for the proper functioning of these organelles. The mitochondrial genome is particularly used in population genetics human, or agronomy. It differs from the rest of the genome of eukaryotic cells through its asexuality , which is causing the phenomenon of cytoplasmic male sterility.

Confined within mitochondria , organelles that generate cellular energy, the mitochondrial genome (mtDNA) is distinct from the DNA contained in the nucleus. The transmission of this DNA is usually called non-Mendelian , in most cases it is transmitted by the mother. But there are many exceptions in plants, fungi and even animals.

Evolution

Origin of the mitochondrial genome

It is now accepted that mitochondria are derived from the endosymbiosis of an -proteobacterium occurred there about 2 billion years. ^{Alteration of the mitochondrial genome}

Although many vital functions (metabolism of DNA , the RNA , protein synthesis , respiration, etc..) always take place within the mitochondria, the ancestral genomes of bacteria were significantly altered had during the evolution. Thus, the mitochondrial genome contains today a very small part of the original genome. The sequences deleted from the mitochondrial genome were either transferred to the nucleus, is permanently lost.

Recombination and repair of mtDNA

It is often said that the organelles reproducing by asexual reproduction, there is no recombination of their genomes. However, recombination to eliminate mutations deleterious genomes, the transfer of mitochondrial genes to the nuclear genome would be advantageously selected for allowing the recombination of these genes (once integrated into the nuclear genome) and thus the elimination of unfavorable mutations. However this is not an absolute rule, the recombination of mitochondrial genomes exists, but its frequency varies greatly from one species to another.

Maintenance of mitochondrial genes

However, there is a part of the mitochondrial genes have never been transferred to the nucleus in the evolution of eukaryotes. This suggests that the transfer of these genes to the nucleus is cons-selected or very difficult to implement. There are two main barriers to the passage of these genes to the nucleus.

First, there are differences between the genetic code of the host and the symbiont. Thus, a nucleotide sequence transferred from the mitochondrion to the nucleus does not necessarily give the same protein, and gene transfer may be associated with loss of function of the protein.

In addition, a number of proteins that have never been transferred during evolution show a high hydrophobicity. This could hinder the passage of these proteins across membranes of organelles, making gene transfer difficult .

Structure and composition

Mitochondrial genomes have undergone numerous changes. This is evident in their sizes, since the genome of a bacterium of the genus Rickettsia is approximately 1 megabase and has nearly 1000 genes, whereas the human mitochondrial genome is only 16kb, and that of Arabidopsis thaliana 367KB. Mitochondrial genomes are particularly heterogeneous, like those of some chaetognaths (to Sagitta, metazoans constituting a large proportion of plankton ) retaining only a dozen genes with no tRNA on just 11kb, others like the corn exceeding 700kb and covering more than 100 genes. Significant changes have taken place in terms of its composition or how it works fine. Thus the majority of known mitochondrial genomes are transcribed by RNA polymerase type virus and not bacteria. Only known exception to this day the mitochondrial genome Reclinomonas americana , which contains the sequences of subunits of RNA polymerase in bacterial type.

The mitochondrial genome is highly dynamic, it is mostly heteroplasmic in plants and animals, that is to say that coexists in different forms within the same mitochondrion . It can be found as circular or linear, double or single stranded. These different forms are, among others, the products of mitochondrial genome replication by a rolling circle mechanism, but also a mechanism of replication-dependent recombination, similar to the replication of phage T4. Mitochondrial genomes are usually represented as circular, called "ring master" which is the molecule that best describes the genome.

Arabidopsis thaliana, this molecule is 367KB and is rich in small repeat sequences , 22 pairs of identical repetitions of more than 100bp, including two major 6.5 and 4.2 kb ( ecotype C24). Only these two regions are involved in frequent events of recombination , creating three circular forms of 134, 233 and 367KB. The ratio between different forms of the genome can vary, but typically form a majority, the small molecules of DNA that can be produced at these events are called sublimate. Recombination events can also be initiated outside the major repeat sequences and these changes may involve the phenomenon of cytoplasmic male sterility or, in mammals, genetic diseases.

