chloroplasts (1).pdf by Dr Jyoti Sharma.

Chloroplast -

1. Chloroplast Genome
Lecture 5

2. Plastids
•Thechloroplastisonememberofaclassofinterrelatedorganellesinhigherplantsknownas
plastids.
•Theseincludeamyloplasts,chromoplasts,etioplasts,andproplastids,inadditionto
chloroplasts.
•Plastidsareself-replicatingorganelles.Theproplastidistheprecursorofallmembersofthis
familyoforganelles,allofwhichcontainthechloroplastgenome.
•Theamyloplastisastarchstorageorganellewhichusuallylacksphotosyntheticpigmentsand
enzymes.
•amyloplastsareabundantlypresentinroots,tubers,andotherstoragetissuesandorgans.
•Chromoplastsareorganellesthathavespecializedinthesynthesisanddepositionofvarious
yellow,orange,andredcarotenoidpigments.Manyfruitsandflowerpetalsowetheirbright
colorstotheseorganelles.Likeamyloplast,chromoplastslackphotosyntheticenzymes.
•Etioplastsaretheplastidsthatformwhenleavesandotherorgansgrowindarkness.
Etioplastsarenotphotosyntheticorganelles,butratherastageinthedifferentiationof
chloroplasts

3. •Chloroplastsarethemetabolicallyactive,semi-autonomousorganellesfoundinplants,
algaeandcyanobacteria.
•Theirmainfunctionistocarryoutthephotosynthesisprocessinvolvingaconversionoflight
energyintotheenergyofchemicalbondsusedforthesynthesisoforganiccompounds.
•TheChloroplasts’proteomeconsistsofseveralthousandproteinsthat,besides
photosynthesis,participateinthebiosynthesisoffattyacids,aminoacids,hormones,
vitamins,nucleotidesandsecondarymetabolites.
•Mostofthechloroplastproteinsarenuclear-encoded.Duringthecourseofevolution,many
genesoftheancestralchloroplastshavebeentransferredfromthechloroplastgenomeinto
thecellnucleus.However,theseproteinswhichareessentialforthephotosynthesishave
beenretainedinthechloroplastgenome.
•chloroplastcontainsribosomesandperformsproteinsynthesisrevealedthatthechloroplast
isgeneticallysemi-autonomous.

4. •Thestructuralcompositionofchloroplastsincludes:
•DoubleMembrane(OuterandInnerMembranes):TheExternalMembraneisasmooth
wrappinglayer,constitutingaphospholipidbilayerseparatefromotherorganellesinthe
cytoplasm.InsidetheExternalMembrane,chloroplastshaveamorecomplexInner
Membranethatislesspermeable.TheinnerpartoftheInnerMembraneformsaseries
offoldsreferredtoascristaethatextendintothecorepartsofthechloroplast.
•Stroma:ThisisthespaceenvelopedbythechloroplastInnerMembraneandfillsthe
innerpartofthechloroplast.Thestromacontainswater,dissolvedions,enzymes,and
othermoleculesessentialfortheorganelle.Thestroma,alsoreferredtoasthematrix
fluid,servesasthesitewherethesynthesisofcarbohydratesoccursbymeansof
photosynthesis.
•ChloroplastDNAandRibosomes:FoundwithinthestromaoftheChloroplast,
theChloroplastDNAencodessomeproteinsessentialforthechloroplast.The
Chloroplastalsocarriesribosomes,responsibleforthetranscriptionandtranslationof
thechloroplastDNA,thussynthesizingtherequiredproteins.
•PigmentBodiesandPigments:Chloroplastscarryamassofchlorophyll,agreenpigment
capableofabsorbinglightenergyandparticipatingintheenergyconversionprocessof
photosynthesis.

6. Chloroplast DNA
•Itisacircularmoleculethatrangesinsizefrom120to247kb.
•PlantcellstypicallycontainmanycopiesofthechloroplastDNA.
•Thenumberofcopiesdependsonthetypeofcellanditsstateofdifferentiation.
•Chloroplastsofmesophyllcellsinrapidlygrowingleaveseachcontain20to40identical
copiesofthechloroplastgenome,andthereareusuallyabout200chloroplastsper
mesophyllcell.
•Incontrast,amyloplastsinpotatotubersorchromoplastsintomatofruitseachcontain
onlyafewcopiesofthechloroplastgenome.
•Nevertheless,theamyloplasts,chromoplasts,andchloroplastsofthesameplantallhave
thecopiesofthesamechloroplastDNA,sotheyhaveidenticalgeneticinformation.
•Oneunusualfeatureofthechloroplastgenomeisthepresenceofaninvertedrepeat.
Thatis,eachchloroplastDNAmoleculecontainstwocopiesofa20-to80-kbsequence,
andthesearearrangedininvertedorder.
•AninvertedrepeatispresentinthechloroplastDNAofnearlyalllandplants,exceptfor
membersofthelegumefamily.hasbeenhighlyconserved.

