It is the transmission of genes that occur outside the nucleus. It is found in most eukaryotes and is commonly known to occur in cytoplasmic organelles such as mitochondria and chloroplasts or from cellular parasites like viruses or bacteria. Mitochondria are organelles which function to produce energy as a result of cellular respiration. Chloroplasts are organelles which function to produce sugars via photosynthesis in plants and algae. The genes located in mitochondria and chloroplasts are very important for proper cellular function, yet the genomes replicate independently of the DNA located in the nucleus, which is typically arranged in chromosomes that only replicate one time preceding cellular division

1. CHLOROPLAST
INHERITANCE
• VIMAL PRIYA subramanian

2. Extranuclear inheritance or cytoplasmic inheritance
• It is the transmission of genes that occur outside the nucleus. It is
found in most eukaryotes and is commonly known to occur in
cytoplasmic organelles such as mitochondria and chloroplasts or from
cellular parasites like viruses or bacteria.
• Mitochondria are organelles which function to produce energy as a
result of cellular respiration. Chloroplasts are organelles which
function to produce sugars via photosynthesis in plants and algae. The
genes located in mitochondria and chloroplasts are very important for
proper cellular function, yet the genomes replicate independently of
the DNA located in the nucleus, which is typically arranged in
chromosomes that only replicate one time preceding cellular division

3. • Three general types of extranuclear inheritance exist. These are vegetative
segregation, uniparental inheritance and biparental inheritance.
• Vegetative segregation results from random replication and partitioning of
cytoplasmic organelles. It occurs with chloroplasts and mitochondria during mitotic
cell divisions and results in daughter cells that contain a random sample of the parent
cell’s organelles. An example of vegetative segregation is with mitochondria of
asexually replicating yeast cells (8).
• Uniparental inheritance occurs in extranuclear genes when only one parent
contributes organellar DNA to the offspring. A classic example of uniparental gene
transmission is the maternal inheritance of human mitochondria. The mother’s
mitochondria are transmitted to the offspring at fertilization via the egg. The father’s
mitochondrial genes are not transmitted to the offspring via the sperm. Very rare cases
which require further investigation have been reported of paternal mitochondrial
inheritance in humans, in which the father’s mitochondrial genome is found in
offspring (4).

4. • Chloroplast genes can also inherit uniparentally during sexual
reproduction. They are historically thought to inherit maternally, but
paternal inheritance in many species is increasingly being identified.
The mechanisms of uniparental inheritance from species to species
differ greatly and are quite complicated. For instance, chloroplasts
have been found to exhibit maternal, paternal and biparental modes
even within the same species (5,6).
• Biparental inheritance occurs in extranuclear genes when both
parents contribute organellar DNA to the offspring. It may be less
common than uniparental extranuclear inheritance, and usually occurs
in a permissible species only a fraction of the time. An example of
biparental mitochondrial inheritance is in the yeast, Saccharomyces
cerevisiae. When two haploid cells of opposite mating type fuse they
can both contribute mitochondria to the resulting diploid offspring
(1,8).

5. Non-Mendelian Inheritance
 Mitochondria
 Chloroplasts
 Examples of non-Mendelian inheritance
 Human mtDNA defects
Other forms of non-Mendelian Inheritance:
 Infectious cytoplasmic inheritance
 Maternal effect
 Genomic (parental) imprinting

6. Extranuclear Genomes:
Mitochondria (animals and plants)
Chloroplasts (plants)
1. Mitochondria and chloroplasts occur outside the nucleus, in the
cytoplasm of the cell.
2. Contain genomes (mtDNA/cpDNA) and genes, i.e.,
extrachromosomal genes, cytoplasmic genes, organelle genes, or
extranuclear genes.
3. Inheritance is non-Mendelian (e.g., cytoplasm typically is inherited
from the mother).

