1. CHLOROPLAST DNA
SUMYYA SADIQ
M.Phil II

2. CHLOROPLAST
 organelle found in plant cells and
eukaryotic algae
 conduct Photosynthesis
 Chloroplasts are green....chlorophyll
pigment

3. STRUCTURE
 Chloroplast ultrastructure:
1. outer membrane
2. intermembrane space
3. inner membrane (1+2+3: envelope)
4. stroma (aqueous fluid)
5. thylakoid lumen (inside of thylakoid)
6. thylakoid membrane
7. granum (stack of thylakoids)
8. thylakoid (lamella)
9. starch
10. ribosome
11. plastidial DNA
12. plastoglobule (drop of lipids)

5. Chloroplast genome
 Chloroplast DNA (cpDNA) is also known as
plastid DNA (ptDNA).
 Circular double stranded DNA molecule
 Ct genomes are relatively larger
 140kb in higher plants.
 200kb in lower eukaryotes.
 Multiple copies of genome per organelle.
Vary in size ,
 But are large enough to code 50-100
proteins as well as rRNAs & tRNAs

6.  cpDNA regions includes Large Single-Copy (LSC)
& Small Single-Copy (SSC) regions, and Inverted
Repeats (IRA & IRB).
 Variation in length mainly due to presence of inverted
repeat (IR)
 Conifers and a group of legumes lack Inverted
Repeats.

8. GENOME SEQUENCING:
 GENOME SEQUENCING Two of the first ct
genome sequenced
- liverwort, Marchantia polymorpha.
- tobacco, Nicotiana tabacum.
 Tobacco DNA is larger , contains 150 genes and
that of liverwort is 134.

9. BASIC GENES:
 Gene for rRNAs, tRNAs, ribosomal
proteins.
 Polypeptide components of the
photosystem- involved in capturing
sunlight.
 Catalytically active subunit of enzyme
RuBP carboxylase.
 4 subunits of chloroplast specific RNA
polymerase.

10. Molecular Systematics on cpDNA
 cpDNA regions can be amplified by means of
PCR.
 The resulted PCR products may be subjected to
RFLP or DNA sequencing.
 Common cpDNA regions used in systematic
study:
 rbcL (1400bp), trnL-trnF (250-800bp), atpB-
rbcL (1000bp), trnL intron (300bp), matK
(2600bp), trnT-trnL (400-800bp), 16S (1400bp),
rpoC (3600bp) etc.

11. Chloroplast replication
 Molecular mechanism is unknow
 Independent of nuclear replication
 plastome copies are greatly amplified in
mesophyll cells of the developing leaf and can
reach values of more than 20,000 cell
 The dual D-loop model for the initiation
of chloroplast DNA replication

12. 1:Unidirectional elongation of nascent strand
initiated from both origins

13. 2:Unidirectional fork movement
toward each other

14. 3: Fusion of D-loops to Cairn type
intermediates

15. 4: Bidirectional, semi-discontinuous
replication

16. 5: Resulting daughter molecules.

17. ENZYMES INVOLVED IN CtDNA REPLICATION
These include :
 DNA polymerase(s),
 DNA unwinding activity (helicase),
 Primase and/or RNA polymerase,
 Single stranded DNA binding protein
 Topoisomerase I and II,
 Origin recognition protein(s).

18. PROPERTIES of ctDNA:
i. Non- mendelian inheritance
ii. Self replication
iii. Somatic segregation in plants
iv. Inherited independently of nuclear
genes
v. Conservative rate of nucleotide
substitution enables to resolve plant
phylogenetic relationships at deep
levels of evolution. eg. familial
level; mono- dicotyledonous