Microbial Communities Flashcards
Microbiome
Microbiota and theatre of activity
Main drivers of microbial communities
Composition and evolution of phage communities a, controls bacterial population and evolutionary dynamics of microbial communities
Phage life cycles
Lytic, lysogenic, chronic
Phages attachment to bacteria
“Walk” into cell wall
Conformational changes to bind and penetrate
BUT some stuff haves attach to pili and “surf” way in (swirl)
Flagellotropic phages
Phages that use flagellum to bind to target bacteria
Usually curled tail fibres that wrap around rotating flagellum
Example of flaggellotropic phage
Infect caulobacter crescentus
1. Flexible filament extending from head to wrap around flagellum
2. Spin down towards cell pole
3. Tail fibre contacts receptor on cell surface and infects
Is flagellum indispensable?
No - just increases chances of tail fibres finding the receptors on moving bacteria
Genome entry
Conformational change, inner tube needles outer membrane and degrades it. Injection, degradation of inner membrane and pierce through to infect
Pseudomonas phage phi6
Unlike most Phages, capsid enters the bacteria cell to protect from rapid cleavage of dsRNA by host ribonucleases
Can replicate within capsid
Similar to human viruses
Pseudomonas phage phi6 steps
- Phage uses protein spikes that protrude from capsid to adsorb to the side of a pills in bacteria
- Protein p6 from phage fuses the phage lipid envelope with bacterial outer membrane
- Resulting Nucleocaspid (no lipid) has exposed endopeptidase that digests a path through the peptidoglycan layer
- Phage has inner and outer capsid surrounding it’s genome. Outer layer cause region of cell membrane nearby to invaginate and constrict to bud off from cell membrane
- Loses outer layer by Inknow process
- Inner capsid remains to protect dsRNA from cleavage
Pseudomonas phage phi6 entry
Bacteria pill alternately extend and retract to allow bacteria to move and phage uses pilinretraction to get closer to outer membrane if the cell
Pseudomonas phage phi6 RNA replication
Each verticals of inner capsid = RNA dependent RNA polymerase (RdRP)
Use dsRNA as template, RdRP transcribe positive sense RNAs that exit from the cassis into cytoplasm where they are directly used for translation of phage proteins or packages into progeny Phages
Decision of lytic or lysogenic
Individual decisions and voting - eg phage lambda
Group decision - eg phage phi3T
Individual decisions and voting
Once inside cell, phage lambda initiates synthesis of early proteins including regulatory protein CII
C1 = lysogeny
CRO = lysis
CII = lysogeny
What would cause high CII levels
More phage in and outside cell so potentially less host strains
Starving of host, smaller cells
Voting
If a phage decides differently to others they go to lysis
If the all decide the same they go to lysogeny
Phage make a group decision
Eg Phi3T - communication between Phages infecting different cells
Infection = production of protein AimP
AimP cleaved from small peptide - arbitrium
Arbitrium exported from bacterial cell
Low levels of arbitrium
Phage infection likely follows lytic cycle
High levels of arbitrium
Phage infection likely follows lysogenic cycle
Too many Phages in environment can lead to sacristy so better to stay Forman
How is arbitrium taken up by neighbouring cells
Bacterial transport proteins (OPP)
Different Phages use different arbitrium so can only communicate with Phages of their own kind!
Molecular mechanism behind group decision (aim)
Early genes aimR and AimP expressed immediately upon infection
AimR activates AimX expression
AimX inhibits lysogeny so causing lytic cycle
AimP expressed, secreted and processed to make arbitrium
Phage infect, AimR binds the arbitrium and cannot activate expression of AimX so lysogeny
Which factors determine the phage lytic vs lysogenic decision
Phage concentration and metabolic status of cell
Which mechanism do Phages use to determine if they follow lytic or lysogenic life cycle
Small peptides to communicate between infected cells
Individual decisions, based among others, on concentrations of phage in the cell
Filamentous Phages overview
Chronic life cycle
SsDNA genome in long cylindrical protein coat
F1 enters cell, capsid disassembles depositing proteins in cell membrane
F1 relies on host proteins for replication
Phage ssDNA to dsDNA to use in transcription and synthesis of new ssDNA genome
F1 produces ssDNA binding protein that costs ssDNA genomes protecting it from degradation
How does the filamentous phage have a chronic life cycle
New f1 genomes find capsid components at cell membrane (some deposited during infection but mainly freshly made and anchored i. Membrane in anticipation)
Most exit via a borrowed host secretion channel but f1 encodes and secretion channel of its own
Using extrusion, filamentous Phages leave host cell intact, so can continually reproduce inside cell without causing significant harm
What tasks must a phage (of chronic life cycle) accomplish to keep lytic cycle going
Outside host cell - capsid must protect genome from environmental dangers, recognise host when collides, irreversibly bind to receptor and deliver genome into cell
Inside host cell- evade host defence, redirect cell metabolism for production of many progeny Phages, replicate phage genome and synthesis correct no of structural proteins, pack new genome into capsids, gine lysis of host for release of new Phages
Virocell
Cell infected by phage
Phages making decisions and utilising machinery
Minimal (“machines”) genome
Leviviridae QB has ssRNA genome that encodes 4 genes
1 gene - RNA replication (replicase)
2 genes - structural proteins forming capsid
1 gene - multifunctional protein termed maturation protein
Overlaps the genes for the capsid proteins - when translating major capsid protein, ~5% of time ribosome reads through leaky stop codon and continues translating yielding longer minor capsid protein
What does the maturation protein in leviviridae QB do?
