ZAFAR HAYAT

REG NO. AUIC-19SG-MPHIL-MB- 2914

SAFI UR REHMAN
REG NO. AUIC-19SG-MPHIL-MB- 2985
AMIR HAMEED
REG NO. AUIC-19SG-MPHIL-MB- 2893
NOBIDA AKHTAR
REG NO. AUIC-19SG-MPHIL-MB- 2936
RIDA SEEMAB
REG NO. AUIC-19SG-MPHIL-MB- 2896
ARIFA MUGHAL
REG NO. AUIC-19SG-MPHIL-MB- 2894
 TOPIC
MITOCHONDRIAL DNA AND CHLOROPLAST DNA IN
BIOTECHNOLOGY
 CONTENTS
 Introduction Of Mitochondrial DNA

 Genome structure and diversity

 Replication

 Genes on the mtDNA and their Transcription

 Regulation of transcription

 Mutation and Diseases

 Mitochondrial sequence databases

 Mitochondrial mutation databases

 References
PREPARED BY NOBIDA AKHTAR
INTRODUCTION
MITOCHONDRIAL DNA

 Mitochondrial DNA is the DNA located in mitochondria, cellular organelles within

eukaryotic cells that convert chemical energy from food into a form that cells can

use, adenosine triphosphate (ATP).1

 Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell, most of the

DNA can be found in the cell nucleus and, in plants and algae, also in plastids such

as chloroplasts. Mitochondria are small structures in cells that generate energy for the cell to

use, and are hence referred to as the "powerhouses" of the cell.

 Mitochondrial DNA includes 16,569 base pairs and encodes 13 proteins.2

 Mitochondrial DNA is the small circular chromosome found inside mitochondria. 3

 The mitochondria, and thus mitochondrial DNA, are passed almost exclusively

from mother to offspring through the egg cell.4

 Mitochondrial DNA (mtDNA) is not transmitted through nuclear DNA (nDNA).

 In humans mitochondrial DNA is inherited only from the mother's ovum.

 Genetic material of a fertilized egg (zygote) derives from each parent.

 Eighty percent of mitochondrial DNA codes for mitochondrial RNA, and therefore most

mitochondrial DNA mutations lead to functional problems, which may be manifested as

muscle disorders (myopathies).

GENOME STRUCTURE AND DIVERSITY

 Six main genome types found in mitochondrial genomes.

 Classified by their structure (e.g. circular versus linear), size, presence

of introns or plasmid like structures.

 In many unicellular organisms (e.g., the ciliate Tetrahymena and

the greenalga, Chlamydomonas reinhardtii, and in rare cases also in multicellular
organisms (e.g. in some species of Cnidaria), the mtDNA is found as linearly
organized DNA.

 Most of these linear mtDNAs possess telomerase-independent telomeres (i.e., the

ends of the linear DNA) with different modes of replication. 9
PREPARED BY SAFI UR REHMAN

REPLICATION

 Mitochondrial DNA is replicated by the DNA polymerase gamma complex which is

composed of a 140 kDa catalytic DNA polymerase encoded by the POLG gene and two 55
kDa accessory subunits encoded by the POLG2 gene.[21]

 The replisome machinery is formed by DNA polymerase, TWINKLE and

mitochondrial SSB proteins.

 TWINKLE is a helicase which unwinds short stretches of dsDNA in the 5′ to 3′

direction.[22] All these polypeptides are encoded in the nuclear genome.

 During embryogenesis, replication of mtDNA is strictly down-regulated from the fertilized

oocyte through the preimplantation embryo.[23]
REGULATION OF TRANSCRIPTION

 The promoters for the initiation of the transcription of the heavy and light strands are located in the main non-
coding region of the mtDNA called the displacement loop, the D-loop.

 There is evidence that the transcription of the mitochondrial rRNAs is regulated by the heavy-strand promoter 1
(HSP1), and the transcription of the polycistronic transcripts coding for the protein subunits are regulated by
HSP2.
GENES ON THE mtDNA AND THEIR TRANSCRIPTION
 Two strands of the human mitochondrial DNA

 Heavy strand

 Light strand.

 The heavy strand is rich in guanine and encodes 12 subunits of the oxidative
phosphorylation system, two ribosomal RNAs (12S and 16S), and 14 tRNAs.