7. Origin of mitochondria and chloroplasts:
Both mitochondria and chloroplasts are believed to be derived from:
Endosymbiotic bacteria = free-living prokaryotes that invaded ancestral
eukaryotic cells and established a mutually beneficial relationship.
1. Mitochondria - derived from a photosynthetic purple bacterium that
entered a eukaryotic cell >billion years ago.
2. Chloroplasts - derived from a photosynthetic cyanobacterium.

8. Organization of the mtDNA genome:
• mtDNAs occur in all aerobic eukaryotic cells and generate energy for
cell function by oxidative phosphorylation (producing ATP).
• Most mtDNA genomes are circular and supercoiled (linear mtDNAs
occur in some protozoa and some fungi).
• In some species %GC is high, allowing easy separation of pure
mtDNA from nuclear DNA by gradient centrifugation.
• mtDNAs lack histone-like proteins (like bacteria).
• Copy number is high, multiple genomes per mitochondria and many
mitochondria per cell (makes mtDNA easy to isolate and PCR).
• Size of mtDNA varies widely.
• Humans and other vertebrates ~16 kb
(all of the mtDNA codes gene products)
• Yeast ~80 kb
• Plants ~100 kb to 2 Mb
(lots of non-coding mtDNA)

9. Replication of the mtDNA genome:
• Replication is semi-conservative (like nuclear DNA replication) and
uses DNA polymerases specific to the mitochondria.
• Occurs throughout the cell-cycle (not just S phase).
• Control region (non-coding) forms a displacement loop (d-loop) that
functions in mtDNA replication.
• Mitochondria (organelle) are not synthesized de novo, but grow and
divide like other cells (e.g., mitosis).

10. Fig. 23.3, mtDNA replication

11. Contents of the mtDNA genome:
• mtDNA contains genes for:
• tRNAs
• rRNAs
• cytochrome oxidase, NADH-dehydrogenase, & ATPase subunits.
• mtDNA genes occur on both strands.
• Functions of all human mtDNA ORFs are assigned.
• Mitochondria’s genetic information also occurs in the nuclear DNA:
• DNA polymerase, replication factors
• RNA polymerase, transcription factors
• ribosomal proteins, translation factors, aa-tRNA synthetase
• Additional cytochrome oxidase, NADH, ATPase subunits.
• Most required mitochondrial (and chloroplast) proteins are coded by
nuclear genes in the nuclear genome.
• Copies of the true mtDNA genes can be transposed to the nucleus (a
distinct set of genes from above):
numtDNA = nuclear mtDNA

12. Fig. 23.4, Physical map of the human mtDNA

13. Transcription of the mtDNA genome:
• mRNAs from the mtDNA are synthesized and translated in the
mitochondria.
• Gene products encoded by nuclear genes are transported from the
cytoplasm to the mitochondria.
• Mammalian and other vertebrate mtDNAs are transcribed as a single
large RNA molecule (polycistronic) and cleaved to produce mRNAs,
tRNAs, and rRNAs before they are processed.
• Most mtDNA genes are separated by tRNAs that signal transcription
termination.
• In plants and yeast (mtDNA is much larger):
• tRNAs do not separate genes
• Gaps between genes are large
• Transcription is signaled by non-tRNA sequences
• Introns occur (do not occur in animal mtDNA)
• Some lack a complete stop codon (3’ end is U or UA; poly (A)
tail completes the stop codon)
• Transcription is monocistronic

14. Translation of the mtDNA genome:
• Mitochondria mRNAs do not have a 5’ cap (yeast and plant mt
mRNAs have a leader).
• Specialized mtDNA-specific initiation factors (IFs), elongation
factors (EFs), and release factors (RFs) are used for translation.
• AUG is the start codon (binds with fMet-tRNA like bacteria).
• Only plants use the “universal” genetic code. Codes for mammals,
birds, and other organisms differ slightly.
• Extended wobble also occurs in tRNA-mRNA base-pairing (22 tRNAs
are sufficient rather than 32 tRNA needed for standard wobble).

