Drivers of microbiol communities Flashcards
Which factors determine the phage lytic vs lysogenic decision?
The concentration of phages and the metabolic status of the cell
Which of the following mechanisms do phages use to determine if they follow the lytic or lysogenic life cycle? Choose all the correct ones.
A) Communication between phages infecting different cells via tail fibers
B) Making individual decisions independently of the number of phages in the cell and environment
C) Using small peptides to communicate between infected cells.
D) Making individual decisions based, among others, on the phage concentration inside a cell
C, D
The smallest phages have a genome that is:
A) Single-stranded RNA (ssRNA)
B) Double-stranded RNA (dsRNA)
C) Double-stranded DNA (dsDNA)
A?
What is the microbiome?
Microbiota + “theatre of activity”
Name the different microbiota
Bacteria
Archaea
Fungi
Protists
Algae
Parts of the “theatre of activity”
Microbiol structural elements: Proteins/peptides, lipids, polysacharides, nucleic acids (DNA/RNA)
Internal/external elements: Environmental conditions, mobile genetic elements, microbial metabolites (signalling moleciles, toxins, (An)organic molecules
Define biome
A reasonably well-defined habitat which has distinct bio-physico-chemical properties
What controls bacterial population and evolutionary dynamics of microbial communities?
Composition and evolution of phage communities
What represent the most abundant biological entities on our planet?
Viruses
in terms of geneic diversity, viruses are
a large reservoir of novel genetic diversity
What drives evolution?
Balance of mutations between bacteria and viruses (prey and preditors)
Stages of the lytic life cycle of a phage
Attachment
genome entry (conformational changes allow this)
replication
assembly
lysis
- Therefore, phage progeny
Stages of the lysogenic life cycle
Attachment
genome entry (conformational changes allow this)
integration
daughter cells with prophages
environmental trigger
- entry to the lytic cycle from replication and assembly onwards
Virulent phages have the …. life cycle; temperate phages undego the …. life cycle
- Lytic
- lysogenic
How does the virion of the pahe interact with bacteria
In a random way, they do not seek to infect (they aren’t living entities)
When they bond, it happes through recognition of tetrapeptides, lipopolysacharides or peptidoglycans proteins and sugars
Explain how some phages “surf their way in” to bacteria
Some bacteria use a flagellum structure for motility.
The flagellum is exploited by phages as their entryway, typically using curled tail fibres that wrap around a rotating flagellum
Phages that use flagellum to bind to a target bacteria are known as flagellotropic phages
Explain how the flagellotropic phage Caulobacter crescentus infect
- A flexible filament extending from their heads is used to wrap around the bacterium’s rotating flagellum
- They then spin along the flagellum towards the cell pole
- Where the tail fibre contacts its receptor on the cell surface, the infection starts
NB: the extra fibre increases the chances of infection
Entry of Pseudomonas phage phi6
Phage phi6 has a dsRNA genome that would be rapidly cleaved by host ribonucleases inside the bacteria.
To avoid this, the phage uses a strategy in which the capsid containing the dsRNA enters the cell:
- Phage has spike proteins to protude from its capsid to absorb the side f a pillus in the bacteria
- protein P6 fuses the phage lipid envelope w the bacterial outer membrane
- this creates a nucleocapsid w exposed endopeptidase that digests a path through the peptidoglycan layer
- using dsRNA as a template, RNA-dependant RNA polymerase (RdRPs) transcribe tje + sense RNAs that exit capsid into cytoplasm where they are directly used for translation of phage proteins, or packaged into progeny phages
+ve vs -ve viral RNA
Positive-sense viral RNA is similar to mRNA and thus can be immediately translated by the host cell.
Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation.
key difference between ssRNA snd dsRNA?
ssRNA has only one strand of RNA while dsRNA is made up of two complementary siRNA or miRNA strands. RNA or ribonucleic acid is a type of nucleic acid which is made up of ribonucleotides.
2 ways of the lytic vs lysogenic decision
Individual decisions and voting – e.g. phage lambda (type of E.coli Phage)
Group decision – e.g. phage phi3T
Individual decisions and voting
Phage lambda life cycle
Once inside the cell, phage lambda quickly initiates synthesis of early proteins including regulatory protein CII
CII’s primary role in the lambda phage regulatory network is to initiate the repressor establishment cascade
The CI protein of bacteriophage lambda is both a repressor and activator of transcription
Cycle:
Phage, infects cell, increases CII, CII, leads to CI, CI leads to lysogeny
CII gets turned off, get lysis pathway activated because you don’t have repression of Cro
Lysogeny module = CI, Lysis module = Cro and CII
Concentration of phages in the infected cell
Higher phage concentration leads to more CII synthesized – more probability of lysogeny
Higher phage concentration (in phage lambda)
more CII synthesized – more probability of lysogeny
Impact on metaboilic state of the host cell on phage lambda lysogeny/lysis decision
Starving cells are smaller, so CII concentration will be higher, favouring lysogeny when the host is starved
two main reasons that phages decide to NOT lyse theie cells (therefore favour lysogeny) are
Based on concentration – too many viruses outside, undergo lysgeny to counteract (caused by gigher CII conc)
Metabolic state – if the metabolic state of the cell isnt optimal (cells are starved and therefore small), CII conc also increases and lysogeny state takes place
Voting
when multiple phages infect a single cell, the decision of all phages is integrated within the cell, such that only a unanimous vote for lysogeny by all phages eventually leads to a lysogenized bacterium
If one phage follows the lytic cycle, the cell will be lysed even if the other phages follow the lysogenic cycle.