 The light strand encodes one subunit, and 8 tRNAs. So, altogether mtDNA encodes
for two rRNAs, 22 tRNAs, and 13 proteins subunits, all of which are involved in the
oxidative phosphorylation process.
PREPARED BY ARIFA MUGHAL

MITOCHONDRIAL DISEASES

 Mitochondrial diseases are a group of disorders caused by dysfunctional mitochondria,

the organelles that generate energy for the cell.

 Mitochondria are found in every cell of the human body except red blood cells, and
convert the energy of food molecules into the ATP that powers most cell functions.

 Mitochondrial diseases are sometimes caused by mutations in the mitochondrial DNA that
affect mitochondrial function. Other mitochondrial diseases are caused
by mutations in genes of the nuclear DNA, whose gene products are imported into the
mitochondria.
EXAMPLES

 Examples of mitochondrial diseases include:

 Leigh syndrome

 Mitochondrial myopathy

 Leber's hereditary optic neuropathy (LHON)

 Neuropathy, ataxia, retinitis pigmentosa, and ptosis (NARP)

 Myoneurogenic gastrointestinal encephalopathy (MNGIE)

 Myoclonic Epilepsy with Ragged Red Fibers (MERRF)

 MELAS syndrome

 Mitochondrial DNA depletion syndrome

LEIGH SYNDROME

 Leigh syndrome (also called Leigh disease and subacute necrotizing encephalomyelopathy)
is an inherited neurometabolic disorder that affects the central nervous system.

 It is named after Archibald Denis Leigh, a British neuropsychiatrist who first described the
condition in 1951. Normal levels of thiamine, thiamine monophosphate, and thiamine
diphosphate are commonly found but there is a reduced or absent level of thiamine
triphosphate.

 This is thought to be caused by a blockage in the enzyme thiamine-diphosphate kinase, and

therefore treatment in some patients would be to take thiamine triphosphate daily.
PREPARED BY AMIR HAMEED
SIGN AND SYMPTOMS

 The symptoms of Leigh syndrome in Infants include diarrhea, vomiting,

and dysphagia (trouble swallowing or sucking), leading to a failure to thrive.

 Children with early Leigh disease also may appear irritable and cry much more than usual.

 Seizures are often seen.

 Excess lactate may be seen in the urine, cerebrospinal fluid, and blood of a person with
Leigh syndrome.

 As the disease progresses, the muscular system is debilitated throughout the body, as the
brain cannot control the contraction of muscles.

 Hypotonic (low muscle tone and strength).

 The eyes are particularly affected; the muscles that control the eyes become weak,

paralyzed, or uncontrollable in conditions. nystagmus (involuntary eye movements).

 The heart and lungs can also fail as a result of Leigh disease.

 Hypertrophic cardiomyopathy (thickening of part of the heart muscle) is also sometimes

found and can cause death.

 In children with Leigh-syndrome associated ventricular septal defects, caused by pyruvate

dehydrogenase deficiency, high forehead and large ears are seen; facial abnormalities are

not typical of Leigh syndrome.

 However, respiratory failure is the most common cause of death in people with Leigh syndrome.

 Neurological symptoms include peripheral neuropathy, loss of sensation in extremities caused by damage to
the peripheral nervous system.
GENOMICS
 Mutations in mitochondrial DNA (mtDNA) and over 30 genes in nuclear
DNA (gene SURF1 and some COX assembly factors) have been implicated in Leigh
disease
 Disorders of oxidative phosphorylation, the process by which cells produce their main
energy source of adenosine triphosphate (ATP), may be caused by mutations in either
mtDNA or in nuclear encoded genes.
 Four out of the five protein complexes involved in oxidative phosphorylation are most
commonly disrupted in Leigh syndrome, either because of malformed protein or because of
an error in the assembly of these complexes. Regardless of the genetic basis, it results in an
inability of the complexes affected by the mutation to perform their role in oxidative
phosphorylation. In the case of Leigh disease, crucial cells in the brain stem and basal
ganglia are affected. This causes a chronic lack of energy in the cells, which leads to cell
death and in turn, affects the central nervous system and inhibits motor functions. The heart
and other muscles also require a lot of energy and are affected by cell death caused by
chronic energy deficiencies in Leigh syndrome.[1]
MITOCHONDRIAL DNA MUTATIONS
 Mitochondria are essential organelles in eukaryotic cells. Their function is to convert the
potential energy of glucose, amino acids, and fatty acids into adenosine triphosphate (ATP)
in a process called oxidative phosphorylation. Mitochondria carry their own DNA, called
mitochondrial DNA (mtDNA). The information stored in the mtDNA is used to produce
several of the enzymes essential to the production of ATP.