15. Useful applications of mtDNA:
• Easy to isolate and PCR (high copy #).
• Most mtDNA is inherited maternally. Can be used to assess
maternal population structure (to the exclusion of male-mediated
gene flow)
• Because it is “haploid” effective population size of mtDNA is 1/4 that
of a nuclear gene.
• As a result, mtDNA substitutions fix rapidly (due to genetic drift)
and typically show higher levels of polymorphism.
Useful for:
• Maternity analysis
• Phylogenetic systematics
• Population genetics (and conservation genetics)
• Forensics (maternal ID)

17. Chloroplast genomes (cpDNA):
• Chloroplast organelles are the site of photosynthesis and occur only
in green plants and photosynthetic protists,
• Like mtDNA, chloroplast genome is:
• Circular, double-stranded
• Lacks structural proteins
• %GC content differs
• Chloroplast genome is much larger than animal mtDNA, ~80-600 kb.
• Chloroplast genomes occur in multiple copies and carry lots of non-
coding DNA.
• Complete chloroplast sequences have been determined for several
organisms (tobacco 155,844 bp; rice 134,525 bp).

18. cpDNA organization:
• Nuclear genome encodes some chloroplast components, and cpDNA
codes the rest, including:
• 2 copies of each chloroplast rRNA (16S, 23S, 4.5s, 5S)
• tRNAs (30 in tobacco and rice, 32 in liverwort)
• 100 highly conserved ORFs (~60 code for proteins required for
transcription, translation, and photosynthesis).
• Genes are coded on both strands (like mtDNA).
cpDNA translation- similar to prokaryotes:
• Initiation uses fMet-tRNA.
• Chloroplast specific IFs, EFs, and RFs.
• Universal genetic code.

19. Fig. 23.7
cpDNA of rice

20. Rules of non-Mendelian inheritance for mtDNA and cpDNA:
• Ratios typical of Mendelian segregation do not occur because
meiotic segregation is not involved.
• Reciprocal crosses usually show uniparental inheritance because
zygotes typically receive cytoplasm only from the mother.
• Genotype and phenotype of offspring is same as mother.
• Paternal leakage occurs at low levels and usually is transient;
mechanisms that degrade paternal mtDNA/cpDNA exist.
• Heteroplasmy (mixture of mtDNA/cpDNA organelles with different
DNA substitutions) results in rare cases.

21. http://bmj-sti.highwire.org/content/77/3/158.full

22. Maternal inheritance
• Maternal inheritance was performed by Correns on the
four o'clock plant.
• This plant can have either green, variegated (white and
green) or white leaves.
• Flower structures can develop at different locations on the
plant and the flower color corresponds to the leaf color.
• When Correns crossed the different colored flowers from
different locations on the female plant with pollen obtained
from flowers of the three different colors, the progeny that
resulted from the cross always exhibited the color of the
leaf of the female.

23. • In comparison to traits controlled by maternal effects, those traits controlled by
maternal inheritance, the female phenotype is always expressed in its
offspring.
• All of the organelle DNA that is found in an embryo is from the female.
• The egg cell is many times larger than the pollen cells, and contain both
mitochondria and chloroplasts.
• Pollen is small and is essentially devoid of organelles, and thus organelle DNA.
So any trait that is encoded by the organelle DNA will be contributed by the
female.
• In the case of the four o'clock plant, the different colors of the leaves is a result
of the presence or absence of chlorophyll in the chloroplast, a trait that can be
controlled by the chloroplast DNA.
• Thus, green shoots contain chloroplasts that have chlorophyll, the chloroplasts
in the white shoots contain no chlorophyll, and the variegated shoots contain
some chloroplasts with chlorophyll and some without chlorophyll.
• Thus, depending upon the location in the plant where the flower comes from,
the egg can have chloroplast with chlorophyll, without chlorophyll or a mixture
of the two types of chloroplasts. This is the biological basis of maternal
inheritance.

