Lecture 2: Basic Features of Bacterial Genomes Flashcards
What is bioremediation?
Bacterial breakdown of hydrocarbons
Describe 7 differences between bacterial and eukaryotic genomes
1) Bacteria have circular DNA, euks have linear
2) bacteria have no introns, euks do
3) bacteria have plasmids, euks don’t
4) bacteria have phage, euks don’t
5) bacteria have operons, euks don’t
6) bacteria are haploid, euks are diploid
7) bacteria don’t reply on histones for DNA organisation as rely on supercoiling, euks do
What are operons?
genes linked together with a single promoter and can move around together
what is the difference between gram positive and negative bacteria?
positive are able to be stained as have thick peptidoglycan layer that dye binds to, negative aren’t
what did cyanobacteria give rise to?
chloroplasts
what did proteobacteria give rise to?
mitochondria
describe the genome of clostridium difficile
semi-conservative replication, bidirectional replication forks. not continuous as DNA polymerases can only move in the 5 to 3 prime direction so one jumps in okazaki fragments
what is strand bias/strandedness?
most genes are coded on the leading strand
What is different about RNA polymerases in bacteria?
They allow replication and transcription to occur at the same time
What is the G+C content
the proportion of G and C in the whole genome
Give an example of a low, medium and high G+C content bacteria
endosymbiotic proteobacteria, E.coli, soil dwelling bacteria
There is a rough correlation between G+C content and genome size, true or false?
True
What are the two views of why G+C content correlates with genome size?
Selectionist: G+C content reflects adaptation
Mutationist: no adaptive value, just mutations
selectionist favoured
bacteria in hosts might have fewer genes, why?
have weaker selection, are cared for so need fewer genes
what is the most frequent mutation? how frequent is it?
C to T, 100x more frequent
What happens if you leave DNA to mutate?
accumulates T and A and G and C declines
What is the GC skew?
on a leading strand there is more G and T, on the lagging strand there is more A and C
Explain why the GC skew occurs
one strand has continuous, the other has discontinuous replication. the discontinuous strand is left more vulnerable to mutation
give the three main causes of intra-species genomic variation
differences in gene order (synteny), gene content and sequence diversity between orthologous genes
What is synteny?
The order of genes on a chromosome
What can cause loss of synteny
genome rearrangements eg inversions, insertion sequences causing rearrangements, selfish DNA elements, translocations, deletions
What is the pan genome?
Describes the full set of genes in a clade
what is the accessory genome?
genes present only in some strains of a species
what is the core genome?
genes present in all strains of a species
Give examples of things coded in the core genome
transcription, translation, cell envelope, replication
give examples of things coded in the accessory genome
pathogenicity, antibiotic resistance
what is different about the GC content of accessory genes?
tend to be lower
What are ORFans?
genes present only in one strain
what three factors determine genome size and structure?
gene acquisition, duplications, deletions
what parts of the body does Staphylococcus Aureus colonise mostly?
skin and nose
what is the open pan genome?
total gene set of all strains increases with number of sequences strains
what is the difference between short read and long read whole genome sequencing?
short read is high throughput, maps for phylogenetics, long read is expensive, complete gene content, gene annotation
