cell bio

1. Mitochondrial molecular genetics 1
• focus on mitochondria: brief overview of their
function and structure
• mtDNA structure and replication:
- animals
- yeast
- plants
• inheritance of mitochondria
- petite mutants of yeast
• biogenesis of mitochondria by fission

2. MITOCHONDRIA
• essential for cell life
- ATP synthesis
- many metabolic intermediates
• essential for cell death
- unprogrammed death: necrosis
( eg, due to loss of energy status)
- programmed cell death
(apoptosis - controlled cell destruction)

3. • Two membranes
• Inner membrane invaginated
• Numbers of mitochondria per cell
vary but usually 100s/cell
Matrix contains the TCA
cycle (and other) soluble
enzymes
Inner membrane
contains metabolite
transporters and the
electron transport chain
Mitochondrial structure

4. The ribosomes can actually be visualized in some mitochondria. In these
figures, they are seen in the matrix as small dark bodies. DNA can also be
visualized in mitochondria. The DNA is circular and resembles that of a
bacterium in its basic structure.
Mitochondria also have their own ribosomes and tRNA:
• 22 tRNAs
• rRNAs (16S and 12S)

5. Mitochondria have their own DNA and Ribosomes
Mitochondria have some of their own DNA, ribosomes, and can make many
of their own proteins. The DNA is circular and lies in the matrix in structures
called "nucleoids". Each nucleoid may contain 4-5 copies of the
mitochondrial DNA (mtDNA).
mitochondrial
DNA

6. To visualize the structure of mitochondrial DNA, we have to extract the
DNA and float it on a water surface. Then, it can be picked up by a plastic
coated grid, and examined in the electron microscope. Mitochondrial
circular DNA is shown in the figure.

7. Human mtDNA
• small, double stranded
circular chromosome
• 16,569 bp in total
• no non-coding DNA
• no introns
• polycistronic replication
which is initiated from
the D (displacement)- loop
region
• followed by splicing of
transcript to form
messages.
Organisation of the
mitochondrial chromosome

8. Human mtDNA. The human mitochondrial DNA consists of 16,568 base pairs and
was the first entire genome sequenced in 1981. It encodes 22 tRNA, the 12 S and
the 16 S rRNA, and 13 peptides forming with the 74 nuclear-encoded polypeptides
the five respiratory chain complexes. The regulatory region is a non coding
sequence, or three stranded D-loop of nearly 600 base pairs. It contains the
promoters of the heavy and light strands (HSP and LSP respectively), and the
origin of replication of Purine-rich Heavy strand (OH). Transcription is polycistronic,
and translation uses a specific code different from the universal. Replication is
asymmetric, starting with the synthesis of the Heavy strand until the origin of the
Light strand (OL) located about 2/3 from OH from which synthesis proceeds
counter-clockwise. Thus, the Heavy strand is single stranded during about half of
the replication cycle which lasts about 2 hours. ND1-6: NADH dehydrogenase
subunits, COX1-3: Cytochrome c oxidase subunits, ATP6 and ATP8: subunits of
ATP synthase, Cyt b: Cytochrome b.

10. human mtDNA
yeast mtDNA
Yeast
mitochondrial
chromosome

11. Human DNA
• 16,569 bp;
• no non-coding DNA
• no introns
• polycistronic replication followed by splicing to form messages.
Yeast mtDNA
• 68-75 kb, similar in structure to bacterial genome
• contains introns and non-regions between genes.
• Same proteins made as in animals
• genes transcribed separately

12. Plant mtDNA
• chromosome size is much bigger but varies dramatically between
species (200-2000 kb)
• arranged as different size circles, sometimes with plasmids.
• The plant mtDNA contains chloroplast sequences, indicating
exchange of genetic information between organelles in plants.
• Much of the plant mtDNA is non-coding, but coding regions are
larger than animals and fungi.
• Number of proteins synthesised not known definitely but more
than in animals and yeast (probably about 50)
Plant mitochondria have specialised functions
• in leaves they participate in photorespiration
• sites of vitamin synthesis (vit C, folic acid, biotin)

13. maize mitochondrial
genome

14. Mitochondrial Inheritance
Yeast has been used extensively to study
mitochondrial inheritance.
There is a Yeast strain, called "Petite" that have
structurally abnormal mitochondria that are incapable
of oxidative phosphorylation. These mitochondria
have lost some or all of their DNA.
Genetic crosses between petite and wt strains
showed that inheritance of this trait did not segregate
with any of the nuclear chromosomes.

15. Mitochondrial Inheritance
Mitochondrial inheritance from yeast is
biparental, and both parent cells
contribute to the daughter cells when the
haploid cells fuse. After meiosis and
mitosis, there is random distribution of
mitochondria to daughter cells. If the
fusion is with yeast that are petite and
yeast that are not, a certain percentage of
the daughter cells will be "petite".

