Plant Mitochondrial and Chloroplast DNA Replication Mechanisms

 
P
l
a
n
t
 
C
h
l
o
r
o
p
l
a
s
t
 
a
n
d
M
i
t
o
c
h
o
n
d
r
i
a
l
 
D
N
A
 
r
e
p
l
i
c
a
t
i
o
n
 
 
Mitochondrial DNA replication
 
MtDNA replication is not directly linked to the plant cell cycle, and mtDNA copy
numbers can vary widely depending on the tissue and stage of development.
MtDNA has been shown to be associated with specific proteins that form nucleoid
complexes within the mitochondrial matrix.
 
In contrast to animals, plant mtDNA contains many more genes and plant
mitochondrial genomes are much larger. Large portions of AT-rich non-coding or
undefined DNA.
A typical plant mitochondrial genome encodes anywhere between 50 and 100
genes. The large genome size is at least partially due to the presence of non-coding
DNA sequences, which consist of introns, repeats, and duplications of regions of the
genome.
The known genes encode rRNA and tRNA genes as well as subunits for oxidative
phosphorylation chain complexes.
The presence of these large non-coding DNA may have a role in lowering the
mutation rate
 
 
Plant Mitochondria
 Plants most likely employ multiple mechanisms
for replication of the mtDNA due to the complex structure of the
mitochondrial genome.
The structure of plant mtDNA makes strand displacement (D-loop)
replication implausible, although there is one report of this
mechanism observed in petunia flowers.
Rolling circle replication and recombination-dependent replication
have also been observed in Chenopodium album, suggesting it could
be a common replication mode in other plant species as well
 
P
l
a
n
t
 
C
h
l
o
r
o
p
l
a
s
t
s
 
R
e
p
l
i
c
a
t
i
o
n
 
 
Plant Chloroplasts Replication
 of cpDNA is better understood than
plant mitochondrial DNA replication.
Chloroplasts utilize a 
double displacement loop strategy
 to initiate
DNA replication. The two displacement loops begin on opposite
strands and begin replicating unidirectionally towards each other until
they join to create a bidirectional replication bubble. DNA replication
continues bidirectionally until two daughter molecules are created.
Rolling circle 
and 
recombination-dependent replication 
have also
been proposed for cpDNA.
Chloroplast genomes exist primarily as homogeneous closed circle
DNA molecules.
 
 
R
e
p
l
i
c
a
t
i
o
n
 
m
e
c
h
a
n
i
s
m
s
 
o
f
 
m
i
t
o
c
h
o
n
d
r
i
a
l
 
a
n
d
C
h
l
o
r
o
p
l
a
s
t
s
 
D
N
A
.
 
Rolling circle 
DNA replication
 is initiated by an 
initiator protein
, which nicks one
strand of the double-stranded, circular DNA molecule at a site called the 
double-
strand origin 
(DSO). The initiator protein remains bound to the 5' phosphate end of
the nicked strand, and the free 3' hydroxyl end is released to serve as a 
primer
 for
DNA synthesis by 
DNA polymerase
. Using the unnicked strand as a template,
replication proceeds around the circular DNA molecule, displacing the nicked strand
as single-stranded DNA. Displacement of the nicked strand is carried out by a helicase
Continued DNA synthesis can produce multiple single-stranded linear copies of the
original DNA in a continuous head-to-tail series called a 
concatemer
(
concatemer
 is
a long continuous 
DNA
 molecule that contains multiple copies of the same DNA
sequence linked in series. These 
polymeric
 molecules are usually copies of an
entire 
genome
 linked end to end and separated by 
cos
 sites). These linear copies can
be converted to double-stranded circular molecules through the following process:
First, the initiator protein makes another nick in the DNA to terminate synthesis of
the first (leading) strand. 
RNA polymerase
 and DNA polymerase then replicate the
single-stranded origin (SSO) DNA to make another double-stranded circle.
The rolling replication is observed 
In 
Chenopodium album
 
 
As a summary, a typical DNA rolling circle replication has five steps:
Circular dsDNA will be "nicked".
The 
3' end
 is elongated using "unnicked" DNA as leading strand
(template); 
5' end
 is displaced.
Displaced DNA is a lagging strand and is made double stranded via a
series of 
Okazaki fragments
.
Replication of both "unnicked" and displaced ssDNA.
Displaced DNA circularizes.
 
