bacterial defence mechanisms

Introduction

bacterial cell walls are made of peptidoglycans made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids, and have the following functions:
- give the bacteria their shape
- provide extra physical protection
- peptidoglycans (PGN) and fragments play important roles in the immune response of higher organisms against bacterial infections, and mediate various symbiotic interactions between bacteria themselves and between bacteria and eukaryotes
there are two main types of bacterial cell wall:
- Gram positive
  - bacteria of the classes Bacillota and Actinomycetota
  - possess a thick cell wall containing many layers of peptidoglycan and teichoic acids.
- Gram negative
  - most other bacteria
  - have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins
penicillin is able to kill bacteria by preventing the cross-linking of peptidoglycan and this causes the cell wall to weaken and lyse

retron systems
- sense when a specific strain of phage has attacked the bacterial cell, and they then unleash a toxic protein to kill the cell which stops the phage before it has a chance to multiply and spread to neighboring cells in the same colony
- most retron systems produce a toxin that, in uninfected cells, is constantly present but deliberately repressed by small, single-stranded DNA molecules which become perturbed when a phage infects the cells allowing the toxin to be released
- type VI retrons act in reverse, they do not produce noticeable levels of single-stranded DNA nor toxin in an uninfected cell, and instead when a phage infects the cell, it starts producing single-stranded DNA which when it builds up interacts with an RNA that has been blocking production of the toxin and thereby allowing toxin production to ramp up - the toxin appears to be a tiny protein that embeds itself into the membrane surrounding the cell, which destabilizes the cells and kills it¹⁾
SIR2-mediated cell death:
- SIR2 protein normally acts as a nuclease in digesting nucleic acids to maintain proper cell functions, however it also has affinity for binding to the protein HerA and then in the presence of a phage, becomes a NADase causing depletion of NAD+ which results in cell death and reduced transmissions of the phage to other bacteria in the colony ²⁾

many microrganisms including bacteria and fungi are able to form communities creating highly resistant biofilms
the critical functionality to achieve this is via formation of fimbriae which is turned OFF by the gene fimE
the fimbriae help bacteria latch onto medical implants, pipes, teeth, etc
when stressed, some plants produce the plant metabolite methylerythritol cyclodiphosphate (MEcPP) which stimulates the fimE gene and thereby inhibits biofilm formation. MEcPP prevents the binding of H-NS to the fimE promoter. ³⁾

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