Lecture 1 Anatomy of Prokarotic Genome 31 Jan 2012

7/31/2019 Lecture 1 Anatomy of Prokarotic Genome 31 Jan 2012

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Prokayotes

Two groups of prokaryotes,

Are distinguished by characteristic genetic and

biochemical features

a. Bacteria, includes most of the commonly found prokaryotes

such as gram-negative (E. coli), gram-positive (Bacillus subtilis),

cyanobacteria (Anabaena), etc.

b. Archaea, are less studied, and mostly found in extreme

environments (hot springs, brine pools, anaerobic lake bottoms).


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Genomes of prokaryotes

Largest prokaryotic is somewhat similar in size of

smallest eukaryotic genomes.

On the whole prokaryotic genomes are much smaller.

For example, the E. coliK12 genome is just 4639 kb,

two-fifths the size of the yeast genome, and has only

4405 genes.


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The prokaryotic genome is single circular DNA

molecule (DNA + DNA binding proteins).

E.coli chromosome, is one of completely sequenced

prokaryoticgenome, is a circular DNA molecule (endless

loop rather than perfect circle) with 4639.221 kbp (4.639

Mb)Encodes ~ 4,300 genes for proteins and ~ 115 genes for

stable RNA molecules.


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No nuclear envelope. Instead, a nucleoid


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Genome can be naturally

compacted by supercoiling it

DNA of 16mm circumference in cell of 1-2m


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Relaxed and supercoiled plasmid DNAs

The molecule in the left most is relaxed; the degree of supercoiling increasingfrom left to right.


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Model for genome organization

E.colinucleoid having 50s of supercoiled DNA loops that radiate from central protein

core. This protein core holds the loops thus results in localized unwinding.


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ssDNA break due to irradiation

by light of 360nm

Trimethylpsoralen binds to

dsDNA at rate directly

proportional to the torssional

stress on the molecule

The amount of trimethylpsoralen

bound is to proportional to the

radiation dose

Thus showed that irradiation

causes ssDNA breaks leading to

domain restricted loss ofsupercoiling


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Plasmid and extra-chromosomal elements complicate

the question of what is the genome


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In addition to large, circular DNA chromosome in nucleoid, many bacteria

contain one or more small extrachromosomal circular DNA molecules called

plasmids.

Plasmids can be a few thousand base pairs to more than 10,000 bp long.

Plasmids coding genes are not present in the chromosomal DNA & are non-

essential to host cells and their sole function appears to be self-propagation.

Some exist independently while others as integrated to chromosomal DNA.

Some plasmids carry genes that are useful to host bacterium.

For example, genes that make a host bacterium resistant to antibacterial agents.

Gene for enzyme -lactamase confer resistance to -lactam antibiotics such as

penicillin and amoxicillin .

Plasmids may pass from an antibiotic-resistant cell to an antibiotic-sensitive cell

of same or another bacterial species, making recipient cell antibiotic resistant.

Mostly NOT CONSIDERED AS A PART OF GENOME.


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Linear & Multipartite genomes

Borrelia burgdoferi, Streptomyces coelicolorandAgrobacterium tumefaciens have

linear chromosomal DNA.

S. coelicolorlinear ends have special DNA binding proteins.

Multipartite genome is divided into two or more DNA molecules

Vibrio cholerae, hastwo circular DNA, 2.96 Mb & 1.07 Mb, where 71% of genes

(3885) encoded by larger one.

Genes for major cellular activities like gene expression, pathogenicity, etc are

present on large DNA.

Small DNA has many essential genes but also has features of plasmids, like

presence of integron set of genes that enable plasmid to capture genes from

bacteriphages and other plasmids.

Megaplasmid accquired from ancestors during course of evolution.


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Prokaryotic genomes are gene-dense

Outer genes transcribed in clockwise direction, inner in anticlockwise


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Genome has lesser intergenic regions thrA &B separated by 1nt, thrB & Cstart

immediately one after other.

IS186 &IS1 are insertional sequences present elsewere in genome (transposons).

Threonine operon


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Gene organization inprokaryotic genomes


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Operon

A set of adjacent genes in a bacterialgenome, transcribed from a single

promoter and subject to the same

regulatory regime.


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There are no introns in the genes

present in this segment of the E. coli

genome.

The infrequency of repetitive sequences

~~ low repeat DNA.


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Overlap by

1 bpOverlap by

1 bpSeparated

by 4 bpSeparated by

12 bp


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Rule breaker: an operon from Aquifex aeolicus

These genes biochemically unrelated.

gatC, glutamyl-tRNA aminotrasferase subunit C; recA, recombination proteinRecA; pilU, twitching mobility protein; cmk, cytidylate kinase; pgsA,phsphotidylglycerophosphate synthase; recJ, single strand specific endonucleaseRecJ


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Lateral/Horizontal gene transfer is rampant

So what is a species?

Blue DNA unique to species

Red DNA acquired by lateral gene transfer.


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Main features of prokaryotic genome

Smaller than eukaryotes.

Single circular, supercoiled DNA.

Presence of operons.

Genes are separated by fewer nt.

Presence of overlapping genes.

Non-discontinous genome.

Unchecked (rampant) lateral or horizontal gene transfer.


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Lecture 1 Anatomy of Prokarotic Genome 31 Jan 2012