Genom Organization

and Gene Expression

KELOMPOK 8
Aisirotul Maisah
4411413006
Firman Heru K
4411413011
Alfiani Umi Farkha
4411413021
Puji Hanani
4411413023
Titi Alfath
4411413032

 The nuclear genom contains most of the gene

required for the plants physiological functions.
The first plant genome to be fully sequenced,
in 2000 was that of a small dicotyledonous
angiosperm called thale cress or Arabidopsis
thaliana
The genom of A. thaliana is made up of only
about 157 million base pairs (157 Mbp) which
are distributed over five chromosome
Within its nuclear genome, A. thaliana holds
some 27.400 protein-coding genes and almost
another 5000 genes that are either
pseudogenes (nonfunctional genes) or parts of
transposon.

The nuclear genome is packaged

into chromatin
The nuclear genom consists of DNA molecules
that are wrapped around histone proteins to
form beadlike structure called nucleosomes.
DNA and histone, together with other proteins
that bind to the DNA, are reffered to as
chromatin.
Two types of chromatin can be distinguished :
euchromatin and heterochromatin
Heterochromatin is usually more tightly
packaged and thus appears darker than the less
condensed euchromatin

 Most genes that are actively transcribed in a

plant are located within the euchromatic
regions of a chromosome, while many genes
located in heterochromatic regions are not
transcribed- these genes are inactive or silent
Compared with euchromatin, heterochromatin
is relatively gene poor. Heterochromatic
regions include the centromeres, several socalled knobs, and the regions immmadiately
adjacent to the telomers, or chromosome
ends, known as the subtelomeric
Heterochromatic structure often consist of
highly repetitive DNA sequence, or tandem
repeats : blocks of nucleotide motifs of about
150 to 180 bp that are repeatd over and over

 A second class of repeats is the

dispered repeats. One types of
dispersed repeats is known as simple
sequence repeats ( SSR) or
microsatellites
These repeats consist of sequence
motifs as short as two nucleotides
that are repeated hundreds or even
thousands of times.
Another dominant group of dispersed
repeat found in heterochromatin is the
jumping genes or transposons

Centromeres, telomeres, and nucleolar

organizers contain repetitive sequence
The most prominent structural landmark on
chromosomes are centromeres, telomeres, and
nucleolar organizers.
Centomers are constrictions of the chromosomes
where sister chromatids adhere to each other and
where spindle fibers attach during cell division
The attachment of fibers to the centromeres is
mediated by the kinetochore, a protein complex
surrounding the centromere
Centromere consist of highly repetitive DNA
regions and inactive transposable elements

 Telomeres are sequence located at the ends of each

chromosome. Telomeres act as caps on the chromosome ends
and prevents loss of DNA during DNA replication
The DNA molecules that make up ribosomes (rRNA) are
transcribed from nucleolar organizer (NO) regions. Because
ribosomes are needed for translation, it is not surprising that
Nos contain hundreds of repeated copies of each rRNA gene
Depending on the plants species, one or several nucleolar
organizers are presents within the genome
Due to their repetitive nature and their high GC content, Nos
can be seen through a light microscope and thus can serve as
chromosome-specific markers
The rDNA of the nucleolar organizer, along with proteins that
transcripts for assembly into ribosomes, forms a prominent
nuclear structure called the nucleolus

Transposons are mobile sequence

within the genome
One dominant type of repetitive DNA within the
heterochromatic regions of the genome is the transposon.
Transposon or transposable elements are alson known as
jumping genes because some of them have the ability to
insert a copy of themselves in a new location within genome
There are two large classes of transposons : the
retroelements or retrotransposon and the DNA transposons
These two classes are distinguished by their mode of
replication and insertion into a new location
Retransposons make an RNA copy of themselves, which is
then reserve-transcribed into DNA before it is inserted
elsewhere in the genom

 DNA transposons, by contrast, move from one position to

another using a cut-and-paste mechanism catalyzed by an
enzyme that is encoded within the transposon sequence
This enzymes, transposase, splices out the transposon and
insertsit elsewhere in the genome, in most cases keeping
the total transposon copy number the same
Transposition into a gene can result in mutations. If a
transposon lands within a coding region, the gene may be
inactivated. Insertion od a transposon close to a gene can
also alter that genes expression pattern