16. Mitochondrial Inheritance in Yeast

17. This led to the suggestion that some
genetic element existed in the cytoplasm
and was inherited in a different manner
from nuclear genes. This is called “non-
Mendelian inheritance” or “cytoplasmic
inheritance”.
In yeast and animals, this indicated
inheritance of mitochondrial genes: in
plants it also includes inheritance of
chloroplast genes
Mitochondrial Inheritance

18. Cytoplasmic Male Sterility
• Definition:
Cytoplasmic male sterility is total or partial male sterility
in plants as the result of
specific nuclear and mitochondrial interactions.Male
sterility is the failure of plants to produce
functional anthers, pollen, or male gametes.
• Function
• example of non mendelian inheritance
• Governed by cytoplasmic factors
• Interplay of nuclear and mitochondrial genomes.
• Restorer of fertility gene

19. Biogenesis of mitochondria
• Non de novo synthesis
• Molecular basis of biogenesis : it involves transcriptional
co activators (peroxisome proliferator activator gamma C
family)PGC- 1α, 1β and PRC, co factors NRF 1 and NRF 2

20. Mitochondrial replication

24. Schematic representation of the human mitochondrial genome.
Richard C. Scarpulla Physiol Rev 2008;88:611-638
©2008 by American Physiological Society

25. Schematic representation of the human mitochondrial genome. Genomic organization
and structural features of human mtDNA are depicted in a circular genomic map
showing heavy (blue) and light (black) strands assigned as such based on their
buoyant densities. Protein coding and rRNA genes are interspersed with 22 tRNA
genes (red bars denoted by the single-letter amino acid code). Duplicate tRNA genes
for leucine (L) and serine (S) are distinguished by their codon recognition
(parentheses). The D-loop regulatory region contains the L- and H-strand promoters
(LSP, HSP1, and HSP2), with arrows showing the direction of transcription. The origin
of H-strand replication (OH) is within the D-loop, whereas the origin of L-strand
replication (OL) is displaced by approximately two-thirds of the genome within a
cluster of five tRNA genes (W, A, N, C, Y). Protein coding genes include the following:
cytochrome oxidase (COX) subunits 1, 2, and 3; NADH dehydrogenase (ND) subinits
1, 2, 3, 4, 4L, 5, and 6; ATP synthase (ATPS) subunits 6 and 8; cytochrome b (Cyt b).
ND6 and the 8 tRNA genes transcribed from the L-strand as template are labeled on
the inside of the genomic map, whereas the remaining protein coding and RNA genes
transcribed from the H-strand as template are labeled on the outside.

26. Mitochondria replicate much like bacterial cells.
When they get too large, they undergo fission.
This involves a furrowing of the inner and then
the outer membrane as if someone was
pinching the mitochondrion. Then the two
daughter mitochondria split. Of course, the
mitochondria must first replicate their DNA. An
electron micrograph depicting the furrowing
process is shown in these figures.
Mitochondrial replication
cell division: random distribution
of mitos between daughter cells
mitochondrial
replication

27. Sometimes new mitochondria are synthesized in centres that are rich
in proteins and polyribosomes needed for their synthesis. The electron
micrograph in the following figure shows such a centre. It appears that
the cluster of mitochondria are sitting in a matrix of proteins and other
materials needed for their production.

28. Certain mitochondrial
proteins are needed
before the
mitochondria can
divide.
This has been shown in a
study by Sorgo and Yaffe,
J Cell Bio. 126: 1361-1373,
1994. They showed the
result of the removal of an
outer membrane protein
from mitochondria called
MDM10. This figure shows
the results. The
mitochondria are able to
take in components and
produce membranes and
matrix enzymes. However,
fission is not allowed and
the result is a giant
mitochondrion.
giant
mitochondrion

29. Despite having their own genome, most mitochondrial
proteins are encoded in the nucleus, made in the cytosol and
imported into the mitochondria

30. In all organisms, only a few of the proteins of the
mitochondrion are encoded by mtDNA, but the precise
number varies between organisms
• Subunits 1, 2, and 3 of cytochrome oxidase
• Subunits 6, 8, 9 of the Fo ATPase
• Apocytochrome b subunit of complexIII
• Seven NADH-CoQ reductase subunits (except in yeast)
The nucleus encodes the remaining proteins which are
made in the cytosol and imported into the mitochondrion.
Most of the lipid is imported.
Synthesis of mitochondrial proteins

31. Rice mitochondrial
and chloroplast
genomes
Plant
mitochondria
contain
chloroplast genes
- suggesting that
genetic transfer
occurs between
the two organelles

32. Mitochondrial DNA of animals and fungi uses a different genetic code
than the “universal” code

33. RNA processing in mitochondria
Plant mitochondria “edit” their RNA transcripts. This
was first noticed when comparing cDNA sequences
with genomic DNA sequences.
The most common change is to replace C with U,
although in some instances other changes can occur.
Matrix enzymes are thought to be responsible for this,
but the reason for the editing is not known.
Most of the DNA in plant mitochondria is non-coding,
only some of which is transcribed. RNA editing
occurs even in non-coding regions such as introns.

34. RNA editing is a molecular process through which some cells
can make discrete changes to specific nucleotide
sequences within a RNA molecule after it has been generated
by RNA polymerase. RNA editing is relatively rare, and
common forms of RNA processing (e.g. splicing, 5'-
capping and 3'-polyadenylation) are not usually included as
editing. Editing events may include the insertion, deletion, and
base substitution of nucleotides within the edited RNA
molecule.

35. Evolution of mitochondria
Mitochondria are generally thought to have
evolved endosymbiotically when an
anaerobic prokaryotic cell engulfed an
aerobic bacterium and formed a stable
symbiosis. Loss of most of the aerobe’s
genome to the nucleus of the host allowed
the latter to control the former.
This is supported by gene sequence analysis
which shows remarkable homology between
bacteria and mitochondrial genes.