Prokaryotic genome ppt

1. Bacterial Genome
Mohana.K

2. What will Bacterial Genomics give us?
• Bacterial genomics can give us a broader
understanding of how a bacteria functions, a bacteria's
origins, and what bacteria live in our world that we
can't study by other means (i.e through obtaining their
DNA from the environment and studying it).
• Of medical interest, bacterial genomics is also
anticipated to play a significant role in speeding up the
development of better therapies and vaccines for
controlling disease-causing bacteria.
• It will also be the cornerstone of anticipated DNA-
based diagnostic tools that will hopefully enable
doctors to make quicker, more accurate diagnoses of
infectious disease.

3. Size of Bacterial Genome
• The size of Bacterial chromosomes ranges from 0.6 Mbp to
over 10 Mbp
• The smallest Bacterial genome identified thus far is from
Mycoplasma genitalium, an obligate intracellular pathogen
with a genome size of 0.58 Mbp (580 Kbp). M. genitalium is
restricted to the intracellular niche because it lacks genes
encoding enzymes required for amino acid biosynthesis and
the peptidoglycan cell wall, genes encoding TCA cycle
enzymes, and many other biosynthetic genes.
• In contrast to such obligate intracellular bacteria, free-living
bacteria must dedicate many genes toward the
biosynthesis and transport of nutrients and building blocks.
The smallest free-living organisms have a genome size over
1 Mbp.
• Currently largest sequenced prokaryotic genome is
streptomyces coelicolor, 8.7 Mb.

4. Gene Content
• Gene portion of bacterial genome is around 85 –
95 %
• Bacteria posess few genes such as in case of
Mycobacterium genitalium (480 genes)
• The highest gene content is present in
Bradyrhizobium japonicum (8317 genes)
• The average gene content is 3,100 genes per
genome.

5. COG
• Genes shared among prokaryote genome by
virtue of common evolutionary descent are
frequently evaluated descent are frequently
evaluated in terms of “Clustered Orthologous
Groups”
It is critical to infer orthologous relationships between genes from different
species.
Orthologs are direct evolutionary counterparts related by vertical descent as
opposed to paralogs which are genes within the same genome related by
duplication.
Typically, orthologous proteins have the samedomain architecture and the same
functioncin prokaryotes

6. Base pair composition
• 22.4 % GC – Wigglesworthia sp
• 72.1 % GC – Streptomyces coelicolor
Average – 46.8 % GC
• GC Skew: Used to indicate biases in the
relative contribution of G or C in an individual
DNA strand
(G – C)
(G + C)

7. • In most bacterial genomes a difference in base
composition between the strands (which could
mean leading vs lagging strand of replication or
coding vs non-coding strand of genes) is
observed, which means that there are different
mutation/substitution processes affecting the
two strands.
• Typically, the leading strand is enriched in G and
T, while the lagging strand is enriched in A and C.
Deviations from the base frequencies A=T and
G=C are called AT- and GC-skews

8. Analysis of GC Skew
• Analysis of GC skew was first utilized for the computational
prediction of ori and ter positions by examining available
genome sequences.
• As GC-skew is positive in the leading strand and negative in
the lagging strand, the GC-skew changes sign at the origin
and terminus where the leading strand becomes the
lagging strand and vice versa.
• This makes GC-skew analysis a useful tool to identify the
origin and the terminus in circular chromosomes. Local
changes, which are visible as diagram distortions, can mark
recent rearrangements such as sequence inversions or
integration of foreign DNA. The loss of DNA would not
change the basic shape of the GC-skew curve, whereas
recent incorporation of external DNA would probably result
in a local deviation.

9. Output of GC Skew analysis

10. General features of Bacterial Chromosomes
• Not all bacteria have a single circular chromosome.
• some bacteria have multiple circular chromosomes.
• Many bacteria have linear chromosomes and linear
plasmids.
• Linear chromosomes and plasmids were not
discovered in bacteria until relatively recently.
• In 1989, pulsed field gel electrophoresis had been
developed, and this new technique provided
convincing evidence that the chromosome of
Borrelia burgdoferi was linear

11. • Agrobacterium tumefacians:
• One linear (2.1 Mb) +
• One circular (3.0 Mb) +
• Two circular plasmids (450 kb + 200 Kb)
• Vibrio cholerae: twocircular chromosomes. One of
these chromosomes contains the genes involved
inmetabolism and virulence, while the other
contains the remaining essentialgenes
• Bacillus thuringiensis:
• One circular (5.7 Mb) +
• Six plasmids (Each > 50 Kb)

12. Genome Packaging in Prokaryotes:
the Circular Chromosome of E. coli
• Prokaryotic cells donot contain nuclei or other
membrane-bound organelles.
• In fact, the word "prokaryote"literally means
"before the nucleus." The nucleoid is simply
the area of a prokaryotic cell in which the
chromosomal DNA is located.

