Prokaryotic Genome Anatomy

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).

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. coli K12 genome is just 4639 kb, two-fifths the size of the yeast genome, and has only 4405 genes.

The prokaryotic genome is single circular DNA

molecule (DNA + DNA binding proteins).

E.coli chromosome, is one of completely sequenced prokaryotic genome, 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.

No nuclear envelope. Instead, a nucleoid

Genome can be naturally compacted by supercoiling it

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

Relaxed and supercoiled plasmid DNAs

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

Model for genome organization

E. coli nucleoid having 50s of supercoiled DNA loops that radiate from central protein core. This protein core holds the loops thus results in localized unwinding.

Main protein components are DNA gyrase & topoisomerase I that are responsible to maintain the supercoiled state. In addition a set of at least 4 proteins are believed to play role in DNA packaging. Most abundant among these is HU proteins (different from histone) form tetramer around which 60 bp of DNA wounds.

There are about 60,000 HU proteins per E. coli cell but can wound only 1/5 of chromosomal DNA.
Its not known if tetramers are evenly spaced or restricted to nucleoid core . Archaea do not have packaging proteins similar to HU rather similar to histones that wound 80 bp of DNA around forming structure similar to eukaryotic nucleosome.

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 of supercoiling

Plasmid and extra-chromosomal elements complicate the question of what is the genome

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 nonessential 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.

Linear & Multipartite genomes

Borrelia burgdoferi, Streptomyces coelicolor and Agrobacterium tumefaciens have linear chromosomal DNA.
S. coelicolor linear 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.

Prokaryotic genomes are gene-dense

Outer genes transcribed in clockwise direction, inner in anticlockwise

Threonine operon

Genome has lesser intergenic regions thrA & B separated by 1nt, thrB & C start immediately one after other. IS186 &IS1 are insertional sequences present elsewere in genome (transposons).

Gene organization in prokaryotic genomes

Genomes of prokaryotes
Operon
A set of adjacent genes in a bacterial

genome, transcribed from a single

promoter and subject to the same regulatory regime.

Genomes of prokaryotes
There are no introns in the genes present in this segment of the E. coli genome. The infrequency of repetitive sequences ~~ low repeat DNA.

64bp 52bp

Overlap by 1 bp

Separated by 4 bp

Separated by 12 bp

Overlap by 1 bp

Rule breaker: an operon from Aquifex aeolicus

These genes biochemically unrelated. gatC, glutamyl-tRNA aminotrasferase subunit C; recA, recombination protein RecA; pilU, twitching mobility protein; cmk, cytidylate kinase; pgsA, phsphotidylglycerophosphate synthase; recJ, single strand specific endonuclease RecJ

Lateral/Horizontal gene transfer is rampant

So what is a species?
Blue DNA unique to species Red DNA acquired by lateral gene transfer.

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.