 Between 20 and 25 percent of Leigh syndrome cases are caused by mutations in

mitochondrial DNA. The most common of these mutations is found in 10 to 20 percent of
Leigh syndrome and occurs in MT-ATP, a gene that codes for a protein in the last complex
of the oxidative phosphorylation chain, ATP synthase, an enzyme that directly generates
ATP. Without ATP synthase, the electron transport chain will not produce any ATP.
 The most common MT-ATP6 mutation found with Leigh syndrome is a point mutation at
nucleotide 8993 that changes a thymine to a guanine. This and other point mutations
associated with Leigh syndrome destabilize or malform the protein complex and keep
energy production down in affected cells. Several mitochondrial genes involved in creating
the first complex of the oxidative phosphorylation chain can be implicated in a case of Leigh
syndrome, including genes MT-ND2, MT-ND3, MT-ND5, MT-ND6 and MT-CO1.

 Mitochondrial DNA is passed down matrilineally in a pattern called maternal

 inheritance — a mother can transmit the genes for Leigh syndrome to both male and female
children, but fathers cannot pass down mitochondrial genes
PREPARED BY ZAFAR HAYAT
MELAS syndrome

 Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is

one of the family of mitochondrial cytopathies which also include MERRF, and Leber's

hereditary optic neuropathy. It was first characterized under this name in 1984. A feature of

these diseases is that they are caused by defects in the mitochondrial genome which is

inherited purely from the female parent.


SIGN AND SYMPTOMS
 MELAS is a condition that affects many of the body's systems, particularly the brain and nervous system
(encephalo-) and muscles (myopathy).
 In most cases, the signs and symptoms of this disorder appear in childhood following a period of normal
development.
 Early symptoms may include muscle weakness and pain, recurrent headaches, loss of appetite, vomiting, and
seizures.
 Most affected individuals experience stroke-like episodes beginning before age 40. These episodes often
involve temporary muscle weakness on one side of the body (hemiparesis), altered consciousness, vision
abnormalities, seizures, and severe headaches resembling migraines.
 Repeated stroke-like episodes can progressively damage the brain, leading to vision loss, problems with
movement, and a loss of intellectual function (dementia). The stroke-like episodes can be mis-diagnosed as
epilepsy by a doctor not aware of the MELAS condition.

GENETICS

 MELAS is mostly caused by mutations in the genes in mitochondrial DNA, but it can also

be caused by mutations in the nuclear DNA.

 NADH dehydrogenase

 Some of the genes (MT-ND1, MT-ND5) affected in MELAS encode proteins that are part

of NADH dehydrogenase (also called complex I) in mitochondria, that helps convert

oxygen and simple sugars to energy.


 INTRODUCTION
PREPARED

CHLOROPLAST DNA
Chloroplasts have their own DNA, often abbreviated as cpDNA.

 It is also known as the plastome when referring to genomes of other plastids.

 NucleoidS

 Each chloroplast contains around 100 copies of its DNA in young leaves, declining to 15–20
copies in older leaves.

 Though chloroplast DNA is not associated with true histones in red algae, a histone-like
chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast
DNA ring into a nucleoid has been found.
PREPARED BY RIDA SEEMAB
MOLECULAR STRUCTURE

 Chloroplast DNAs are circular, and are typically 120,000–170,000 base pairs long.

 They can have a contour length of around 30–60 micrometers, and have a mass of
about 80–130 million daltons.

 Most chloroplasts have their entire chloroplast genome combined into a single large
ring, though those of dinophyte algae are a notable exception—their genome is
broken up into about forty small plasmids, each 2,000–10,000 base pairs long. Each
minicircle contains one to three genes, but blank plasmids, with no coding DNA,
have also been found.

PROTEIN SYNTHESIS

 Protein synthesis within chloroplasts relies on an RNA polymerase coded by the

chloroplast's own genome, which is related to RNA polymerases found in bacteria.

 RNA polymerase that is encoded by the plant's nuclear genome. The two RNA polymerases

may recognize and bind to different kinds of promoters within the chloroplast genome.