Lyses host cell so assembled virions can exit
Protects the encapsulated genome from RNase
Recognises and adsorbs go the receptor in it’s host
Why is the RNA genome of leviviridae QB efficient?
Copies of positive sense RNA genome function as mRNA for translation of phage proteins so DNA synthesis is expendable
Microviridae φx174
Circular ssDNA genome (5386 nt) encoding 11 genes
Several genes overlap by using different reading frames
6 genes used for assembly of capsid
In lab 2 genes not essential for replication and function still unknown
Why do most Phages have larger genomes?
Eg phage T4 used 169kbp genome encoding 300 genes
More genes = more capabilities eg
Structural proteins (capsid, tail and tail fibres)
Basic life cycle steps with greater fitness
Counter host defences
Compete with other Phages or battle mobile genetic elements
Obtain extra cellular resources eg phosphate
Precisely manipulate hosts metabolism
Expand host range
Thrive under environmental conditions
Temperate Phages cardi metabolic genes that benefit host (serving Phages interests)
MOST PHAGE GENE FUNCTIONS UNKNOWN
How Phages evolve
Accumulate mutations
Evolve through recombination events in which they exchange genetic material with other Phages
Mosaic structure that arises when genomes of Phages compared
What is mosaic structure of genome
Genomes of 2 Phages compared
Nearly identical sequences alternate with sequences that are merely similar or even completely divergent
Shiga toxin
In salmonella
Phage infects, phage now has shiga toxin
Phages cause evolution of bacteria
Smallest Phages have a genome that is:
Single stranded RNA
What are temperate Phages
Bacteriophages that can pick life cycles and are important vectors of horizontal gene transfer among bacteria
How do temperate Phages alter and benefit bacteria
Protect bacteria against lytic infection of other Phages by superinfection exclusion
Providing virulence factors (eg extra cellular toxins)
Providing genes encoding antimicrobials
Aiding with biofilm formation
Suppressing mammalian immunity against the bacterium
Biofilms
Key to pathogenicity of many bacteria making them difficult to fight
Temperate Phages and biofilms
Temperate Phages important in production of biofilms By various bacterial species
Biofilms steps
Reversible attachment
Irreversible attachment
Biofilm maturation
Biofilm dispersion
Biofilm of pseudomonas aeruginosa and Pf Phages
Pf Phages give stability to biofilm by:
Causing lysis of a few cells, release of DNA into extracellular space (eDNA) advising structural interfaith to biofilm
Accumulate in biofilm matrix where they spontaneously align and give biofilm matrix liquid crystalline properties (enhance biofilm adhesion, survival to desiccation, provides height antibiotic tolerance by sequestering antibiotic)
Eg cystic fibrosis
Phages and mammalian immunity to bacteria
Absence of phage: bacteria ligands (eg LPS) stimulate immune response in mammalian cells
Pf phage present: taken up by mammalian cells by endocytosis
Production of phage RNA that triggers signalling pathways that inhibit immune response to bacteria (TNF production and phagocytosis)
Steps of infection without Pf phage
1) recognition of bacterial ligands
2) NFkB translocation
3) TNF secretion
4) TNF stimulates bacterial phagocytosis
Infection with Pf phage
1) recognition of Pf phage RNA by TLR3 mediated TRIF signalling
2) TRIF activation leads to type 1 interferon production
3) type 1 interferon inhibits TNF secretion and bacterial phagocytosis