 Plants and other organisms seem to be able to regulate the

activity of transposons through the methylation of DNA and
histones
As more genomic noticed large numbers of highly methylated
transposons in heterochromatic region.
Studies of mutants that are unable to maintain genome
methylation have shown that slow loss of proper methylation
over generations can activate dormant transposons and increase
the frequency of transpositional mutations
Therefore, methylation and the formationof hererochromatin
appear to play important roles in the stability of the genom

Polyploids contain multiple copies of

the entire genome
Ploidy level- the number of copies of the entire genome in
a cell-is another important aspect of genome structure that
may have implications for both physiology and evolution
In many organism, but especially in palnts, the entire
diploid (2n) genome can undergo one or more additional
rounds of replication without undergoing cytokinesis to
become polyploid
Two forms of polyploidy are distinguished : autopolyploidy
and allopolyploidy.
Autopolyploids contain multiple complete genomes of a
single species, while allopolypoids contain multiple
complete genomes derived from two or more separate
species

 Both types of polyploidy can result from

incomplete meiosis during gametogenesis.
During meiosis, the chromosomes of a diploid
germ cell undergo DNA replication followed by
two rounds of division
If chromosome duplication is not followed by cell
devision during meiosis, diploid gametes result
Within a species or in a self-fertilizing individual,
if a diploid egg is fertilized by diploid sperm, the
resulting zygote contains four copies of each
chromosome and is said to be autotetraploid

Allopolyploids usually form in one of

two ways :
1.A haploid sperm from one species
and a haploid egg from another
species may form a diploid
interspecies hybrid
2.Diploid gametes from two different
species may join to form a tetraploid
zygote.

 Diploid interspecies hybrids occur naturally, but they are

frequently sterile because their chromosome cannot pair
properly during prophase 1 of meiosis
The lack of fertility in interspecies hybrids is in stark
contast to the phenomenon known as hybrid vigor or
heterosis : the increase vigor often observed in the
offspring of crosses between two inbred varieties of the
same plants species
Heterosis can contributed to larger plants, greater
biomass, and higher yields in agricultural crops
Polyploidy can also be induced artificially by treatment
with the natural cell toxin colchicine, which is derived
from the autumn cronus (Colchicum autumnale)

Phenotypic and physiological responses to polyploidy

are unpredictable

Allopolyploids differ from their parental diploid

progenitor species in two major ways :
1.Their genomes, like those of autopolyploids, are
duplicated
2.They are hybrid between two different species
Allopolyploids are frequently more vigorous or
higher yielding than their parent species and are
very common among agriculturally important
plantssuch allopolyploids includecanola and
collars, coffee, cotton, wheat, rye, oat, and
sugarcane

Some of the genetic changes that have been

observed in newly formed allopolyploids compared
with their parent species are the following :

Restructing of the chromosome,

including loss of DNA sequence
Changes in epigenetic modifications
Changes in gene transcriptional
activity
Activation of previously dormant
transposable elements through loss
of gene silencing

 Polyploidy is in striking contrast to a

condition called aneuploidy.
Aneuploids are organisms whose genomes
contain more or fewer individual
chromosomes (not entire chromosome
sets) than normal
Such states are known as trisomies if one
type of chromosome is tripled or
monosomies if only one chromosome of a
given type is presents.

Plant Cytoplasmic Genomes :

Mitochondria and Chloroplasts
In addition to the nuclear genome, plant cells contain
two additional genome, which they share with animal
cells, and the chloroplast genome.
Cytoplasmic genome are probably the evolutionary
remnants the genomes of bacterial cells that were
engulfed by another cell.
The endosymbiotic theory, postulates that the original
mitochondrion was an oxygen-using bacterium that
was absorbed by another prokaryotic organism.