 
 
Rolling circle 
DNA replication
 
 
D-loop replication
 is a proposed process by which circular DNA
like 
chloroplasts
 and 
mitochondria
 replicate their genetic material. An
important component of understanding 
D-loop
 replication is that
many 
chloroplasts
 and 
mitochondria
 have a single
circular 
chromosome
 like 
bacteria
 instead of the
linear 
chromosomes
 found in 
eukaryotes
. However,
many 
chloroplasts
 and 
mitochondria
 have a linear chromosome, and D-
loop replication is not important in these organelles. Also, not all circular
genomes use D-loop replication as the process of replicating its genome.
In many organisms, one strand of 
DNA
  comprises
heavier 
nucleotides
 (relatively more 
purines
adenine
 and 
guanine
). This
strand is called the 
H (heavy) strand
. The 
L (light) strand
 comprises lighter
nucleotides (
pyrimidines
thymine
 and 
cytosine
). Replication begins with
replication of the heavy strand starting at the 
D-loop
.
 
 
 
 
 
 
Each D-loop contains an 
origin of replication
 for the heavy strand. Full
circular DNA replication is initiated at that origin and replicates in only one
direction. The middle strand in the D-loop can be removed and a new one
will be synthesized that is not terminated until the heavy strand is fully
replicated.
As the heavy strand replication reaches the origin of replication for the
light strand, a new light strand will be synthesized in the opposite direction
as the heavy strand.
There is more than one proposed process through which D-loop replication
occurs, but in all of the models, these steps are agreed upon. The portions
not agreed upon are what is the importance of maintaining a D-loop when
replication is not in progress, because it is energetically expensive to the
cell, and what mechanisms, during replication, preserve the detached
strand of DNA that is waiting to be replicated.
 
 
 
 
 
 
 
To date, two organellar DNA polymerases, 
Poly I-A and Poly I-B
, resembling
bacterial 
DNA Poly I
, have been discovered in both mitochondria and
chloroplasts. Although 
Poly I-A and Poly I-B 
are similar to each other,
notable differences between the two have been observed.
Poly I-B
 knockout plants were shown to have fewer genome copy numbers
per organelle and grew slowly, a predominant role of 
Poly I-B
 in cpDNA
damage repair.
Recent studies show that 
Poly I-A 
replicates DNA with high fidelity.
heterozygous plants containing a single copy of either 
Poly I-A
 or 
Poly I-B
were able to grow to maturity
Structural analysis of these DNA polymerases indicate that they are distinct
from the animal 
mtDNA polymerase gamma 
and other animal nuclear DNA
polymerases, and that they show the greatest phylogenetic relationship
with bacterial Poly I.
 
 
primase preferentially incorporates CTP and GTP, which is curious as
nearly all plant mitochondrial and chloroplast genomes are highly A/T
rich. Why then would a plant organellar primase preferentially
incorporate CTP and GTP? This G–C rich sequence is hypothesized to
provide stability during primer extension
Unlike animal mitochondria, which utilize a single RNA polymerase
[primase], plant organelles require multiple RNAPs: at least two for
plastids and one for mitochondria. In Some plants the activity of
helicase and primase 
is accomplished by one complex (
Twinkle
).
 Twinkle mutant plants have no clear phenotype, indicating that in
contrast to the role of Twinkle in animal mitochondria, there is no
absolute requirement for this gene in Arabidopsis.
In humans there is a second DNA helicase, DNA2 nuclease/helicase,
localized to the nucleus and mitochondria
 
 
In E. coli, RNA primers are removed from DNA–RNA hybrids by the 5’-3’
exonuclease activity of 
DNA polymerase I
. Since 
Poly I-A and Poly I-B 
lack 5’-3’
exonuclease activity, primer removal must be carried out by another enzyme.
Recent work has shown 
RNase H-like
 activity both in mitochondria and
chloroplasts
Plants utilize at 
least two types of single stranded DNA binding proteins
 (SSBs
) in
their organelles. The first one is similar to bacterial SSBs. Arabidopsis encodes at
least two of these genes, called 
SSB1
 and 
SSB2
, although little is known about
SSB2.
The second class of SSB proteins is called 
organellar single-stranded DNA binding
proteins (OSB
). OSB proteins are distinct from the bacterial SSB versions and are
unique to plant organelles.
four OSB genes are transcribed in Arabidopsis with OSB proteins localizing to both
the mitochondria and chloroplasts.
organellar single-stranded DNA binding proteins (OSB) These proteins are 
unique
to plant organelles.
Slide Note
Embed
Share

Plant mitochondria and chloroplasts have intricate DNA replication processes. Mitochondrial DNA replication is independent of the plant cell cycle and is associated with specific proteins in nucleoid complexes. Plant mtDNA contains more genes than animal mtDNA, with a complex structure involving introns and repeats. Plant cpDNA replication utilizes a double displacement loop strategy, while rolling circle replication is observed in both mitochondria and chloroplasts.