 The ribosomes in chloroplasts are similar to bacterial ribosomes

DNA REPLICATION
 Leading model of cpDNA replication

 The mechanism for chloroplast DNA (cpDNA) replication has not been
conclusively determined, but two main models have been proposed.
 Scientists have attempted to observe chloroplast replication via electron
microscop since the 1970s.
 The results of the microscopy experiments led to the idea that
chloroplast DNA replicates using a double displacement loop (D-loop).
As the D-loop moves through the circular DNA, it adopts a theta
intermediary form, also known as a Cairns replication intermediate, and
completes replication with a rolling circle mechanism.
 Replication starts at specific points of origin.

 In addition to the early microscopy experiments, this model is also supported by the amounts
of deamination seen in cpDNA.

 Deamination occurs when an amino grouP is lost and is a mutation that often results in base changes.
When adenine is deaminated, it becomes hypoxanthine. Hypoxanthine can bind to cytosine, and when
the XC base pair is replicated, it becomes a GC (thus, an A → G base change).

 In cpDNA, there are several A → G deamination gradients.

 DNA becomes susceptible to deamination events when it is single stranded. When replication forks
form, the strand not being copied is single stranded, and thus at risk for A → G deamination.
REFERENCES
 Siekevitz P (1957). "Powerhouse of the cell". Scientific American. 197 (1): 131–
40. Bibcode:1957SciAm.197a.131S. doi:10.1038/scientificamerican0757-131.
 ^ Iborra FJ, Kimura H, Cook PR (May 2004). "The functional organization of mitochondrial
genomes in human cells". BMC Biology. 2: 9. doi:10.1186/1741-7007-2-
9. PMC 425603. PMID 15157274.
 ^ Sykes B (10 September 2003). "Mitochondrial DNA and human history". The Human
Genome. Wellcome Trust. Archived from the original on 7 September 2015. Retrieved 5
February 2012.
 ^ Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich
DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. (1981). "Sequence and
organization of the human mitochondrial genome". Nature. 290 (5806): 457–
65. doi:10.1038/290457a0. PMID 7219534.
 ^ Boursot P, Bonhomme F (1 January 1986). "[Not Available]". Génétique, Sélection,
Évolution. 18 (1): 73–98. doi:10.1186/1297-9686-18-1-73. PMC 2713894. PMID 22879234.
 ^ Delsuc F, Stanhope MJ, Douzery EJ (August 2003). "Molecular systematics of armadillos
(Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of
mitochondrial and nuclear genes". Molecular Phylogenetics and Evolution. 28 (2): 261–
75. doi:10.1016/s1055-7903(03)00111-8. PMID 12878463.
 Hassanin A, An J, Ropiquet A, Nguyen TT, Couloux A (March 2013). "Combining multiple
autosomal introns for studying shallow phylogeny and taxonomy of Laurasiatherian
mammals: Application to the tribe Bovini (Cetartiodactyla, Bovidae)". Molecular
Phylogenetics and Evolution. 66 (3): 766–
75. doi:10.1016/j.ympev.2012.11.003. PMID 23159894.
 ^ Wiesner RJ, Rüegg JC, Morano I (March 1992). "Counting target molecules by
exponential polymerase chain reaction: copy number of mitochondrial DNA in rat
tissues". Biochemical and Biophysical Research Communications. 183 (2): 553–
9. doi:10.1016/0006-291X(92)90517-O. PMID 1550563.
 ^ Jump up to:a b c Johnston IG, Williams BP (February 2016). "Evolutionary Inference across
Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention". Cell
Systems. 2 (2): 101–11. doi:10.1016/j.cels.2016.01.013. PMID 27135164.
 ^ van der Giezen M, Tovar J, Clark CG (2005). "Mitochondrion‐Derived Organelles in Protists
and Fungi". A Survey of Cell Biology. International Review of Cytology. 244. pp. 175–
225. doi:10.1016/S0074-7696(05)44005-X. ISBN 978-0-12-364648-4. PMID 16157181.