 Two main lines of evidence are often cited in support

of the endocymbiotic theory :
1. Both mitochondria and chloroplasts are enclosed by
an outer and an inner membrane, and the inner
membrane is continuous with additional membranebound compartments inside the organelle.
2. Both organella genomes show sequence similarity to
procaryotic genomes.
. The organelar genomes, like those of procaryotes are
not enclosed in a nuclear envelope and are called
nucleoids.

 Organellar genomes consist mostly of linear

chromosomes.
For many years organelar chromosomes had been thought
to contain a genome-sized DNA molecule in circular form,
similar to the circular plasmids of bacteria.
Most of the DNA in both plant mitochondria and
chloroplasts is found in linear molecules that my contain
more than one copy of the genome.
Organelar genomes are complex in structure and they
usually consist of multiple copies of the genome on the
same DNA molecul

 Organellar genetics do not obey Mendelian laws.

The genetics of organellar gene are governed by two
principles that distinguish them from Mendelian genetics.
1. Both mitochondria and plastid generally show uniparental
inheritance ( sexual offspring (via pollen and eggs) only
inherit organelles from one parent). Among the
Gymnosperms from paternal parent, for Angisperms from
maternal parent.
2. Both chloroplasts and mitochondria can segregate
vegetatively ( vegetative cell (as opposed to a gamete) can
give rise to another vegetative cell via mitosis that is
genetically different.
. Organellar genetics do not obey Mendelian laws, but usually
show uniparental inheritance and vegetative segragation.

Transcriptional Regulation of Nuclear Gene

Expression.
The path from gene to protein is a multistep process
catalyzed by many enzymes.
Each step is subject to regulation by the plant to control
the amount of protein that is produced by each gene.
Regulation of the first step, transcription, determines
when and whether an mRNA is made.
This level of regulation, which is referred to as
transcriptional regulation, includes the control of
trancription initiation, maintenance, and termination.

 The next level in the regulation of gene expression,

known as posttranscriptional regulation, occurs after
transcription includes controls on mRNA stability,
translation efficiency and degradation.
Finally, protein stability (posttranslational regulation)
plays an important role in the overall activity of a gene
or its product.

 RNA polymerase II binds to the promoter region of most

protein-coding genes.
Gene transcription is facilitated by an enzyme called RNA
polymerase, which binds to the DNA to the DNA to be
transcribed and makes an mRNA transcript complementary
to the DNA sequence.
The region of the gene that binds RNA polymerase is
called the promotor.
The structure of the eukaryotic promoter into two part :
1. Core promoter or minimum promoter, consisting of the
minimum upstream sequence required for gene
expression.
2. Regulatory sequence, which control the activity of the
core promoter.

 In addition to RNA polymerase and the general transcription

factors, most genes, especially those that play important roles
in development, require specific transcription factors ( also
often called gene regulatory proteins) for RNA polymerase to
become active.
These regulatory proteins bind to the DNA and become part of
the transcription initiation complex.

Epigenetic modifications help determine gene

activity
Transcription can be initiated only if the DNA is accessible to
the RNA polymerase and other required binding protein.
To make the DNA accessible, its packaging has to be
looseened, a process mediated by covalent modifications of
both DNA and histones.
Because these modifications can change a genes behavior
without changing the DNA sequence of the gene its self, they
are referred to as epigenetic modifications.

 Epigenetic modifications, such us methylation of DNA and

methylation and acetylation of histone proteins, help the
determine gene activity.

Posttranscriptional Regulation of Nuclear Gene

Expression
An organism often produceds mRNA in response to a specific
situation. In order to remain useful as a specific respone to a
specific situation, individual mRNAs must have a finite
lifetime.
RNA stability can be influenced by cis-elements.
One mechanism by which mRNA stability is regulated
depents on the presence of certain sequence within the
mRNA molecule it sel, called cis-elements.
These cis-elements can be bound by RNA-binding
proteins, which may either stabilize the mRNA or promote
its degradation by nuclease.

 Noncoding RNAs regulate mRNA activity via the RNA

interference (RNAi) pathway.
Another mechanism for regulating mRNA stability is the
RNA Interference (RNAi) pathway.
The RNAi pathway is a set of cellular reactions to the
presence of double-stranded RNA (dsRNA) molecules.
Recall that mRNA is usually a single-stranded molecule
(ssRNA).
In plant cells, dsRNA usually occur as a result of one of
three types of events

1. The presence of microRNAs (miRNAs), which are involved

innormal developmental processes.

