User:Kinkreet/Autophagy

Most cells must be capable of recycling non-functing proteins, mRNAs, nucleic acids and other wastes and debris, to reuse the material as well as to minimize the production of faulty proteins, which can interfere with the complex framework of signalling within the cell. This process is called autophagy, and involves transporting the molecules inside autosomes to be merged with lyzosomes, where the hydrolases, other enzymes and the acidic condition will degrade the molecules. Autophagy is required to breakdown signalling molecules to regulate development, break down cytokines and growth factors and/or their receptors to regulate inflammation and the immune response, and break down defective and reactive proteins to delay aging.

When bacteria is detected by a cell, especially phagocytes, they are phagocytosed inside a vesicular department, called autophagosome, to be transported to the lyzosome for degradation, employing the same mechanism of autophagy.

However, cytosolic bacteria can either avoid or interfere with the autophagy mechanism in order to survive in the cytosol of the infected cell. Because the bacteria exists in the cytosol, antibodies produced against it would not produce a humoural response. Neutrophils assists in the early stages of infection but do not clear the infection. The organism must then rely on activated macrophages.

First, we will look at the mechanism of autophagy against bacteria, and then see how some bacteria can acoid or interfere with it.

First, a double-membraned phagophore forms around the waste/defective molecules/bacteria and elongates until it has fully enclosed them and form an autophagosome which is 0.3-1/0 μm in diameter. The autophagosome then becomes acidified and reactive intermediates (reactive oxygen intermediates, ROI, and reactive nitrogen intermediates, RNI) are generated. Interferon-γ (IFNγ) is a cytokine that activates macrophages by making it produce more of these reactive species, and so making them more able to break down the microbe it is phagocytosing. The autophagosome then merges with lyzosome(s), which further degrade the bacteria. This process requires a set of autophagy (ATG) proteins, of which 35 are conserved in yeast and humans. Some ATG proteins (p62, NBR1, NDP52, OPTN) bind specifically to ligands, and may modify the ligands, commonly by ubiquitination. Other ATG proteins act as receptors for the bound ATG proteins, or for the ubiquitin moiety; these receptors form a new category of pattern recognition receptors (PRRs) called sequestosome 1/p-62-like receptors (SLRs).

Bacteria such as Shigella and Listeria survive by escaping from the autophagosome, whereas bacteria such as Mycobacteria and Salmonella survive by interfering with the autophagy machinery.

Escape
Bacteria that survive by the escape mechanism must satisfy two conditions:
 * 1) It must be able to break free from the autophagosome; and
 * 2) It must prevent recognition and degradation in the cytosol.

Listeria
Listeria monocytogenes is a bacteria that causes Listeriosis. Upon recognition by macrophages, it is phagocytosed using the zipper mechanism. Listeria escape using listeriolysin (LLO), a pore-forming cytotoxin, and phospholipases to form pores which allows molecules between 500-10000 MW to pass. By allowing the macrophages to endocytose Listeria along with dyes of different molecular weight, and using time-lapse microscopy tracking the localization of dyes, it is shown that the pores expand with time. LLO is cholesterol-dependent and also acts to inhibit lyzosome fusion. Once inside the cytosol, it forms an actin tail which enables Listeria motility, which it utilizes to try break out from the cell, possibly into other cells, all while damaging the cell. If there are no adjacent cells, Listeria would continue to move until there is a neighbouring cell, where it will push and break the two membranes and into the other cell.

The macrophage attempt to prevent Listeria from escape by using the phagocyto oxidase complex, oxidizing NADPH in the cytosol to produce superoxide and other ROIs. It appears acidification is required for Listeria to escape; cells treated with bafilomycin, a drug the inhibits acidification, prevented escape of the bacteria for less than 30 minutes.

Questions
Where do the breakdown products go? Just into the cytosol or transported elsewhere?