Download Organization of the eukaryotic genomes

Prokaryotic Genome

The term Genome was created in 1920 by Hans Winkler,[2]
professor of botany at the University of Hamburg,
Germany.

The Oxford English Dictionary suggests the name to be a
blend of the words gene and chromosome.

In modern molecular biology and genetics, the genome is
the entirety of an organism's hereditary information. It is
encoded either in DNA or, for many types of viruses, in
RNA.

The genome includes both the genes and the non-coding
sequences of the DNA/RNA.[1]
Genome size
Genome size is the total number of DNA base pairs
in one copy of a haploid genome.
The genome size is positively correlated with the
morphological complexity among prokaryotes and
lower eukaryotes; however, after mollusks and all
the other higher eukaryotes above, this correlation
is no longer effective.[13][15]
The genome size is positively correlated with the morphological complexity
among prokaryotes
Table 8.3 Genomes 3 (© Garland Science 2007)
Genome Size and Gene Numbers in
Various Organisms
The number of genes in bacterial and archael genomes is
proportional to the genome size
7
Comparative Genome Sizes
Relationship of Gene Number and Genome Size
While the number of genes in prokaryotes correlates well with the
sizes of their genome, the number of genes in eukaryotes does not
correct well with their genome sizes
Size range
BACTERIA
E. coli:
Example
species
Ex. Size
1-10 Mb
4.639 Mb
FUNGI
10-40 Mb
S. cerevisiae
13 Mb
INSECTS
100-5000 Mb
D. melanogaster
165 Mb
BIRDS
1000-1500 Mb
Chicken
1300 Mb
PLANTS
FLOWERING
100 to 100,000 Mb
Corn
2500 Mb
MAMMALS
3000-4000 Mb
Human
3000 Mb
1 Mb = 1 million base pairs. (Probably the number of
essential genes does not differ greatly among various
multicellular organisms. Most estimates are that humans
have about 40,000 genes.)
Prokaryotic and
Eukaryotic
Chromosomes



Not only the genomes of eukaryotes are more
complex than prokaryotes, but the DNA of
eukaryotic cell is also organized differently from
that of prokaryotic cells.
The genomes of prokaryotes are contained in
single chromosomes, which are usually circular
DNA molecules.
In contrast, the genomes of eukaryotes are
composed of multiple chromosomes, each
containing a linear molecular of DNA.

In prokaryotes, most of the genome (85-90%) is non-repetitive
DNA, which means coding DNA mainly forms it, while noncoding regions only take a small part.[12]

On the contrary, eukaryotes have the feature of exon-intron
organization of protein coding genes; the variation of
repetitive DNA content in eukaryotes is also extremely high.

When refer to mammalians and plants, the major part of
genome is composed by repetitive DNA.[1

The DNA of eukaryotic cell is tightly bound to small
basic proteins (histones) that package the DNA in
an orderly way in the cell nucleus.

For e.g., the total extended length of DNA in a
human cell is nearly 2 m, but this must be fit
into a nucleus with a diameter of only 5 to 10µm.

Although DNA packaging is also a problem in
bacteria, the mechanism by which prokaryotic DNA
are packaged in the cell appears distinct from that
eukaryotes and is not well understood.

When talking about genome composition, one should
distinguish between prokaryotes and eukaryotes as
the big differences on contents structure they have.

Prokaryotes
 Most genome is coding
 Small amount of non-coding is regulatory sequences

Eukaryotes
 Most genome is non-coding (95%)
▪ Regulatory sequences
▪ Introns
▪ Repetitive DNA
• Haploid circular genomes (0.5-10 MB,
500-10000 genes)

The
prokaryotes
usually have only one
chromosome, and it
bears
little
morphological
resemblance
to
eukaryotic
chromosomes.
The typical prokaryotic genome is a ring of DNA that is not
surrounded by a membrane and that is located in a nucleoid
region

Some species of bacteria also have
smaller rings of DNA called
plasmids

Among prokaryotes there is
considerable
variation
in
genome length bearing genes.




