The document provides an overview of mitochondrial genomes, detailing their structure, function, and evolutionary relevance based on the endosymbiont hypothesis. It highlights mitochondrial processes such as the Krebs cycle, electron transport, and unique features like the presence of ribosomal RNA and genes for respiratory functions. Additionally, it discusses the complexity of plant mitochondrial DNA and its interactions with chloroplast DNA.

1. Mitochondrial Genome

2. Introduction
• membrane-bound organelle (eukaryotic
only!)
• Each cell contains hundreds to thousands of
mitochondria.
• Site of Krebs cycle and oxidative
phosphorylation (the electron transport
chain, or respiratory chain).
• Power House – Synthesis of ATP
• Two membranes: outer and inner.
• Folds of the inner membrane, where most
of oxidative phosphorylation occurs, are
called cristae.
• Inside inner membrane = matrix
• Between membranes = intermembrane
space
• Mitochondrial DNA is inside the inner
membrane.

3. Mitochondria
•Analysis of mitochondrial Genome helps in
•Understanding the molecular basis of cytoplasmic
mutations
•Susceptibility to systemic insecticides
•Sensitivity to fungal toxins

4. Endosymbiont Hypothesis
•Endosymbiont hypothesis: originally proposed in
1883 by Andreas Schimper, but extended by Lynn
Margulis in the 1980s
•Mitochondrial ribosomal RNA genes and other genes
show that the original organism was in the alpha-
proteobacterial family (similar to nitrogen-fixing
bacteria)

5. Endosymbiont Hypothesis
• Evidence
• Mitochondria have their own DNA (circular)
• The inner membrane is more similar to prokaryotic membranes than to
eukaryotic.
• By the hypothesis, the inner membrane was the original
prokaryotic membrane and the outer membrane was from the
primitive eukaryote that swallowed it.
• Mitochondria make their own ribosomes, which are of the prokaryotic 70s
type, not the eukaryotic 80s type.
• Mitochondria are sensitive to many bacterial inhibitors that don’t affect the
rest of the eukaryotic cell, such as streptomycin, chloramphenicol, rifampicin.
• Mitochondrial protein synthesis starts with n-formyl methionine, as in the
bacteria but unlike eukaryotes.

6. •Most of the original bacterial genes have
migrated into the nucleus.
•Eukaryotes that lack mitochondria generally
have some mitochondrial genes in their
nucleus, evidence that their ancestors had
mitochondria that were lost during evolution.

7. Endosymbiont Hypothesis
This is actually a secondary endosymbiosis: the largest cell is engulfing a photosynthetic
eukaryote, which already contains chloroplasts.

8. Mitochondrial Function
Krebs cycle:
• Pyruvate, the product of glycolysis, is produced in the
cytoplasm.
• It is transported into the mitochondrial matrix (inside the
inner membrane).
• There, it is converted into acetyl CoA.
• Fatty acids, from the breakdown of lipids, are also
transported into the matrix and converted to acetyl CoA.
• The Krebs cycle then converts acetyl CoA into carbon dioxide
and high energy electrons. The high energy electrons are
carried by NADH and FADH2.

9. Electron Transport:
• The high energy electrons are removed from NADH and
FADH2, and passed through three protein complexes
embedded in the inner membrane.
• Each complex uses some of the electrons’ energy to pump H+
ions out of the matrix into the intermembrane space.
• The final protein complex gives the electrons to oxygen,
converting it to water.
• The H+ ions come back into the matrix, down the
concentration gradient, through a fourth complex, ATP
synthase (also called ATPase), which uses their energy to
generate ATP from ADP and inorganic phosphate.
• In brown fat, the synthesis of ATP is uncoupled from the flow
of H+ ions back into the matrix. The H+ ions flow through a
protein called thermogenin, and not through the ATPase. The
energy is converted into heat: the primary way we keep warm
in cold weather.

10. Mitochondrial Function

11. Size and organization
•Plant Mt.DNA – Much larger and more complex
•Size : 200 – 2500 Kb
•Analyses of cucurbit mtDNAs
• seven-fold range in genome size within this family,
• 330 kb in watermelon to approximately 2500 kb in muskmelon
•Changes in size occurs very rapidly
•Closely related species will have quite different
mitochondrial genome size
•Physical form of genome is not well understood
• Circular DNA
• Mitochondrial plasmid DNA
• Collection of circle- Exist as a population of subgenomic circles

12. Organization – Key feautures
Several general features of higher plant mitochondrial genomes
1. The genomes are larger than those from mammals and fungi.
2. Organized as multiple circular molecules, with conversion of circle types
mediated by recombination between repeated sequences.
3. Mitochondrial genomes from closely related species are highly conserved in
primary sequence, but vary greatly in linear gene order.
4. Chloroplast DNA sequences are found in mitochondrial DNA.
5. In addition to high molecular weight mtDNA, plasmid-like molecules are
present in mitochondria.

13. Chloroplast sequences in mitochondrial genome
•Sequences highly homologous to chloroplast DNA are
present in the mitochondrial genomes of many species
•Maize has inverted repeat sequences(12 Kb)of
chloroplast genome in mitochondrial genome
• Carries several tRNA and 16s rRNA sequences
•Sequence homologous to the chloroplast ribulose-l ,5-
bisphosphate carboxylase large subunit gene was also
found in mtDNA
•These studies demonstrate that DNA transfer from
chloroplasts to mitochondria is common in higher plants
and that most of the events are recent
•No direct evidence on mechanism

14. GENE CONTENT. STRUCTURE AND EXPRESSION
Special features of mitochondrial genome
• Ribosomal protein gene, rRNA, tRNA for mitochondrial translation system
• Proteins in ETC and ATP ase complex
• rRNA arrangement pattern is similar in yeast
• 26s rRNA – separated from 18s and 5s rRNA segments by a long distance
• Intron less sequences : COI(cytochrome c oxidase), COB gene
(apocytochrome B)
• Mitochondrial tRNA is diverse – differs in structure from prokaryotes and
eukaryotes
• Mitochondrial Ribosomes – 77-78s units in plants
• No Polyadenylation
• Multiple Termination, Initiation and Processing sites
• Genetic code is also different
• Eg: CGG – Tryptophan (plants) {TGG- Mammals, TGC/UGA- yeast}

15. Mitochondrial genes
Genes for respiratory chain
functions
• Complex I, the NADH-dehydrogenase
(nine polypeptides, genes nad1–7, nad4L
and nad9) –
The NAD10 subunit of complex I,
which is encoded mitochondrially in some
fungi and algae.
• Complex II, the succinate dehydrogenase
(1 subunit, sdh4)
Genes for three subunits of complex II
are found in the mitochondrial genomes of
some red and brown algae, two units in M.
polymorpha, but only one in Arabidopsis.
• Complex III, the cytochrome-c reductase
(1 polypeptide, cytb)
• Complex IV, the cytochrome-c oxidase
(three subunits, cox1–3).

16. Mitochondrial DNA replication
• Replication have been identified by sequence homology and from proteomic
data.
• Among those, plant organellar DNA polymerases were identified by their
similarities to the known mitochondrial DNA polymerase of animals and
yeast.
• In A. thaliana, there are two organellar DNA polymerases, Pol1A and Pol1B,
which are dual targeted to both mitochondria and plastids and which are
apparently redundant in their functions .
• Individually, each of them is dispensable, because the mutants show no
visible phenotypes, apart from a small reduction in mtDNA and chloroplast
DNA (cpDNA) copy numbers.
• Conversely, the double mutant is not viable, showing that the two
polymerases are redundant for organellar genome replication.

17. THANK YOU