MO Viruses and viral genomes Flashcards
The most common biological entity on the earth?
Virusses
Virusses
- Viruses infectious agent that replicates only inside the living cells of an organism (can infect all living organisms)
- DNA or RNA enclosed in a protein coat (capsid).
- They cannot replicate or perform life processes independently; they require a host cell.
- Not considered living organisms due to lack of independent metabolism or reproduction -> Hijack the host cell’s machinery to reproduce.
Bacteriophages (or phages)
are viruses that specifically infect bacteria.
* Can be RNA or DNA
* Phages attach to bacterial cells, inject their genetic material, and hijack the bacteria’s machinery to reproduce.
* two life cycles: the lytic cycle (destroying the host cell) or the lysogenic cycle (integrating their genome into the host without immediate destruction)
* Over 200kb genome size -> Jumbo phage
* Can be used as antibiotic, kills bacteria
Lifecycle Lyctic bacteriophage
- Recognition of host
- Bind to host
- Inject genetic material (DNA/RNA) in cytoplasm
- Host wil replicate genetic material
- Production&Assembly of phage proteins
- Burst and lysis of bacterial cell
Binding to the host
They attatch to cellwall, have specificity for their host
Difference gram + and -: positive has bigger peptoglycan layer which make it harder for the phage to regognise the small membrane protein, negative presents proteins on outside and are easy recognisable for phage.
MIMETAS chip
- helps identify new phages out of the environment in a more efficient way
- two channels, Perfusion (for the phages) and ECM fluorescent bacteria. When the phages destroy the bacteria the fluorescence dies out.
Phage therapy
- they are drugs that can amplify themselves, ar enot harmfull to humans (they will die when their bacterial host is no longer around), fewer side effects compared to other therapies and is highly specific so keeps the microbiome intact
Defence mechanisms of Bacterial cell
- Adsoption block: stopping the phage from binding to bacteria via masking with biofilm (making hard to reach) or mutation of receptor or OMW (outer membrane vesicles) used as decoys
- Uptake block: can bind but DNA injection blocked
- Restriction-Modification system: Restriction enzymes recognize phage DNA and cut / Modification enzymes add methyl groups to the host’s own DNA at the same recognition sites, protecting it from cleavage.
- CRISPR: store fragments of viral DNA from past infections and CAS protein use stored sequences to recognize/cut the DNA
- Abortive infection: infection sensed by bacteria so suicide, the last fail safe if everything else fails
Phages can bind to what parts
Effluc pumps, Porins, Flagella, Pili (normally used for exchange of DNA, they block/hinder binding of phage with thick glycosylated layer on pilis. phages can circomvent this using degrading enzymes or have specific fibers to be able to bind), LSP
OMW (outer membrane vesicles)
They are used as decoys and allow phages to inject their genetic material inside as they poses the receptors for binding but then do nothing with it
a problem can be whe the OMW with th phages DNA merges with a phage resistant bacteria. This allowes phages to infect these bacteria that would normally be resistant to it
Bacterial resistance comes at a cost
- phage resistance for efflux pump binding can increase antibiotic susceptability -> anitbiotic + phage therapy works better then
- Phages that bind to structural virulence factors decrease virulence of bacteria
So either way phage resistance is not optimal for bacteria as they become more sensitive to antibiotics and less virulent
Uptake block
Happens when the bacteria is already infected with the same or closely related phage -> SIE (super infection exclusion)
Lysogenic lifecycle bacteriophage
- Recognition of host
- Bind to host
- Inject genetic material (DNA/RNA) in cytoplasm
- Phage DNA intergrates into host chromosome using intergrase-> prophage and is copied when cell devides
When cell gets stressed (UV light) then DNA will be excised (removed) from host chromosome and begin Production&Assembly of phage proteins - Burst and lysis of bacterial cell
Lysogenic phages produce two proteins, SP (Superinfection Protein) and Imm (Immunity Protein), that prevent additional phage DNA from entering the already infected cell.
CRISPR-Cas
Immune memory. Store fragments of viral DNA from past infections (in the spacer sequence) and CAS protein use stored sequences to recognize/cut the DNA
Cluster of Regularly Interspaced Short Palindromic Repeats
- Adaptation : The Cas1-Cas2 complex integrates foreign DNA into the CRISPR array of the host.
- crRNA Maturation : The CRISPR array is transcribed and processed to form mature crRNAs.
- Interference : The mature crRNA guides Cas nucleases to target foreign DNA, which is then cleaved.
Diverse pre-spacers lead to diverse spacer aquisition and therefore diversity in CRISPR spacers in the population. The higher spacer diversity (among bacterial population) the better the resistance to phages as they die out because they can not evolve resistance to all spacers.
If everything else fails
1. activity depends on two proteins, RexA and RexB
2. Phage binds to RexA and thereby activates it
3. Active RexA activated RexB, membrane-bound ion channel
4. Creation of pores in the cell -> Cell death
You also have TA systems (Toxin/anti-toxin). The bacterial cell contains equal amount of both, during infection the phage inhibits (deactivates) the antitoxin which leads to increase of free toxin -> cell death
