Genom Organization

and Gene Expression
Aisirotul Maisah
Firman Heru K
Alfiani Umi Farkha
Puji Hanani
Titi Alfath

• The nuclear genom contains most of the gene
required for the plant’s physiological functions.
• The first plant genome to be fully sequenced,
in 2000 was that of a small dicotyledonous
angiosperm called thale cress or Arabidopsis
• 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

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
• 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

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

• 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 .

telomeres. and nucleolar organizers contain repetitive sequence • The most prominent structural landmark on chromosomes are centromeres. 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.Centromeres.


• Telomeres are sequence located at the ends of each chromosome. it is not surprising that Nos contain hundreds of repeated copies of each rRNA gene • Depending on the plants species. Nos can be seen through a light microscope and thus can serve as chromosome-specific markers • The rDNA of the nucleolar organizer. Because ribosomes are needed for translation. one or several nucleolar organizers are presents within the genome • Due to their repetitive nature and their high GC content. 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. along with proteins that transcripts for assembly into ribosomes. forms a prominent nuclear structure called the nucleolus .

which is then reserve-transcribed into DNA before it is inserted elsewhere in the genom . • 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.Transposons are mobile sequence within the genome • One dominant type of repetitive DNA within the heterochromatic regions of the genome is the transposon.


by contrast. the gene may be inactivated. transposase. Insertion od a transposon close to a gene can also alter that gene’s expression pattern . splices out the transposon and insertsit elsewhere in the genome.• DNA transposons. 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. 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.

• 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 .• 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.


but especially in palnts.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. 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. while allopolypoids contain multiple complete genomes derived from two or more separate species . • Autopolyploids contain multiple complete genomes of a single species.Polyploids contain multiple copies of the entire genome • Ploidy level.


the resulting zygote contains four copies of each chromosome and is said to be autotetraploid . diploid gametes result • Within a species or in a self-fertilizing individual.• Both types of polyploidy can result from incomplete meiosis during gametogenesis. 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. if a diploid egg is fertilized by diploid sperm. During meiosis.

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

• 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)


are duplicated 2.Their genomes. rye. like those of autopolyploids. cotton.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. wheat. oat.Phenotypic and physiological responses to polyploidy are unpredictable Allopolyploids differ from their parental diploid progenitor species in two major ways : 1. coffee. 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. • The endosymbiotic theory. plant cells contain two additional genome. • Cytoplasmic genome are probably the evolutionary remnants the genomes of bacterial cells that were engulfed by another cell. which they share with animal cells. . postulates that the original mitochondrion was an oxygen-using bacterium that was absorbed by another prokaryotic organism. and the chloroplast genome.

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

– For many years organelar chromosomes had been thought to contain a genome-sized DNA molecule in circular form.• Organellar genomes consist mostly of linear chromosomes. – Organelar genomes are complex in structure and they usually consist of multiple copies of the genome on the same DNA molecul . – 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. similar to the circular plasmids of bacteria.


• Organellar genetics do not obey Mendelian laws. Among the Gymnosperms from paternal parent. . 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. for Angisperms from maternal parent. Organellar genetics do not obey Mendelian laws. but usually show uniparental inheritance and vegetative segragation. Both mitochondria and plastid generally show uniparental inheritance ( sexual offspring (via pollen and eggs) only inherit organelles from one parent). 1. 2. – The genetics of organellar gene are governed by two principles that distinguish them from Mendelian genetics. –.


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

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


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

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


they are referred to as epigenetic modifications. its packaging has to be “looseened”. • To make the DNA accessible.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. . • Because these modifications can change a gene’s behavior without changing the DNA sequence of the gene its self. a process mediated by covalent modifications of both DNA and histones.

.• Epigenetic modifications. such us methylation of DNA and methylation and acetylation of histone proteins. help the determine gene activity.


– These cis-elements can be bound by RNA-binding proteins. which may either stabilize the mRNA or promote its degradation by nuclease. 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. called cis-elements.Posttranscriptional Regulation of Nuclear Gene Expression • An organism often produceds mRNA in response to a specific situation. – One mechanism by which mRNA stability is regulated depents on the presence of certain sequence within the mRNA molecule it sel. .

– Another mechanism for regulating mRNA stability is the RNA Interference (RNAi) pathway. dsRNA usually occur as a result of one of three types of events . – In plant cells. – 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).• Noncoding RNAs regulate mRNA activity via the RNA interference (RNAi) pathway.

which are involved innormal developmental processes. . The presence of microRNAs (miRNAs).1.

The production of short interfering RNAs (siRNAs).2. which silence certain genes .

The introduction of foreign RNAs.3. either by viral infection or via transformation by foreign gene .

• 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. We turn next to the stability of proteins an the mechanisms that regulate a protein’s life span. mRNA stability plays an important role in the ability of the gene to produce a functional protein. 76-amino acid polypeptide called ubiquitin.Posttranslational regulation determines the life span of proteins • As we have seen. .

• 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. .

so the change in the mutant’s nucleotide sequence must result in an altered phenotype. .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.

explain a method called map based cloning.• There are several ways to map a mutation to its chromosome and ultimately clone the affected gene. . 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.

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


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 gene’s 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 .

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


the promoter-GFP fusion genes we described earlier . 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.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.

.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) .

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