seminar 3: Harrison Flashcards
what are mobile genetic elements?
sets of genes that have a transmission advantage over rest of genome
- can be horizontally transmitted
give points about the bacterial virus phage
- drive bacterial mortality
- used in C cycling
- form local adaptations and maintain diversity
- kill about 40% bacteria in oceans every day
what is phage therapy?
used by humans to tackle bacterial infections
what are prophages?
phages that can jump into the chromosome so are powerful mutualists
- attack and kill other bacteria
- can carry virulence traits
- often carry important toxins
what do plasmids and ICEs do?
dont exit the cell
- manipulate cellular host to form bridges/pilli that fuse to cell membrane of another cell to send DNA to infect new cell
what type of gene transfer do plasmids use and what do they often carry lots of?
horizontal
lots of bacterial genes from different hosts/chromosomes
what are satellite/nested elements? (4)
- jump between genomes/host via bigger elements
- package into other viruses
- hitchhike on pilli
- can spread through entire microbial community
what are the 2 main ways microbes and their mobile genetic elements evolve?
- plasmid preference
- simultaneous interactions shaping evolutionary outcomes
give 3 reasons why plasmids are considered costly
- metabolic burden
- disruptive (produce own regulatory proteins)
- epistasis (genes may have bad relationships with other genes)
what was the study bacteria and its plasmid +size?
P.fluorescens
large plasmid 1/10th size genome containing mercury resistance operon
what is the relationship between the plasmid and bacteria dependent on?
context- the environment
how can it be considered a parasitic relationship?
when contains the plasmid but no mercury there is a 50% reduction in fitness and reduced growth rate
when mercury is added how does the relationship between plasmid and bacteria alter?
becomes mutualistic and benefits of resistance outweigh costs
what was the brief procedure to begin with when looking at evolution along the parasitism-mutualism continuum? (3)
- 6 gradings of mercury
- tracked plasmid frequency
- 450 bacterial generations
sequence evolved clones
what was found for the parallel evolution at 2 loci? (3)
- no mutation in the plasmid
- same gene targeted across and within treatments
- 3/4 population evolved a mutation in Gac S/A
how was a knockout strain created and how does this compare to the wild type?
removing genes from ancestral bacteria
cost removed in knock out strain
what do Gac S/A form and how do they work together?
2 component regulator of extracellular protein production
- control downstream regulation of other genes
how does the ancestral strain compare to the evolved strain in terms of parallel transcriptomic response to plasmid?
ancestral
- 1/5th bacterial genome upregulated
evolved
- gene expression profile eventually returns to ancestral state as response regulators targeted
briefly explain the steps of the Gac system (5)
- GacS receives signals
- Gac A activated
- sRNAs produced that inhibit RNA binding proteins rsmA
- rsmA grabs mRNA but is triggered to release it so is translated
- extracellular proteins produced
what can sometimes be introduced to the Gac system from plasmids and what does this result in?
plasmid carries encoded rsmA
- causes bad copy of the binding protein to be produced
- likely non functional proteins created
- likely excess extracellular proteins produced that the cell does not need to aid in plasmid transfer
how do cells tackle the plasmid causing excess protein production?
knocks out Gac S/A genes with stop codons and frame shifts
- prevents repression of binding proteins
- reduces extreme upregulation of these proteins
what constantly occurs across the parasitism mutualism continuum?
compensatory evolution
- plasmids benefits
- evolution and mutations act to reduce costs of plasmid
- so resistance gene likely maintained
what are bacteria phage interactions seen as?
antagonistic coevolution
what was the experimental set up for studying how competing selection pressures alter evolution of outcome? (4)
- set up with bacteria only, bacteria and plasmid only, bacteria and phage only, bacteria, plasmid and phage
- 150 generation batch transfer
- grow bacteria on agar with milk
- zones of clearing around bacteria with functioning Gac
what do the enzymes that the bacteria excrete do?
degrade proteins to gain metabolites
with the plasmid and bacteria only what frequency of Gac colonies was reached?
- how did this differ when the phage was involved?
high
- low, no fixation
what was it discovered that phages constrain?
plasmid Gac A/S compensatory evolution
what was discovered when doing a streak assay with phage and bacterial colonies on agar plate?
- bacterial colonies that can grow and pass through the line of phage is resistance
- bacteria that doesn’t spread pas is susceptible
what did plasmids alter to do with phages?
alter bacteria phage coevolution
are bacteria that evolved with or without the plasmid less susceptible?
without
what are phages with plasmid population?
less infective
if the host is very resistant what will evolution drive?
higher rates of infectivity in coevolving populations
what has plasmid presence restricted?
evolution of resistance in bacteria and infectivity in phage
what did plasmid with phage fighting populations evolve? and when is the rate of these higher?
mucoid bacterial culture phenotype
- higher with plasmid and phage together compared to in absence of plasmid
when sequencing clones from each population of treatments - were genes shared across all treatments?
- what showed up as predicted?
- what does the fact it is antagonistic coevolution mean?
- what does changing LPS genes do?
- what did bacteria with plasmid and phage show?
- none across all treatments
- repeated compensatory mutations in Gac A/S genes
- drives faster evolution and more LPS genes targeted
- hides bacteria from the phage as phages recognise these
- different targets of mucoid and no Gac mutations
what was the summary result for:
a) bacteria and phage
b) bacteria, phage, plasmid
c) bacteria, plasmid
a) strong phage resistance via LPS
b) weak phage resistance via mucoidy and no compensatory mutations
c) bacteria evolve compensatory mutations
what is the protein causing mucoid phenotype? and what does it do?
alginate
slows access of phages to cell surface
what does loss of Gac A/S to the system mean and what is this known as?
when is this of particularly high cost?
loss of phage defence
antagonistic pleiotropy
- when in presence of phages
what alters the outcome for pairwise relationships?
selection from multiple symbionts
what is key to understand for understanding horizontal gene transfer?
mobile genetic elements in terms of evolving symbionts