14. The scales of Genome Organisation

15. DNA Supercoiling
• One way prokaryotes compress their DNA into
smaller spaces is through supercoiling.
• Genomes can be negatively
supercoiled, meaning that the DNA is twisted
in the opposite direction of the double
helix, or positively supercoiled, meaning that
the DNA is twisted in the same direction as
the double helix. Most bacterial genomes are
negatively supercoiled during normal growth.

16. Proteins Involved in Supercoiling
• Multiple proteins act together to fold and condense prokaryotic DNA.
• In particular, one protein called HU, which is themost abundant protein in
the nucleoid, works with an enzyme called topoisomerase I to bind DNA
and introduce sharp bends in the chromosome, generating the tension
necessary for negative supercoiling.
• Integration host factor (IHF), can bind to specific sequences within the
genome and introduce additional bends.
• The folded DNA is then organized into a variety of conformations that are
supercoiled and wound around tetramers of the HU protein, much like
eukaryotic chromosomes are wrapped around histones.
• Once the prokaryoticgenome has been condensed, DNA topoisomerase I,
DNA gyrase, and other proteins help maintain the supercoils.
• One of these maintenance proteins, H-NS, plays anactive role in
transcription by modulating the expression of the genes involved in the
response to environmental stimuli.
• Another maintenance protein, factor for inversion stimulation (FIS), is
abundant during exponential growth and regulates the expression of more
than 231 genes, including DNA topoisomerase I .

17. Accessing Supercoiled Genes
• It has been determined that prokaryotic DNA
replication occurs at arate of 1,000 nucleotides
per second, and prokaryotic transcription occurs
at arate of about 40 nucleotides per second .
• During transcription, small regions of the
chromosome can be seen to project from the
nucleoid into the cytoplasm
• Because there is nonuclear membrane to separate
prokaryotic DNA from the ribosomes within the
cytoplasm, transcription and translation occur
simultaneously in these organisms

18. Operons
• When different genes are to be expressed in
exactly the same amount because they are part of
a complex, transcription of all genes in a single
transcript diminishes gene expression noise and
ensures more precise stoichiometry.
• Pairs of divergently oriented operons show correlated
expression levels this is because sometimes they share
bidirectional regulatory regions that allow coregulation
of the two operons.

19. Replication-Associated Gene
Dosage Effects
• The possibility of starting a new round of replication before the
previous round finishes, i.e., of having simultaneous replication
rounds, allows cells of E. coli to double every 20 min, whereas the
chromosome takes three times longer to replicate. The estimated
number of simultaneous replication rounds (R) is the ratio between
the time required to replicate the chromosome and the time
between two successive cell divisions.
• If R is close to zero, then chromosome replication rarely takes place
in the cell.
• IfRis 1, one replication round starts when the previous ends.
• When R > 1, cells experience multiple simultaneous replication
rounds.

20. Problems faced by linear DNA
• 1. Free double-stranded DNA ends are very
sensitive to degradation by intracellular
nucleases, there must be a mechanism to
protect the ends.
• 2. Ends of linear DNA molecules must have a
special mechanism for DNA replication.

21. • Protected by both types of telomeres:
palindromic hairpin loops are protected by
the lack of free double-stranded ends, and
invertron telomeres are protected by proteins
that bind to the 5'-ends.

22. Table : Prokaryotic versusEukaryotic Chromosomes
Prokaryotic Chromosomes Eukaryotic Chromosomes
•Many prokaryotes contain a single circular •Eukaryotes contain multiple linear
chromosome. chromosomes.
•Prokaryotic chromosomes are condensed in •Eukaryotic chromosomes are condensed in a
the nucleoid via DNA supercoiling and the membrane-bound nucleus via histones.
binding of various architectural proteins. •In eukaryotes, transcription occurs in the
•Because prokaryotic DNA can interact with the nucleus, and translation occurs in the
cytoplasm, transcription and translation occur cytoplasm.
simultaneously. •Most eukaryotes contain two copies of each
•Most prokaryotes contain only one copy of gene (i.e., they are diploid).
each gene (i.e., they are haploid). •Some eukaryotic genomes are organized into
•Nonessential prokaryotic genes are commonly operons, but most are not.
encoded on extrachromosomal plasmids. •Extrachromosomal plasmids are not
•Prokaryotic genomes are efficient and commonly present in eukaryotes.
compact, containing little repetitive DNA. •Eukaryotes contain large amounts of
noncoding and repetitive DNA.