7. Cytoplasmic inheritance. Mitochondrial genome in eukaryotes.

Cytoplasmic inheritance refers to the transmission of genetic information that

is located in the cytoplasm of a cell, rather than in the nuclear DNA. While the
majority of an organism's genetic material is found in the cell nucleus, certain
genetic elements, such as mitochondrial DNA and chloroplast DNA, are
present in the cytoplasm. Cytoplasmic inheritance is primarily associated with
the transmission of genetic material through these cytoplasmic organelles.

Mitochondria are organelles which function to transform energy as a result of

cellular respiration. The genes located in mitochondria and chloroplasts are
very important for proper cellular function. The mitochondrial DNA and other
extranuclear types of DNA replicate independently of the DNA located in the
nucleus, which is typically arranged in chromosomes that only replicate one
time preceding cellular division. The extranuclear genomes of mitochondria
and chloroplasts however replicate independently of cell division. They
replicate in response to a cell's increasing energy needs which adjust during
that cell's lifespan. Since they replicate independently, genomic recombination
of these genomes is rarely found in offspring, contrary to nuclear genomes in
which recombination is common. Studies show that in most organisms
mtDNA replicates throughout the interphase. At mitosis each daughter cell
receives approximately the same number of mitochondria, but since there is
no mechanism for apportioning exactly equal numbers of mitochondria to the
daughter cells, some cells contain more mtDNA than others.

By isolating mitochondria from cells and analyzing the DNA extracted from
them, it can be seen that each mitochondrion contains multiple mtDNA
molecules. Thus the total amount of mtDNA in a cell depends on the number
of mitochondria, the size of the mtDNA, and the number of mtDNA molecules
per mitochondrion. Each of these parameters varies greatly between different
cell types. Circular molecules of mtDNA consist of two strands of DNA called
the heavy strand (or H-strand) and the light strand (or L-strand).
The two strands have different masses due to different proportions of heavier
nucleotides. While this difference is not known to have any functional
significance, it can be used in the laboratory to segregate the strands of
denatured DNA, and hence to analyze the strands separately.
Studies of mutants in yeasts and other single-celled organisms first indicated
that mitochondria exhibit cytoplasmic inheritance and thus must contain their
own genetic system. The mtDNA is located in the matrix and is sometimes
found attached to the inner mitochondrial membrane.
The entire mitochondrial genome has now been cloned and sequenced from a
number of different organisms, and mtDNAs from all these sources have been
found to encode a similar set of rRNAs, tRNAs, and essential mitochondrial
proteins. Mitochondria encode RNAs, which form mitochondrial ribosomes,
although all but one or two of the ribosomal proteins (depending on the
species) are imported from the cytosol. All of the tRNAs used for protein
synthesis in the mitochondrion are encoded by mtDNAs. As far as is known,
all transcripts of mtDNA and their translation products remain in the
organelles; there is no export of RNAs or proteins. Hybridization studies have
shown that virtually all RNAs found in the mitochondrion are synthesized
there on mtDNA templates. A nuclear-encoded RNA is imported into the
mitochondrion in only one known case: a 135-bp RNA forms an essential
component of a site-specific endonuclease involved in the metabolism of a
primer RNA for mtDNA replication.
Mitochondrial ribosomes differ from cytoplasmic ribosomes in their RNA and
protein compositions, small size, and sensitivity to certain antibiotics. For
instance, cycloheximide inhibits protein synthesis by eukaryotic cytoplasmic
ribosomes but does not affect protein synthesis by mitochondrial ribosomes.
All proteins are synthesized on mitochondrial ribosomes in the presence of
cycloheximide and are encoded by mtDNA.

Surprisingly, the size of the mtDNA, the number and nature of the proteins it
encodes, and even the mitochondrial genetic code itself vary greatly between
different organisms. The mtDNAs of most multicellular animals are around
16-kb circular molecules that encode intronless genes compactly arranged in
both DNA strands. Vertebrate mtDNAs encode the two mRNAs found in
mitochondrial ribosomes, the 22 tRNAS used to translate mitochondrial
mRNAs, and 13 proteins involved in electron transport and ATP synthesis.
All proteins encoded by mtDNA are synthesized on mitochondrial ribosomes.
Most mitochondria-synthesized polypeptides identified thus far are subunits
of multimeric complexes used in electron transport, ATP synthesis, or
insertion of proteins into the inner mitochondrial membrane or
intermembrane space. However, most of the proteins localized in
mitochondria, are encoded by nuclear genes, synthesized on cytosolic
ribosomes, and imported into the organelle by some processes. As far as is
known, all RNA transcripts of mDNA and their translation products remain in
the mitochondrion in which they are produced, and all mDNA-encoded
proteins are synthesized on mitochondrial ribosomes.
Mitochondrial DNA encodes the rRNAs that form mitochondrial ribosomes,
although most of the ribosomal proteins are imported from the cytosol. In
animals and fungi, all the tRNAs used for protein synthesis in mitochondria
also are encoded by mtDNAs. However, in plants and many protozoans, most
mitochondrial tRNAs are encoded by the nuclear DNA and imported into the
mitochondrion.

The severity of disease caused by a mutation in mtDNA depends on the nature

of the mutation and on the proportion of mutant and wild-type mtDNAs
present in a particular cell type. Generally, when mutations in mtDNA are
found, cells contain mixtures of wild-type and mutant mtDNAs – a condition
known as heteroplasmy. Each time a mammalian somatic or germ-line cell
divides, the mutant and wild-type mDNAs segregate randomly into the
daughter cells, as occurs in yeast cells. Thus, the mtDNA genotype, which
fluctuates from one generation and from one cell division to the next, can drift
toward predominantly wild-type or predominantly mutant mtDNAs. Since all
enzymes required for the replication and growth of mammalian mitochondria,
such as the mitochondrial DNA and RNA polymerases, are encoded in the
nucleus and imported from the cytosol, a mutant mtDNA should not be at a
“replication disadvantage”; mutants that involve large deletions of mtDNA
might even be at a selective advantage in replication because they can replicate
faster.
Recent research suggests that the accumulation of mutations in mtDNA is an
important component of aging in mammals. Mutations in mtDNA have been
observed to accumulate with aging, perhaps due to a decrease in the
proofreading ability of DNA polymerase. To study this hypothesis, researchers
used gene "knock-in" techniques to replace the nuclear gene encoding
mitochondrial DNA polymerase with normal proofreading activity with a
mutant gene encoding a polymerase defective in proofreading. Mutations in
mtDNA accumulated much more rapidly in homozygous mutant mice than in
wild-type mice, and the mutant mice aged at a highly accelerated rate.