Lecture 1. Bacterial Genomes Flashcards
What is our traditional view of prokaryotic genomes based on?
Everything we know about E. coli
Circular singular DNA molecule that is located in the nucleoid (doesn’t stain well as full of DNA)
Is there any difference between prokaryote DNA and eukaryote DNA?
DNA essentially the same (in the B form)
Two polynucleotide chains are in opposite orientation
Regular right-handed double helix
Diameter of 2 nm and making a complete turn every 3.4 nm.
There are ~10.5 base pairs per turn of the helix
What are the certain flexibilities within the basic B-form?
The number of base pairs per turn of the helix can be altered
The helix in the cell is not straight but coiled in 3D space
There are certain sequence features where bends occur
How does the DNA coil on top of itself?
Through supercoiling
When does supercoiling occur?
When additional turns are introduced into the DNA double helix (positive supercoiling) or if turns are removed (negative supercoiling) which makes the elements of the genome more accessible for proteins but tightens up the genome
What is supercoiling controlled by?
The cell, the cell manages their genome constantly reshaping it for their needs
What enzymes help rearrange the genome?
Topoisomerases
How is the torsional stress in the molecule accommodated?
Two ways
Formation of superhelices
Altering number of base pairs per turn of helix
What is the linking number (L)?
Total number of times that the two strands of the double helix of a closed molecule cross each other when constrained to lie in a plane
What is the role of type I topoisomerases?
Break one strand of DNA, pass the other complete strand through the gap and seal the break
Linking number changed by ±1
Topoisomerase I of E. coli, relaxes negatively supercoiled DNA
Make supercoiling more severe
What is the role of type II topoisomerases?
Break both strands of the DNA, pass another part of the helix through the gap and change the linking number by ±2
What enzyme creates negative supercoils in E. coli?
DNA gyrase
What do type I topoisomerases remove?
Reduces supercoiling by removing negative supercoils
What is the role of DNA gyrase?
DNA gyrase of E. coli is a heterotetramer of 2 subunits (A and B)
Creates negative supercoils (using ATP)
Opens up strands and is essential for DNA replication
How is DNA organised in E. coli?
The single circular DNA molecule is organised into a series of supercoiled loops (40-50) that radiate from a central protein core
Highly organised structure
Organse and control genome like eukaryotes that is controlled by the protein core
What does the protein component of the E. coli nucleoid include?
DNA gyrase and DNA topoisomerase I that maintain the supercoiled state of the DNA
At least four proteins, the most abundant being HU (heat unstable), that are involved in packaging the DNA (we now know there are many more than just 4)
HU forms a tetramers around which the DNA is wound – approximately in units of 60 bp, cover about/binds to 1/5 of the genome
How many HU protein are in a single E. coli cell?
~13,000 HU proteins in a single E. coli cell
What do archaea have instead of proteins related to HU (heat unstable)?
Proteins related to eukaryotic histones
One of the pieces of evidence used to suggest that eukaryotes descended form archaea
Why is the idea that prokaryotic genome based on E. coli isn’t entirely correct?
Some bacteria have a linear not circular genome (Borrelia burgdorferi (Lyme disease), Streptomyces coelicolor (antibiotic producer), Agrobacterium tumefaciens (plant tumours))
Others have multipartite genomes (genomes divided into two or more DNA molecules)
With multipartite genomes, what is it difficult to distinguish?
It can be difficult to distinguishing a genuine component of the “essential” genome from a plasmid
What are plasmids?
A plasmid is a (often small) DNA molecule that usually codes for non-essential genes
Some very large plasmids may also carry essential genes
What are essential parts for Vibrio cholerae?
Main chromosome (2.961 Mb - million bp)
Megaplasmid (1.072 Mb)
The megaplasmid in Vibrio cholerae is larger than chromosome 2 in Deinococcus radiodurans (nomenclature is confused)
What is the importance of circular plasmid cp32 in Borrelia burgdorferi?
Always 5 or 6 copies within the cell, implies important to the cell all of the time
What is it important to remember when talking about microbes in the real environment?
Not every microbe is E. coli
May be carrying multiple copies of nearly identical copies of genes
What is an example of a genome that is smaller than many megaplasmids?
Nasuia deltocephalinicola, a leafhopper symbiont, genome size 112kbp, 137 genes
Relies on the host as symbiote so can shorten genome
What are important components of the genome of bacteria?
Horizontal gene transfer (HGT)
Acquisition of all antimicrobial resistance genes spreads by horizontal gene transfer
Why is horizontal gene transfer (HGT) important?
Important in bacterial evolution
‘evolution in quantum leaps’
What are prophages?
Phage-like elements found inside bacterial genomes
Linked to pathogenesis and other important phenotypes
What are examples of toxins that are encoded by prophages?
Diptheria toxin (C. diptheriae)
Shiga toxin (E. coli)
Cholera toxin (V. cholerae)
Neurotoxin (presence of prophage is the only difference between C. botulinum and benign clostridium)
Leukocidin (s. aureus)