The genome length is smallest in
RNA viruses
In this case, the organism is
provided with only a few genes
in its chromosome.
The number of gene may be as
high as 150 in some larger
bacteriophage genome.
Table 8.2 part 1 of 2 Genomes 3 (© Garland Science 2007)
Package of DNA in Microorganisms
•
•
In viruses, genomic
DNA
molecule
is
associated
with
protein molecules and
packaged inside the
viral capsids.
In bacteria and fungi,
the genomic DNA is
associated
with
proteins
and
is
packaged
as
a
compact mass inside
the center of the cell.
It
is
called
as
“nucleoid”
E.coli, about 3000 to 4000 genes are organized
into its one circular chromosome.

The chromosome exists as a highly folded
and coiled structure dispersed throughout
the cell.

The folded nature of chromosome is due to
the incorporation of RNA with DNA.

During replication of DNA, the coiling must
be relaxed. DNA gyrase is necessary for the
unwinding the coils.

There are about 50
loops
in
the
chromosome
of
E.coli. These loops
are highly twisted
or
supercoiled
structure
with
about four million
nucleotide pairs.
Its
molecular
weight is about 2.8
X109
Single, circular DNA molecule
located in the nucleoid region of cell
Most common type
of supercoiling
Helix twists on
itself in the opposite
direction; twists to
the left
Model for genome organization
Figure 8.3 Genomes 3 (© Garland Science 2007)
Mechanism of folding of a bacterial
chromosome
There are many supercoiled loops (~100 in E. coli) attached to a central core.
Each loop can be independently relaxed or condensed.
Topoisomerase enzyme – (Type I and II) that introduce or remove
supercoiling.
Gene organization in
prokaryotic genomes
• Bacterial genes are organized in by gene systems known
as
Operons: polycistronic transcription units
• Transcription and translation take place in the same
compartment
Example: E. coli
89% coding
4,285 genes
122 structural RNA genes
• Environment-specific genes on plasmids and other
types of mobile genetic elements
EPFL Bioinformatics I – 09 Jan 2006
Figure 8.8a Genomes 3 (© Garland Science 2007)
Figure 8.8b Genomes 3 (© Garland Science 2007)

Its an easy place to start
 history
 we know more about it
▪ systems better understood
 simpler genome
 good model for control of genes
▪ build concepts from there to eukaryotes
 bacterial genetic systems are exploited in
biotechnology

Single circular chromosome
 haploid
 naked DNA
▪ no histone proteins
 ~4 million base pairs
▪ ~4300 genes
▪ 1/1000 DNA in eukaryote

No nuclear membrane
 chromosome in cytoplasm
 transcription & translation are coupled
together
▪ no processing of mRNA
 no introns
 but Central Dogma
still applies
▪ use same
genetic code
2005-2006

Replication of bacterial
chromosome

Asexual reproduction
 offspring genetically
identical to parent
2005-2006

Without meiosis prokaryotes loos an
important source of genetic variation.

Rapid reproduction and horizontal gene
transfer facilitate the evolution of
prokaryotes in changing environments

Sources of variation
 spontaneous mutation
 Transformation
 transduction
 conjugation
 transposons
bacteria shedding DNA




▪
▪
Spontaneous mutation is a significant source of
variation
in rapidly reproducing species
Example: E. coli, human colon
(large intestines) 2 x 1010 (billion) new
E. coli each day!
 spontaneous mutations
▪ for 1 gene, only ~1 mutation in 10 million replications
▪ each day, ~2,000 bacteria develop mutation in that gene
but consider all 4300 genes, then:
4300 x 2000 = 9 million mutations
per day per human host!
There are have three different
mechanisms of genetic recombination:
- transformation – genes are taken from
the surrounding environment;
- conjugation – direct gene transfer
from one prokaryote to another;
- transduction – the gene transfer by
viruses.
.
5/12/2017
Plasmids