25. Examples of non-Mendelian inheritance: maternal inheritance
• Variegated-shoot phenotypes in four o’clocks
Fig. 23.8b
Normal chloroplast
Green
photosynthetic
Mutant chloroplast
White
non-photosynthetic
Mixed chloroplasts
White/green

26. Fig. 23.9
Chloroplasts are inherited
via the seed cytoplasm
3 types of eggs (female):
Normal
Mutant
Mixed
Assumption:
Pollen (male) contributes
no information

27. Examples of non-Mendelian inheritance:
• Mutant [poky] Neurospora possess altered mtDNA cytochrome
complements that lead to slow growth.
• [poky] phenotype is inherited with the cytoplasm.
Fig. 23.10, Reciprocal crosses of poky and wild-type Neurospora.
protoperitheca (sexual mating type)
conidia
(asexual mating type)

28. Examples of maternally inherited human mtDNA defects:
• Leber’s hereditary optic neuropathy (LHON), OMIM-535000
• Mid-life adult blindness from optic nerve degeneration.
• Mutations in ND1, ND2, ND4, ND5, ND6, cyt b, CO I, CO II, and
ATPase 6 inhibit electron transport chain.
• Kearns-Sayre Syndrome, OMIM-530000
• Paralysis of eye muscles, accumulation of pigment and
degeneration of the retina, and heart disease.
• Deletion of mtDNA tRNAs.
• Myoclonic epilepsy & ragged-red fiber disease (MERRF), OMIM-
545000
• Spasms and abnormal tissues, accumulation of lactic acid in the
blood, and uncoordinated movement.
• Nucleotide substitution in the mtDNA lysine tRNA.
Most individuals with mtDNA disorders possess a mix of normal and
mutant mtDNA, therefore severity of diseases varies depending on
the level of normal mtDNA.

29. Exceptions to maternal inheritance:
• Heteroplasmy, mice show paternal DNA present at 1/10,000 the
level of maternal DNA.
• Occurs when mtDNA from sperm leak into egg cytoplasm at the time
of fertilization.
• In these cases, maternal and paternal mtDNA can recombine!
• Paternal inheritance of chloroplasts commonly occurs in some plants
(e.g., gymnosperms).
www.sciencemusings.com/

30. Maternal effect:
Some maternal phenotypes are produced by the nuclear genome rather
than the mtDNA/cpDNA genomes.
• Proteins or mRNA (maternal factors) deposited in the oocyte prior
to fertilization; these are important for development.
• Genes for maternal factors occur on nuclear chromosomes; no
mtDNA is involved (not epigenetic).
• e.g., shell coiling in the snail Limnaea peregra.
• Determined by a pair of nuclear alleles; D produces dextral
(right-handed) coiling, d produces sinistral (left-handed)
coiling.
• Shell coiling always is determined by the maternal genotype,
not the alleles that the progeny carry or maternal phenotype.
• If coiling were controlled by extranuclear gene (e.g., mtDNA),
progeny would always have the same phenotype as mother.
• Cause-female snail deposits products in the egg that regulate
orientation of mitotic spindle and direction of cell cleavage.

31. Fig. 23.17
dextral sinistral
*****dextral ***** *****dextral *****

32. Maternal effect:
• mRNAs coded by maternal genes (not offspring) are essential for
normal structural development and axis orientation.
• Placement of bicoid mRNA determines anterior end of developing
Drosophila embryo.
http://scienceblogs.com/pharyngula/2006/06/maternal_effect_genes.php

33. Genomic (parental) imprinting:
• Expression of genes (or alleles) is determined by whether the gene
is inherited from the father or mother.
• Results in expression of single allele (either from father or mother);
other allele frequently suppressed by methylation.
Mechanisms differ between maternal effect and imprinting:
• Maternal effect: dextral/sinistral coiling of snail shells.
• Genomic imprinting: genes from one sex suppressed by methylation
(Prader-Willi syndrome, OMIM-176270).

34. Transovarial disease transmission - a type of maternal inheritance:
• Infected cytoplasm infects the egg and is transmitted to offspring.
• Many insect-vectored diseases show transovarial transmission.
• Example - eggs and larvae of mosquitoes infected with West Nile
Virus also are infected.
http://gsbs.utmb.edu/microbook/ch056.htm