 ^ Adams KL, Palmer JD (December 2003). "Evolution of mitochondrial gene content: gene
loss and transfer to the nucleus". Molecular Phylogenetics and Evolution. 29 (3): 380–
95. doi:10.1016/S1055-7903(03)00194-5. PMID 14615181.
 ^
 Björkholm P, Harish A, Hagström E, Ernst AM, Andersson SG (August 2015). "Mitochondrial
genomes are retained by selective constraints on protein targeting". Proceedings of the
National Academy of Sciences of the United States of America. 112 (33): 10154–
61. Bibcode:2015PNAS..11210154B. doi:10.1073/pnas.1421372112. PMC 4547212. PMID 26195
779.
 ^ Allen JF (August 2015). "Why chloroplasts and mitochondria retain their own genomes and
genetic systems: Colocation for redox regulation of gene expression". Proceedings of the
National Academy of Sciences of the United States of America. 112 (33): 10231–
8. Bibcode:2015PNAS..11210231A. doi:10.1073/pnas.1500012112. PMC 4547249. PMID 262869
85.
 ^ Jump up to:a b c Kolesnikov AA, Gerasimov ES (December 2012). "Diversity of mitochondrial
genome organization". Biochemistry. Biokhimiia. 77 (13): 1424–
35. doi:10.1134/S0006297912130020. PMID 23379519.
 ^ Nosek J, Tomáska L, Fukuhara H, Suyama Y, Kovác L (May 1998). "Linear mitochondrial
genomes: 30 years down the line". Trends in Genetics. 14 (5): 184–8. doi:10.1016/S0168-
9525(98)01443-7. PMID 9613202.
 ^
1. de Vries J, Archibald JM (April 2018). "Plastid genomes". Current Biology. 28 (8): R336–
R337. doi:10.1016/j.cub.2018.01.027. PMID 29689202.
2. ^ C.Michael Hogan. 2010. Deoxyribonucleic acid. Encyclopedia of Earth. National Council for Science and
the Environment. eds. S.Draggan and C.Cleveland. Washington DC
3. ^ Sakamoto W, Takami T (June 2018). "Chloroplast DNA Dynamics: Copy Number, Quality Control and
Degradation". Plant & Cell Physiology. 59 (6): 1120–1127. doi:10.1093/pcp/pcy084. PMID 29860378.
4. ^ Jump up to:a b c Dann L (2002). Bioscience—Explained (PDF). Green DNA: BIOSCIENCE EXPLAINED.
5. ^ "Chloroplasts and Other Plastids". University of Hamburg. Archived from the original on 25 September 2012.
Retrieved 27 December 2012.
6. ^ Jump up to:a b c d e f g h i j Sandelius AS (2009). The Chloroplast: Interactions with the Environment. Springer.
p. 18. ISBN 978-3-540-68696-5.
7. ^ Jump up to:a b c d Clegg MT, Gaut BS, Learn GH, Morton BR (July 1994). "Rates and patterns of chloroplast
DNA evolution". Proceedings of the National Academy of Sciences of the United States of America. 91 (15):
6795–801. Bibcode:1994PNAS...91.6795C. doi:10.1073/pnas.91.15.6795. PMC 44285. PMID 8041699.
 ^ Björkholm P, Harish A, Hagström E, Ernst AM, Andersson SG (August 2015). "Mitochondrial
genomes are retained by selective constraints on protein targeting". Proceedings of the
National Academy of Sciences of the United States of America. 112 (33): 10154–
61. Bibcode:2015PNAS..11210154B. doi:10.1073/pnas.1421372112. PMC 4547212. PMID 26195
779.
 ^ Allen JF (August 2015). "Why chloroplasts and mitochondria retain their own genomes and
genetic systems: Colocation for redox regulation of gene expression". Proceedings of the
National Academy of Sciences of the United States of America. 112 (33): 10231–
8. Bibcode:2015PNAS..11210231A. doi:10.1073/pnas.1500012112. PMC 4547249. PMID 262869
85.
 ^ Jump up to:a b c Kolesnikov AA, Gerasimov ES (December 2012). "Diversity of mitochondrial
genome organization". Biochemistry. Biokhimiia. 77 (13): 1424–
35. doi:10.1134/S0006297912130020. PMID 23379519.
 ^ Nosek J, Tomáska L, Fukuhara H, Suyama Y, Kovác L (May 1998). "Linear mitochondrial
genomes: 30 years down the line". Trends in Genetics. 14 (5): 184–8. doi:10.1016/S0168-
9525(98)01443-7. PMID 9613202.
 ^ Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR
(January 2012). "Rapid
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