7. •The first two plants in which the chloroplast genome(cpDNA) was successfully sequenced were
tobacco (Nicotiana tabacum, Ohyama etal. 1986) and liverwort (Marchantia polymorpha,
Shinozaki etal. 1986).
•These two organisms are very distantly related, although both are thought to have evolved
from a common algal ancestor. They are separated by approximately a hundred million years
of evolution. Yet, their chloroplast genomes are similar, indicating that the chloroplast genome
has evolved very slowly.
•The inverted repeats of tobacco are each 25,339 bp and they are identical in base sequence.
In all cases, the inverted repeat contains the chloroplast rRNA genes and some of the
chloroplast tRNA genes.
•Except for the inverted repeat, the chloroplast genome consists of unique-sequence DNA.
•Outside the inverted repeat each gene is present only once in the genome.
• As a result, the inverted repeat separates the chloroplast genome into large single-copy (LSC)
and small single-copy (SSG) regions

9. Nucleoids
•Each chloroplast contains around 100 copies of its DNA in young leaves, declining to 15–20
copies in older leaves.
•They are usually packed intonucleoidswhich can contain several identical chloroplast DNA
rings. Many nucleoids can be found in each chloroplast.
•Though chloroplast DNA is not associated with truehistones,inred algae, a histone-like
chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast
DNA ring into anucleoidhas been found.
•In primitivered algae, the chloroplast DNA nucleoids are clustered in the center of a
chloroplast, while in green plants andgreen algae, the nucleoids are dispersed throughout
thestroma.

11. Gene structure
•The average chloroplast genome contains about 120 kb of unique sequence, which is
enough to encode 120 genes if one assumes that an average gene contains about 1 kbMost
chloroplasts have their entire chloroplast genome combined into a single large ring, though
those ofdinophyte algaeare a notable exception—their genome is broken up into about
forty smallplasmids, each 2,000–10,000base pairslong
•In most plant species, the chloroplast genome encodes approximately 120 genes.

•The genes primarily encode core components of the photosynthetic machinery and factors
involved in their expression and assembly.
•Across species of land plants, the set of genes encoded by the chloroplast genome is fairly
conserved. This includes fourribosomal RNAs, approximately 30tRNAs, 21ribosomal
proteins, and 4 subunits of the plastid-encodedRNA polymerasecomplex that are involved
in plastid gene expression.
•The largeRubiscosubunit and 28 photosyntheticthylakoidproteins are encoded within the
chloroplast genome

14. •Over time, many parts of the chloroplast genome were transferred to thenuclear
genomeof the host,a process calledendosymbiotic gene transfer. As a result, the
chloroplast genome is heavilyreduced compared to that of free-living
cyanobacteria.
•Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more
than 1500 genes in their genome
•In land plants, some 11–14% of the DNA in their nuclei can be traced back to the
chloroplast,up to 18% inArabidopsis, corresponding to about 4,500 protein-coding
genes.
•There have been a few recent transfers of genes from the chloroplast DNA to the
nuclear genome in land plants.

15. •The tobacco chloroplast genome contains a total of about 90 different genes.
•These include all 4 genes encoding chloroplast ribosomal RNAs, 20 genes encoding
ribosomal proteins, and 30 genes encoding tRNAs.
•Many of the proteins that are important for photosynthesis consist of several polypeptides,
each the product of a different gene.
•In several cases the genes encoding some of the polypeptides are in the nuclear genome; in
other cases, the genes are in the chloroplast genome. Six of the nine genes encoding
subunits of the chloroplast ATP synthase enzyme are in the chloroplast, as are all three of
the genes encoding subunits of the chloroplast RNA polymerase.
•The chloroplast DNA encodes genes for three photosystem I proteins, nine photosystem II
proteins, and three photosynthetic electron transport proteins. Fifteen of these genes
contain introns.

