How the bacteria undergo lysis?

Discussion in 'Chemistry' started by Eagle9, Apr 24, 2014.

  1. Eagle9 Registered Senior Member

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    Citation:
    http://www.igenericdrugs.com/?s=Ampiox
    Is it known the biochemical pathways of lysis in E.Coli? This bacterium do not contain lysosomes that are generally responsible for “breaking down virtually all kinds of biomolecules, including proteins, nucleic acids,carbohydrates, lipids, and cellular debris” (http://en.wikipedia.org/wiki/Lysosome ). So what triggers the lysis in this bacterium?

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  3. origin Trump is the best argument against a democracy. Valued Senior Member

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  5. Eagle9 Registered Senior Member

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    Let's see:
    Well, this information is interesting but there is nothing written how exactly the antibiotic works. Imagine that we added the Penicillin, then what? There is written that the “drug causes the bacterium to form a defective cell wall”. But if the ADDITIONAL (defective) cell wall is created then what happens with the real/non-defective one? Is it removed? Or what happens when other antibiotics acts on gram-negative bacteria (particularly E.coli)? I need the detailed information

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  7. Read-Only Valued Senior Member

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    No, you simply misunderstood - there is no additional cell wall, the wall it creates is the ONLY wall present and leads to the destruction of the bacteria cell. And that is the end of your pursuit because it gives to the full details.
     
  8. Trippy ALEA IACTA EST Staff Member

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    You want the specific chemical pathways?

    Bacterial cell walls (but no those of Archaea) are made up of petidoglycan. Peptidoglycan is a chain like polymer, it consists of units of N-acetyl muramic acid alternating with units of N-acetyl glucosamine. The units of N-acetyl glucosamine are cross linked by peptide bridges.

    Transpeptidase, the enzyme that penicillin acts upon is responsible for maintaining those peptide bridges, it has a serine active site. It acts on a diamino acid linked to a cross bridge. In S. aureus the diamino acid is L-lysine (the most common) and the bridge is a sequence of 5 Glycine units. The amino acids used for both positions vary, but the function is the same, and the mechanism of the enzyme is the same:

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    The peptide bridge that forms the cross link occurs between the terminal amino acid in th cross bridge and the penultimate alanine, with the elimination of the terminal alanine. In order to do this, the first step is the binding of the serine active site to the penultimate alanine unit, and, as I recall, the last step involves the replacement of the now terminal alanine with a hydroxyl group.

    Now we have penicillin:

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    Penicillin binds irreversibly to the transpeptidase, preventing the transpeptidase from repairing the cell wall:

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    When this happens, osmosis begins to take over and the bacterium fill up with water and eventually explodes.

    As I recall, penicillin resistance came about because some proportion of the bacteria had a naturally occuring mutation that caused the transpeptidase to have a more open structure than normal. This more open structure allows the hydrolysis of the bond between the serine and the penicillin, meaning that the transpeptidase binds reversably to the penicillin.
     
  9. origin Trump is the best argument against a democracy. Valued Senior Member

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    Geeze Trippy, that was an awesome post, thanks! I am so lost when it comes to biology - and strangely enough my daughter is in her last undergrad year of molecular genetics.:bugeye:
     
  10. Eagle9 Registered Senior Member

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    Thanks

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    I read the “a defensive cell wall” and not the “a defective cell wall” and I thought that there was an additional one.

    Trippy
    Yes
    So, the gene in bacterial DNA which is responsible for transpeptidase changes, right? I would like to know, is this change significant? I mean, does its nucleotide sequence changes significantly? If it changes insignificantly then it is believable that such mutation can happen randomly……….
    But where does it happen? Does the Penicillin need to enter INSIDE the cell and to bind to transpeptidase in the cytoplasm? Or does it happen directly on the membrane?

    And: what does mean “repairing the cell wall”? The wall (and anything other) needs repair when it is damaged, right? So, why does the wall need to be repaired? Or maybe its peptidoglycans need to be replaced regularly, from time to time?

    And: this was Penicillin’s mechanism of action. But what about Ampiox? In the first post I wrote:
    So, the mechanism is essentially the same as in case of Penicillin, right?

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  11. Trippy ALEA IACTA EST Staff Member

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    Presumably the change in the nucleotide sequence is small. As I understand it the change in the enzyme structure is small, it's just a slight change in the way transpeptidase folds resulting in a more open structure at the active site. It's not that much more open, however, it's enough of a change.

    I believe the peniciliin actually needs to enter the cell to be effective.

    On the one hand, the bacteria are in a hostile environment.

    Ampiox, as near as I can tell, is a mixture of Ampicillin and Oxacillin.

    Now, consider this structure:

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    It's the core structure of penicillin - I've hilighted the active 'center' in red - the differences are in the 'R' group. When you see a structure with an R like that it pretty much means "Anything goes here". Penicillin G has a benzyl group attached at this location.