Composition genes

There are three main types in the gene composition of mitochondrial genomes. In yeast and plants , the size and organization of the mitochondrial genome are highly variable. In mammals , the mitochondrial genome is very compact. Finally, it is compact, scalable and has an area rich in adenine and thymine in arthropods.

human mitochondrial genome

Organization of the mitochondrial DNA of mammals

In the human , the human mitochondrial genome is circular. It contains 37 genes , which encode 13 proteins , 22 transfer RNAs and 2 ribosomal RNA. Genes are arranged one after the other, and are only separated by short noncoding regions. The genes encoding the proteins are separated from each other by genes encoding transfer RNA. A regulatory region of 600pb includes the origins of transcription and replication origin.

mitochondrial genome of Drosophila

In the Drosophila , the mitochondrial genome is 19.5 kb composite. It contains 37 genes encoding 13 proteins , 22 transfer RNAs and 2 ribosomal RNA. Mitochondria have the same genes in Drosophila and mammals, but the arrangement of genes in the mitochondrial genome is different in both species. The coding sequences account for 57% of the genome.

mitochondrial genome of yeast

The yeast mitochondrial genome has a 86kb long with 43 genes encoding 19 proteins , 25 transfer RNAs and 2 ribosomal RNA. The coding sequences account for 23% of the genome.

mitochondrial genome of Arabidopsis thaliana

Arabidopsis thaliana mitochondrial genome is 367KB, it comprises a total of 60 genes , 33 encoding proteins , three encoding ribosomal RNA and 21 encoding transfer RNA . These genes cover only 10% of the genome, an additional 10% are represented by 74 ORFs over 300 bp with no homology with known genes specific, and for which no protein product has been observed so far. Genes are often organized in small units of transcription , which gives a very particular mitochondrial genome. Indeed, it has a low density of genes, about a gene for 8kb, and clustering of these genes on small sequences, creating areas of the genome of up to 27kb with only a few or putative ORFs tRNA. Repeated three areas cover 7% of the genome, 8% are found in introns , 5% are traces of transposons or locally chloroplast , thus leaving 60% of the genome with no obvious function or origin. The collection of transfer RNA is not complete, it covers only 14 amino acids and 22 codons , tRNAs corresponding to the remaining six amino acids must be imported into the nucleus ( alanine , arginine , histidine , leucine , phenylalanine , threonine and valine ). It should be noted that of the 22 tRNAs included in the mitochondrial genome, 4 are from chloroplast. Of the 33 protein-coding genes, six encode proteins of ribosome , a gene encodes a maturase , a protein not yet known function (mttB), and all the other genes encode subunits of the chain transfer electron or proteins involved in the synthesis of cytochrome C. So there is no gene for the transcription, or RNA polymerase or transcription factor , all proteins involved in these processes must be imported from the nucleus.

Variation of the genetic code

The mitochondria use a genetic code different from the universal genetic code used by the vast majority of living organisms. In fact there are 17 different genetic codes, including 11 for the mitochondria of different organisms . It should be noted that associations between species and mitochondrial genetic code are changing at the whim of new sequencing mitochondrial genomes. For example code # 5 called "invertebrate mitochondrial code" is confirmed for species such as Caenorhabditis elegans or Drosophila (with the exception of the absence of codon AGG), but such is not the case for urchins , which have their own code (No. 9).

cytoplasmic male sterility

The male sterile cytoplasm is a phenomenon whereby a dioecious plant finds himself unable to produce fertile male gametes. The term cytoplasm refers to the fact that the phenotype is caused by a factor carried by the mitochondrial genome. This process has two major interests in agronomy: facilitate the production of hybrid offspring from naturally pollinated plants, and thus benefit from the phenomenon of heterosis or hybrid vigor, but also for distributing seed plants that can yield offspring used for a new seedlings. In nature the phenomenon of cytoplasmic male sterility is counterbalanced by the appearance of factors of fertility restoration, encoded by the nucleus.

Genetic Analysis

The mitochondrial genome is used for two types of genetic analysis at least. They allow the study of mother-child affiliations on the one hand and the other dating lines. Thus studies of the early 2000s showed that all mitochondria human would have a common African origin, dated about 150,000 years .

The principle of these dates is that mitochondrial DNA mutate spontaneously and uniformly over the generations. Thus the frequency of mitochondrial DNA differences between two evaluates the date on which these two DNAs were identical. There is no exchange, at least in humans, since these genes come only from the mother.

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