For the lysogeny cycle to take place (voting)
all phages infecting the bacteria have to be synchronized in the decision of lysogeny
Group decisions e.g. phi3T
choice is influenced by communication between phages infecting different cells
During infection phages produce the phage protein AimP
AimP is cleaved to form a small peptide – Arbitrium
Arbitrium is exported from the bacterial cell
it is taken up by neighbourinhg cells via tranport protein OOP
Low levels of arb.. = lytic
high “ = lysogenic
Low vs high levels if arbitrium in phi3T
Low levels of arbitrium present in a cell: phage infection likely follows the lytic cycle
Not that many phages in the environment, so it is still advantageous to the phage to replicate
High levels of arbitrium present in a cell: phage infection likely follows the lysogenic cycle
Too many phages in the environment can lead to scarcity of host cells, so it is more advantageous to remain in a dormant state
When it comes to group decisions, how do phages only communicate with their own kind?
Different phages use different arbitriums
Molecular mechanism behind arbitrium
Early genes aimR and aimP are expressed immediately upon infection
AimR activates AimX expression. AimX is an inhibitor of lysogeny, directing the phage to a lytic cycle
AimP is also expressed, secreted and processed to produce Arbitrium
Arbitrium is internalized into other bacteria by the OPP transporter
Now, when the phage infects the bacterium, AimR binds the Arbitrium molecules and cannot activate the expression of AimX, leading to lysogeny preference
Filamentous phages and the chronic life cycle
When the f1 genome enters the cell, the capsid disassembles, depositing the proteins in the cell membrane.
f1 then relies on host proteins for replication - they convert the phage ssDNA into dsDNA to use in transcription and synthesis of new ssDNA genomes.
f1 also produces a ssDNA-binding protein that coats the ssDNA genomes, protecting them from degradation.
When the f1 genome enters the cell, it does not leave the capsid outside, nor does it bring the capsid along with it into the cell - the capsid disassembles, depositing the proteins in the cell membrane for reuse later to coat progeny as they exit.
What is the third type of phage lifecycle
Chronic state infections
Normally driving by viruses called Inoviridae
Inoviridae are more abundant in the environment
Chronic state…
does not lead to cell death
Most filamentous phages exit through a borrowed host secretion channel, but f1 encodes a secretion channel of its own:
g4p secretin
Two mechanisms that viruses have for protection against defense mechanisms in bacteria
1 – Capsid – enters the cell to protect against ribonucleases
2 – ssDNA binding proteins – coats the genome, protecting them from degradation
What are the tasks that a phage must accomplish to keep their lytic cycle turning?
Outside the host cell
-Capsid must protect the genome from environmental dangers (e.g. UV, nucleases)
-Quickly recognize a host when it collides with one
-Irreversibly bind to its receptor and deliver the phage genome into the cell
Once the phage adsorbs to the cell, the phage and cell together are known as a virocell
Inside the host cell
-Evade host defences (lecture 2)
-Redirect the cell metabolism for the production of many progeny phages
-Replicate the phage genome and synthesise a correct number of structural proteins (e.g. capsid)
-Pack the new genomes into the capsids
-Time the lysis of the host for release of the new phages
How many genes are required to carry out these life cycle steps? e.g. Leviviridae Qβ
ssRNA genome that encodes only 4 genes
RNA genome (4212 nt) is efficient because copies of the positive-sense RNA genome function also as mRNA for translation of phage proteins – DNA synthesis is expendable!
- 1 gene for RNA replication – the replicase
- 2 genes for structural proteins that form the capsid
- 1 gene for a multifunctional protein termed maturation protein
The smallest DNA phage genomes are found among
the (tailless) Microphage.
Microviridae φX174
circular ssDNA genome of 5,386 nt that encodes 11 genes
6 of the genes are used for the assembly of a capsid more complex than that of phage Qβ
In the lab, 2 of the genes are not essential for phage replication and their function is still unknown
Temperate phages are important vectors of horizontal gene transfer among bacteria.
By doing so, they can alter and benefit the bacteria by, for example:
Protecting bacteria against lytic infection of other phages, by superinfection exclusion
Providing virulence factors (e.g. extracellular toxins)
Providing genes encoding for antimicrobial
Aiding with biofilm formation
Suppressing mammalian immunity against the bacterium
Pf phages give stability to the Pseudomonas aeruginosa biofilm by:
Causing lysis of a few of the cells, which leads to the release of DNA
into the extracellular space (eDNA), which adds structural integrity to the biofilm
Accumulating in the biofilm matrix where they spontaneously align and
give the biofilm matrix liquid crystalline properties that
-Enhances biofilm adhesion
-Survival to desiccation
-Provides high antibiotic tolerance (by sequestering antibiotics)
Phages and mammalian immunity to bacteria
In the absence of phage, bacterial ligands e.g. LPS, stimulate the immune response in mammalian cells
If Pf phage is present, it is taken uo by the mammalian cells by endocytosis
This leads to the production of phage RNA that triggers specific signalling pathways (type 1 interferon) that inhibit the immune response to bacteria (inhibit TNF production and phagocytosis)