Plasmids, small rings of DNA consist of only a few
genes, present in some prokaryotes
▪ 5000 - 20,000 base pairs
▪ self-replicating
 carry extra genes
▪ 2-30 genes
▪ rapid evolution
 can be exchanged between bacteria
▪ bacterial sex!! ( sexual reproduction)
2005-2006
Plasmids
Plasmid genes provide:a- resistance to antibiotics
b- direct metabolism of
unusual nutrients
c- other special functions
Plasmids replicate,
a- independently of the
chromosome
b- can be transferred
between partners during
conjugation
Table 8.1 Genomes 3 (© Garland Science 2007)
Bacterial Conjugation is genetic recombination
in which there is a transfer of DNA from
a living donor bacterium to a recipient
bacterium. Often involves a sex pilus.

The 3 conjugative processes
+
I. F conjugation
II. Hfr conjugation
III. Resistance plasmid conjugation

Direct transfer of DNA between 2 bacterial cells
that are temporarily joined
 results from presence of F plasmid with F
factor
▪ F for “fertility” DNA
2005-2006
I) F+ Conjugation Process
F+ ConjugationGenetic recombination in which there is a
transfer of an F+ plasmid (coding only for
a sex pilus) from a male donor bacterium
to a female recipient bacterium.
Other plasmids present in the cytoplasm of
the bacterium, such as those coding for
antibiotic
resistance,
may
also
be
transferred during this process.
1. The F+ male has an F+ plasmid coding
for a sex pilus and can serve as a genetic
donor
2. The sex pilus adheres to an F- female
(recipient). One strand of the F+ plasmid
breaks
3. The sex pilus retracts and a bridge
is created between the two bacteria.
One strand of the F+ plasmid enters
the recipient bacterium
4. Both bacteria make a complementary
strand of the F+ plasmid and both are
now F+ males capable of producing a
sex pilus.
Note: There was no transfer of donor
chromosomal
DNA
although
other
plasmids the donor bacterium carries
may also be transferred during F+
conjugation.
http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/f.htm l
Genetic recombination in which fragments of
chromosomal DNA from a male donor
bacterium are transferred to a female recipient
bacterium, following insertion of an F+ plasmid
into the nucleoid of the donor bacterium.
Involves a sex (conjugation)pilus.
1. An F+ plasmid inserts
into the donor bacterium's
nucleoid to form an Hfr
male.
2. The sex pilus adheres to
an F- female (recipient).
One donor DNA strand
breaks in the middle of the
inserted F+ plasmid.
3. The sex pilus retracts and a bridge
forms between the two bacteria. One
donor DNA strand begins to enter the
recipient bacterium.
a portion of the donor's DNA strand
is usually transferred to the recipient
bacterium.
4. The donor bacterium makes a
complementary copy of the remaining
DNA strand and remains
an Hfr
The recipient bacterium
complementary
strand
transferred donor DNA.
makes a
of
the
male.
5. Since there was transfer of some donor
chromosomal DNA but usually not a complete F+
plasmid, the recipient bacterium usually remains Fhttp://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/hfr.htm l
Genetic recombination in which there
is a transfer of an R plasmid (a
plasmid coding for multiple antibiotic
resistance and often a sex pilus) from
a male donor bacterium to a female
recipient bacterium.
Involves a sex (conjugation) pilus
4 steped Resistant Plasmid Conjugation
1. The bacterium with an Rplasmid is multiple antibiotic
resistant and can produce a
sex pilus (serve as a genetic
donor).
2. The sex pilus adheres to an
F- female (recipient). One
strand
of
the
R-plasmid
breaks.
4 stepped Resistant Plasmid Conjugation (cont’d)
3. The sex pilus retracts and a
bridge is created between the two
bacteria. One strand of the Rplasmid
enters
the
recipient
bacterium.
4.
Both
bacteria
make
a
complementary strand of the Rplasmid and both are now multiple
antibiotic resistant and capable of
producing a sex pilus.
http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/r.html
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