16. Organization ofgenes intheA. thaliana chloroplast genome
•Arabidopsis thaliana is one of the best-known model plants, for decades widely used in
various studies.
•Its cpDNA complete nucleotide sequence has been demonstrated in 1999 (Sato etal. 1999).
•Depending on the different factors, the chloroplast genome of A. thaliana can take both the
spatial form, namely circular and linear DNA molecule. (Oldenburg and Bendich 2015)
• It is composed of 154,478 base pairs and are more than 2 times smaller than the
mitochondrial genome (mtDNA),which has about 367,000bp.
•The A. thaliana cpDNA contains two IRs of 26,264bp each and separating them LSC and SSC
of 84,197 and 17,780bp, respectively.
•The total content of adenine and thymine (A + T) in the A. thaliana cpDNA is 63.7% and is
similar to the cpDNA of tobacco (62.2%), rice (61.1%) or maize (61.5%)(Maier etal. 1995) or
Thunberg pine (61.5%) (Wakasugietal. 1994).

17. Structure of a typical chloroplast genome (on example of
Arabidopsis thaliana). SSCR-Small Single Copy Region, LSCR-
Large Single Copy Region, IR-A and IR-B-inverted repeats.
Length of plastome and its parts in kbp.

18. •The A. thaliana cpDNA contains 87 open reading frames(ORF) including ORF77 (YCF15)
duplicated gene or 85 without that gene. Due to the duplication of 8 genes with in the IRs, it is
believed that the cp DNA encodes a total of 79 proteins. In addition to eight duplicated genes
encoding chloroplast proteins, three duplicated ribosomal RNA genes localized in IRs region can
be distinguished.
•As many as 37 genes encoding tRNA molecules are located within the regions of LSC and SSC
•One duplicated gene namely ORF77 (YCF15) is not included in all sources. 45 genes of the cpDNA
encode proteins related to the photosynthesis process.
•Among them,6 genes coding for protein subunits of the cytochrome b6fcomplex, 5 genes coding
for proteins being a part of the photosystem I (PS I), 15 genes coding for proteins being a part of
the photosystem II (PS II), 6 genes encoding the ATPase chloroplast subunits, 12 genes encoding
the NADH dehydrogenase subunits and one gene encoding the RuBisCo large subunit.
•In addition, the A. thaliana cpDNA includes 29 genes related to the gene expression processes,
including 4 genes encoding the chloroplast RNA polymerase subunits and 25 genes encoding
protein components of the ribosomes(Sato etal. 1999). The list of chloroplast genes
supplements 12 genes with other and also not known yet, physiological functions

19. A graphic presentation of theA. thalianacpDNA
map with marked lengths of two sequences of
inverted repeats (IRs), long unique sequence (LSC)
and short unique sequence (SSC). The color coding
indicates fallowing genes: small subunit ribosomal
proteins (yellow), large subunit ribosomal proteins
(orange), hypothetical chloroplast open reading
frames (lemon), protein-coding genes either
involved in photosynthetic reactions (green) or in
other function (red), ribosomal RNAs (blue),
transfer RNAs (black). Grey color indicates introns
(Original picture author: prof. Emmanuel Douzery)

20. Aspect Mitochondrial DNA (mtDNA) Chloroplast DNA (cpDNA)
Location in the Cell Found in Mitochondria Found in Chloroplasts
Cell Type Presence Present in Animal and Plant Cells Mainly in Plant Cells
Origin Believed to have evolved from ancient
prokaryotes
Evolved from cyanobacteria
Inheritance Pattern Maternal inheritance Maternal inheritance
Genetic Autonomy Independent of nuclear DNA Independent of nuclear DNA
Structure Circular DNA molecule Circular DNA molecule
Function in the Cell Energy production (ATP synthesis) Photosynthesis (glucose production)
Role in Energy Production Vital for oxidative phosphorylationCrucial for converting light energy into
chemical energy
Protein Encoding Encodes proteins involved in electron
transport chain
Encodes proteins involved in photosynthesis
Genetic Diversity High mutation rate, high genetic diversityModerate mutation rate, moderate genetic
diversity
Applications Forensic analysis, understanding genetic
disorders
Plant breeding, phylogenetic studies
Number in a Cell Multiple mitochondria per cell Multiple chloroplasts per cell
Energy Source Produces ATP through oxidative
phosphorylation
Harnesses sunlight to produce glucose
Cellular Function Energy production and regulation Photosynthesis and energy storage
Carbon Fixation Does not fix carbon dioxide Fixes carbon dioxide
Size Smaller in size compared to chloroplastsLarger in size compared to mitochondria
Replication Mechanism Independent replication Independent replication
Role in Eukaryotic Cells Powerhouse of the cell Essential for photosynthesis
Medical Implications Mitochondrial disorders due to mutationsNot associated with medical disorders
Environmental Significance Not significant in terms of environmental
impact
Significant for oxygen production and plant
life
Challenges in Study Rapid mutation rates, complex interactionsModerate mutation rates, complex
interactions
Genetic Variation Analysis Useful for tracing human migrationsUseful for plant evolutionary studies