Uploaded on Jul 17, 2024 | 1 Views


Download Presentation

Please find below an Image/Link to download the presentation.

The content on the website is provided AS IS for your information and personal use only. It may not be sold, licensed, or shared on other websites without obtaining consent from the author. Download presentation by click this link. If you encounter any issues during the download, it is possible that the publisher has removed the file from their server.

E N D

Presentation Transcript


  1. Plant Chloroplast and Plant Chloroplast and Mitochondrial DNA replication

  2. Mitochondrial DNA replication MtDNA replication is not directly linked to the plant cell cycle, and mtDNA copy numbers can vary widely depending on the tissue and stage of development. MtDNA has been shown to be associated with specific proteins that form nucleoid complexes within the mitochondrial matrix. In contrast to animals, plant mtDNA contains many more genes and plant mitochondrial genomes are much larger. Large portions of AT-rich non-coding or undefined DNA. A typical plant mitochondrial genome encodes anywhere between 50 and 100 genes. The large genome size is at least partially due to the presence of non-coding DNA sequences, which consist of introns, repeats, and duplications of regions of the genome. The known genes encode rRNA and tRNA genes as well as subunits for oxidative phosphorylation chain complexes. The presence of these large non-coding DNA may have a role in lowering the mutation rate

  3. Plant Mitochondria Plants most likely employ multiple mechanisms for replication of the mtDNA due to the complex structure of the mitochondrial genome. The structure of plant mtDNA makes strand displacement (D-loop) replication implausible, although there is one report of this mechanism observed in petunia flowers. Rolling circle replication and recombination-dependent replication have also been observed in Chenopodium album, suggesting it could be a common replication mode in other plant species as well

  4. Plant Chloroplasts Replication Plant Chloroplasts Replication Plant Chloroplasts Replication of cpDNA is better understood than plant mitochondrial DNA replication. Chloroplasts utilize a double displacement loop strategy to initiate DNA replication. The two displacement loops begin on opposite strands and begin replicating unidirectionally towards each other until they join to create a bidirectional replication bubble. DNA replication continues bidirectionally until two daughter molecules are created. Rolling circle and recombination-dependent replication have also been proposed for cpDNA. Chloroplast genomes exist primarily as homogeneous closed circle DNA molecules.

  5. Replication mechanisms of mitochondrial and Replication mechanisms of mitochondrial and Chloroplasts DNA. Chloroplasts DNA. Rolling circle DNA replication is initiated by an initiator protein, which nicks one strand of the double-stranded, circular DNA molecule at a site called the double- strand origin (DSO). The initiator protein remains bound to the 5' phosphate end of the nicked strand, and the free 3' hydroxyl end is released to serve as a primer for DNA synthesis by DNA polymerase. Using the unnicked strand as a template, replication proceeds around the circular DNA molecule, displacing the nicked strand as single-stranded DNA. Displacement of the nicked strand is carried out by a helicase Continued DNA synthesis can produce multiple single-stranded linear copies of the original DNA in a continuous head-to-tail series called a concatemer(A concatemer is a long continuous DNA molecule that contains multiple copies of the same DNA sequence linked in series. These polymeric molecules are usually copies of an entire genome linked end to end and separated by cos sites). These linear copies can be converted to double-stranded circular molecules through the following process: First, the initiator protein makes another nick in the DNA to terminate synthesis of the first (leading) strand. RNA polymerase and DNA polymerase then replicate the single-stranded origin (SSO) DNA to make another double-stranded circle. The rolling replication is observed In Chenopodium album

  6. As a summary, a typical DNA rolling circle replication has five steps: Circular dsDNA will be "nicked". The 3' end is elongated using "unnicked" DNA as leading strand (template); 5' end is displaced. Displaced DNA is a lagging strand and is made double stranded via a series of Okazaki fragments. Replication of both "unnicked" and displaced ssDNA. Displaced DNA circularizes.

