This document discusses organelle genomes, focusing on chloroplast and mitochondrial DNA. It provides details on the structure and content of chloroplast genomes, noting they typically contain 110-120 genes and are characterized by inverted repeats and single copy regions. Mitochondrial genomes are more variable in gene content and size. The structure and replication of human mitochondrial DNA is described, involving displacement loop formation during semi-conservative replication of the circular genome. Mutations in mitochondrial DNA can cause a variety of neuromuscular diseases by interfering with energy production.

1. NAME - SAMADRITA BANIK
ST. GEORGE COLLEGE
M.Sc MICROBIOLOGY
2ND SEMESTER
ORGANELLE GENOME

2. INTRODUCTION
The organelle genomes are part of the NCBI
Reference Sequence project that provides
curated sequence data and related
information for the community to use as a
standard.

3. ORGANELLE GENOME
Mitochondria and chloroplasts play a critical role in eukaryotic cells
by ensuring aerobic respiration and photosynthesis, respectively.
More than just a collection of complete organelle genome sequences,
the articles featured in this topical series help to shed some light on
specific traits and idiosyncrasies of these exceptional genomes, and
highlight their value for taxonomic and phylogenic studies.

4. 2 Main Types of Organellar DNA
• Chloroplast DNA (cp DNA):
Each chloroplast contains 20-200 copies of a circular double stranded
DNA molecule, which may also be linear as found in maize, cp DNA
is characterized

5. • (i) Two inverted repeats (IR), each 10-24 kb long and carrying
ribosomal genes,
• (ii) A short single copy (SSC) sequence, 18-20 kb long,
• (iii) A long single copy (LSC) sequence

6. Most chloroplast genomes appear to possess the same set of genes.
Each molecule of cp DNA is encoded with 110-120 genes and code
for about 125 proteins. In maize the genes on cp DNA contains both
small and large rRNA genes and sequence for tRNA. It also
synthesizes mRNA for some proteins involved in photosynthesis like
enzyme rubisco.
Two and eight genes respectively for the polypeptides of PS I and PS
II have been identified. Some herbicide resistant genes have also
been located in cp DNA.

7. A circular genetic map was proposed by Ruth Sager (1972) in
Chlamydomonas . Chloroplast genetics in higher plants including crops
like pea, maize, rice, etc. has also been studied. Bendich (2004)
emphasized that cp DNA in plants is generally found as multi-genomic
complex and branched linear DNA molecules and not as mono-genomic
circular molecules.

8. • Mitochondrial DNA (mt DNA):
Like chloroplasts, mitochondria also contain 5-100 copies DNA
molecules which are usually circular, but may essentially be also
linear. Remarkable variation exists in the size of mt DNA, ranging
from 6- 2500 l<b. mt DNA contributes only about less than 1 % of
cellular DNA except yeast (18%)

9. Mitochondrial genomes display greater variability in gene content.
The cloning and sequencing of the entire mt DNA have now been
made in several organisms including human (Fig. 2.60). It contains
genes for rRNA, tRNA, ribosome associated protein, mitochondrial
proteins and enzymes.
A substantial fraction of mt DNA in yeast represents unidentified
reading frames containing introns of split genes and appear to code
for proteins required for mRNA splicing, called maturates.

10. Genetic Map of Human Mitochondrial DNA
In higher plants, smaller circular (sometimes linear also) DNA
molecules present in addition to the main circular mt DNA. The
master circle contains repetitive sequences and due to extensive
recombination between these repeats, smaller molecules originate.
One interesting feature of mt DNA is its unidirectional and highly
asymmetric replication. The daughter L-strand starts synthesis when
two-third of H-strand is already synthesized. Another interesting
point of plant mt DNA is that it can move between organelles which
are called promiscous DNA. mt DNA is associated with the male
sterility character of plants as in maize.

11. DNA REPLICATION OF MITOCHONDRIA
Mitochondrial DNA replication is semi-conservative and uses DNA
polymerases that are specific to the mitochondria. The mtDNA replicates
throughout the cell cycle, independently of nuclear DNA synthesis which
takes place in S phase of cell cycle. Observations on mtDNA replication in
animal mitochondria in vivo have resulted in a model referred to as the
displacement loop (D loop) model as follows.
The two strands of mtDNA in most animals have different densities because
the bases are not equally distributed on both strands, called H (heavy) and L
(light) strands. The synthesis of a new H strand starts at the replication
origin for the H strand and forms a D-loop structure.
As the new H strand extends to about halfway around the molecule,
initiation of synthesis of a new L strand takes place at a second replication
origin. Synthesis continues until both strands are completed. Finally, each
circular DNA assumes a supercoiled form.

12. STRUCTURE OF MITOCHONDRIAL DNA
REPLICATION

13. he mtDNA is maternally inherited and has a very high mutation rate.
When a new mtDNA mutation occurs in a cell, a mixed intracellular
population of mtDNAs is generated, known as heteroplasmy. During
replication in a heteroplasmic cell, the mutant and normal molecules
are randomly distributed into daughter cells.
When the percentage of mutant mtDNAs increases, the mitochondrial
energy producing capacity declines, production of toxic reactive
oxygen species increases, and cells become more prone for
apoptosis. The result is mitochondrial dysfunction. Tissues most
sensitive to mitochondrial dysfunction are brain, heart, kidney and
skeletal muscle.
The mtDNA mutations are associated with a variety of
neuromuscular disease symptoms, including various
ophthalmological symptoms, muscle degeneration, cardiovascular
diseases, diabetes mellitus, renal function and dementias.

14. The mtDNA diseases can be caused either by base substitutions or
rearrangement mutation. Base substitution mutations can either alter
protein (missense mutation) or rRNAs and tRNAs (protein synthesis
mutations). Rearrangement mutations generally delete at least one
tRNA and thus cause protein synthesis defects.
Missense mutations are associated with myopathy, optic atrophy,
dystonia and Leigh’s syndrome. Base substitution mutations in
protein synthesizing genes have been associated with a wide
spectrum of neuromuscular diseases, and the more severe typically
include mitochondrial myopathy.
Mitochondrial diseases are also associated with a number of different
nuclear DNA mutations. Mutations in the RNA component of the
mitochondrial RNAse have been implicated in metaphyseal
chondrodysplasia or cartilage hair hypoplasia which is an autosomal
recessive disorder resulting from mutation in nuclear chromosome 9
short arm position (9p13).

15. CONCLUSION
The phenomenon of extra-nuclear inheritance based on transmission of visible
phenotypes through mitochondria and chloroplasts. Studies in the 70s revealed
presence of DNA in these organelles. Both mitochondria and chloroplasts are
present only in cells of lower and higher eukaryotic organisms. Detailed studies
established that DNA in these organelles is similar to the DNA in prokaryotic
bacteria.
The genomes of both mitochondria and chloroplasts code for all of their RNA
species and some proteins that are involved in the function of the organelles.
The DNA is in the form of a circular duplex molecule, except in some lower
eukaryotes in which mitochondrial DNA is linear.