2. The production of short interfering RNAs (siRNAs), which

silence certain genes

3. The introduction of foreign RNAs, either by viral infection or

via transformation by foreign gene

Posttranslational regulation determines the life

span of proteins
As we have seen, mRNA stability plays an important
role in the ability of the gene to produce a functional
protein. We turn next to the stability of proteins an the
mechanisms that regulate a proteins life span.
The cytoplasmic pathways of protein turnover
involves the ATP-dependent formation of a covalent
bond between the protein that is to be degraded and a
small, 76-amino acid polypeptide called ubiquitin.

 Ubiquitination is initiated when the ubiquitin

activating enzyme (E1) catalyzes the ATP dependent
adenylylation of the C terminus of ubiquitin. The
adenylylated ubiquitin is then transferred to a
cysteine residue on a second enzyme, the ubiquitin
conjugating enzyme (E2). Proteins destined for
degradation are bound by a third type of protein, a
ubiquitin ligase (E3)

Tools for Studying Gene Function

Individuals that contain specific changes in
their DNA sequence are called mutants. The
analysis of mutants is an extremely powerful
tool that can help scientists infer the function
of a gene or map its location on the
chromosoms.

Mutant analysis can help to elucidate gene

function
The use of mutants for gene identification
relies on the ability to distinguish a mutant
from a normal individual, so the change in the
mutants nucleotide sequence must result in an
altered phenotype.

 There are several ways to map a mutation to

its chromosome and ultimately clone the
affected gene, explain a method called map
based cloning, which uses crosses between a
mutant and a wild type palnt and genetic
analysis of the offspring to narrow down the
location of the mutation to a short segment of
the chromosome, which is then sequenced.

Molecular techniques can measure the

activity of genes
Once a gene of interest has been identified, scientists
are usually interested in where and when the gene is
expressed.
For example, a gene may be expressed only in
reproductive tissues, or only I vegetative ones.
All microarray techniques use a solid support, such as
a glass slide, onto which DNA sequences are spotted
that are representative of single genes of a given
species.

Gene fusions can introduse reporter

genes
A gene fusions is an artificial
construct that combines part of the
gene of interest with another gene
that produces a readily detectable
protein
A genes expression is regulated by
transcription factors that fine-tune its
activity and allow it to be trancsribed
only where and when its needed.

Genetic modification of crop plants

In contrast to classical selective
breeding, bioengineering allows the
transfer of specific gene ora gened
between spiceis that cannot be
crossed succesfully

 Biotechnological tools circumvent

this problem by allowing insertion of
only the desired genes into the
recipient plant, most often either by
Agrobacterium-mediated
transformation or by biolistics.
Plants produced in this way are
commonly referred to as genetically
modified organisms (GMOs)

There are three essesntial differences between

GMOs and conventionally bred varieties of crops
Gene transfer into GMOs occurs in the
laboratory and does not require crossbreeding
The donor genes of GMOs can be derived from
any organism, not just those with which the
recipient can be succesfully crossed
GMOs may carry gene constructs that are the
product of splicing a variety of genetic
components together to produce genes with
altogether new functions (for example, the
promoter-GFP fusion genes we described
earlier

Transgenes can confer resistance to

herbicides or plant pets
Any gene articially tranferred into an
organism is referred to as a
transgene
Plants carrying a transgene for
glyphosate resistance will survive a
field application of glyphosate (the
commercial herbicide Roundup),
which kills weeds but does not harm
resistant crop plants.

 Another commonly used transgene

encodes an inseticidal toxin from th
soil bacterium Bacillus thuringiensis
(Bt)

Genetically modified organisms are

controversial
The development of GMOs has not
been greeted with universal
enthusiasm and support . In spite of
their enoumous humanitarian
potential, many individuals, as well
as the government of some
countries, look on GMOs with
suspicion and cocern.