  7. Rolling circle DNA replication

  8. D-loop replication is a proposed process by which circular DNA like chloroplasts and mitochondria replicate their genetic material. An important component of understanding D-loop replication is that many chloroplasts and mitochondria circular chromosome like linear chromosomes found many chloroplasts and mitochondria have a linear chromosome, and D- loop replication is not important in these organelles. Also, not all circular genomes use D-loop replication as the process of replicating its genome. In many organisms, one heavier nucleotides (relatively more purines: adenine and guanine). This strand is called the H (heavy) strand. The L (light) strand comprises lighter nucleotides (pyrimidines: thymine and cytosine). Replication begins with replication of the heavy strand starting at the D-loop. have instead eukaryotes. a single the bacteria in of However, strand of DNA comprises

  9. Each D-loop contains an origin of replication for the heavy strand. Full circular DNA replication is initiated at that origin and replicates in only one direction. The middle strand in the D-loop can be removed and a new one will be synthesized that is not terminated until the heavy strand is fully replicated. As the heavy strand replication reaches the origin of replication for the light strand, a new light strand will be synthesized in the opposite direction as the heavy strand. There is more than one proposed process through which D-loop replication occurs, but in all of the models, these steps are agreed upon. The portions not agreed upon are what is the importance of maintaining a D-loop when replication is not in progress, because it is energetically expensive to the cell, and what mechanisms, during replication, preserve the detached strand of DNA that is waiting to be replicated.

  10. To date, two organellar DNA polymerases, Poly I-A and Poly I-B, resembling bacterial DNA Poly I, have been discovered in both mitochondria and chloroplasts. Although Poly I-A and Poly I-B are similar to each other, notable differences between the two have been observed. Poly I-B knockout plants were shown to have fewer genome copy numbers per organelle and grew slowly, a predominant role of Poly I-B in cpDNA damage repair. Recent studies show that Poly I-A replicates DNA with high fidelity. heterozygous plants containing a single copy of either Poly I-A or Poly I-B were able to grow to maturity Structural analysis of these DNA polymerases indicate that they are distinct from the animal mtDNA polymerase gamma and other animal nuclear DNA polymerases, and that they show the greatest phylogenetic relationship with bacterial Poly I.

  11. primase preferentially incorporates CTP and GTP, which is curious as nearly all plant mitochondrial and chloroplast genomes are highly A/T rich. Why then would a plant organellar primase preferentially incorporate CTP and GTP? This G C rich sequence is hypothesized to provide stability during primer extension Unlike animal mitochondria, which utilize a single RNA polymerase [primase], plant organelles require multiple RNAPs: at least two for plastids and one for mitochondria. In Some plants the activity of helicase and primase is accomplished by one complex (Twinkle). Twinkle mutant plants have no clear phenotype, indicating that in contrast to the role of Twinkle in animal mitochondria, there is no absolute requirement for this gene in Arabidopsis. In humans there is a second DNA helicase, DNA2 nuclease/helicase, localized to the nucleus and mitochondria

  12. In E. coli, RNA primers are removed from DNARNA hybrids by the 5-3 exonuclease activity of DNA polymerase I. Since Poly I-A and Poly I-B lack 5 -3 exonuclease activity, primer removal must be carried out by another enzyme. Recent work has shown RNase H-like activity both in mitochondria and chloroplasts Plants utilize at least two types of single stranded DNA binding proteins (SSBs) in their organelles. The first one is similar to bacterial SSBs. Arabidopsis encodes at least two of these genes, called SSB1 and SSB2, although little is known about SSB2. The second class of SSB proteins is called organellar single-stranded DNA binding proteins (OSB). OSB proteins are distinct from the bacterial SSB versions and are unique to plant organelles. four OSB genes are transcribed in Arabidopsis with OSB proteins localizing to both the mitochondria and chloroplasts. organellar single-stranded DNA binding proteins (OSB) These proteins are unique to plant organelles.

Related


More Related Content

giItT1WQy@!-/#giItT1WQy@!-/#giItT1WQy@!-/#giItT1WQy@!-/#giItT1WQy@!-/#giItT1WQy@!-/#giItT1WQy@!-/#