Week 1 part 2

• Bacteria are rarely found in isolation. They can either be beneficial or toxic towards other organisms
• Bacteria can positively or negatively communicate with each other through chemical signals. Ex: positive --> biofilm, negative --> antibiotic production

  
• bacterias live in communities for many reasons such as protection and metabolic cross-feeding

  
• Quorum sensing --> Bacteria communicate with each other by using chemical signals. Bacteria can make very defined chemical molecules that can identify many different things: sensing who is in the community and also sensing enemies.

  
• Gram-negative bacteria use AHLs (acyl homoserine lactones || Autoinducer-1)

  
• Gram-positive bacteria use ALPs (oligopeptides ||autoinducing peptides)

  
• interspecies of bacteria uses autoinducer-2

  
• AHLs are hydrophobic signals that come from gram-negative bacteria. They freely diffuse through the cell membrane
• ALPs are peptides that require a transport protein to get through the membrane. Gram-positive bacteria make it.
• Quorum sensing: A signalling pathway that is used to orchestrate gene expression programs that underlie collective behaviours among bacteria. Many group behaviours are regulated by quorum sensing.
• AHLs are made by the LuxI family signal synthases. LuxI is a cytoplasmic enzyme that catalyzes the formation of AHLs by combining fatty acyl chains with homoserine.

  
• AHLs are able to freely diffuse across membranes and enter other bacterial cells.
• AHL pathway: the pathway starts with LuxI being made by the Lux genes. LuxI then creates AHLs with the use of HSL. AHL then diffuses out of the bacteria. It accumulates outside and binds to the LuxR. LuxR is a transcription factor that makes more LuxR and LuxI (positive feedback loop)

  
• Luciferase enzyme is made up of subunits made by the LuxA and LuxB genes. through a chemical reaction, light is produced as the end product. (bacteria create bioluminescence).

  
• expression of the lux operon is cell-density dependent. This phenomenon is seen in the bobtail squids as they will only glow (using bacteria) when a population threshold is reached.
• Gram-positive bacteria use peptide-based signals: agrD gene makes AgrD peptide that tjen goes to the AgrB active transporter. AgrB is responsible for the cyclization of the peptide and exporting it out of the bacteria. This process turns AgrD into AIP. AIP is sense by nearby (like) bacteria by binding to AgrC. AgrC is a kinase that self phosphorylates upon activation and moves the phosphate to AgrA. phosphorylated AgrA is transcription factor that turns on the agr genes and RNAIII genes.
• RNAIII is an inhibitor of Rot. Rot represses many types of toxins. By stopping this function AIP is able to indirectly result in depression of virulence genes.

  
• AIPs from different strains can inhibit non-cognate AgrC sensors. This restricts the signals from firing.

  
• We can use AIPs as a probiotic. By ingesting beneficial bacteria and growing more of it in the gut it can help detect bad bacteria and attack it. Bacillus subtilis is an example