    Now:
    This is the structure of Ampicillin:

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    And this is the structure of Oxacillin:

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    Now, you will notice that Ampicillin and Oxacillin both have the penicillin core, and the same active center - the β-Lactam ring. The difference between them being in the composition of the R group. The difference the R group makes is, as I recall, how it interacts with some of the amino acids around the active site of the enzyme. So yes, the mode of action of Ampicillin and Ampiox is, in fact, the same as that of penicillin, because they are both penicillin derivatives.
     
  12. Aqueous Id flat Earth skeptic Valued Senior Member

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    I think it was clever of you to think that antimicrobials might unleash the lipase stored internally to kill the bacteria. Imagine how toxic such a substance would be! My guess is that it could never evolve naturally since the lysosomes of the host would not conceivably have any immunity to it. But interesting hypothesis!

    Keep in mind that a cell wall will rupture under all kinds of syndromes. Obviously lipase is effective against healthy cell walls, hence it is the digestive juice of choice for cells that eat other cells (and it can be assisted by other enzymes and peroxides). But note also, if some other internal damage is done to a cell then it's conceivable that it will rupture for lack of the ability to keep the cell wall repaired. Also keep in mind bacteria are quasi-colonial organisms; therefore for the colony to maintain its integrity it may be preferable for the individual cells to undergo apoptosis (programmed cell death) to keep a majority of younger, more robust cells in place. I'm thinking of bacterial colonial forms that form fibers, mats and films. For those structures to serve their purpose, apoptosis seems like a logical solution. Obviously the cell wall of a dying cell will eventually erode, causing the cell to lyse. I mention this since, as many pathogenic bacteria evolved immunity to the agents used to control infections, it became necessary to seek other ways to either kill the cell or else to disrupt its cell wall maintenance functions. Thus there are drugs which indirectly cause lysis without necessarily harming the cell wall at all.

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    http://www.ncbi.nlm.nih.gov/books/NBK7986/

    As a brain teaser, consider the attachment of E. coli to the human gut. You might want to know what enzymes or acids are present in and around the intestinal mucous membrane in order to determine whether E. coli had to co-evolve to survive such hazards. You might ask yourself whether the cell wall of E. coli is more robust than, say, more primitive bacteria, and what kind of molecular, structural and/or systemic features it evolved. Since it's a leading cause of several deadly infections (peritonitis, some pneumonia) it has received considerable attention since penicillin was first discovered. There should be a wealth of information which speaks to this.

    A lot of what I posted may be beyond the scope of your question. But I was curious why you specifically were interested in lysis rather than cell death in general. I'm assuming you're treating E. coli strictly as a pathogen, recognizing the fact that it's natural presence in humans is mostly harmless.
     
  13. Eagle9 Registered Senior Member

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    Trippy
    And is it possible to find the exact sequence of mutational and non-mutational sequence of DNA of E.coli? It would be interesting to compare them.
    I think the same, but is not there an evidence of this?

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    And therefore bacteria’s cell wall’s molecules (those peptidoglycans) need to be updated/replaced regularly, from time to time?
    Ok, thanks

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    Aqueous Id
    Of course lipase can actually kill bacteria but are you sure that antibiotics generally unleash the lipase? Does it happen?
    E.coli is also quasi-colonial organism? Do they live together? I keep them in little Eppendorfs and sometimes I see their colonies, more precisely some bacteria form a sediment on the bottom of the eppendorf.
    Huge amount of information! But apparently very interesting

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    Now I am earning my master’s degree, the thesis is about action mechanism of various antibiotics and phages to E.coli’s proliferation and observing the results. Actually, it is not crucial for me to know the exact biochemical mechanisms how the antibiotic works, but still I wanted to know something more

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  14. Trippy ALEA IACTA EST Staff Member

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    Dammit Jim, I'm a chemist, not a biologist!

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    In all honesty I have no idea, presumably, it may have even been done.

    Given that it has to act on the transpeptidase, and the transpeptidase is manufactured inside the cell to be used on the cell wall...

    Presumably - after all, when we stop transpeptidase from doing that they fill with water and explode, right?
     
  15. Eagle9 Registered Senior Member

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    Trippy
    Well, it sounds very logic, but maybe Penicillin is embedded IN the cell wall (that is does not enter INSIDE the cytoplasm), encounters the transpeptidase and acts on it there. In such situation Penicillin simply does not need to enter the cell.
    What do you think, is it possible?

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    Sounds right, thanks

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  16. Trippy ALEA IACTA EST Staff Member

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    I think it's a fine hair to be splitting.

    This may be of interest to you Effect of β-Lactamase Location in Escherichia coli on Penicillin Synergy
     
  17. Trippy ALEA IACTA EST Staff Member

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  18. Eagle9 Registered Senior Member

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    Trippy
    Ok, thanks a lot

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  19. Eagle9 Registered Senior Member

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    Trippy
    Aqueous Id
    Guys, could you please tell me how the Gentamicin (Sulfate) causes lysis in E.Coli? In Wikipedia it is written:
    Ok, Gentamicin (Sulfate) causes interrupting the protein synthesis, then what? In my experiments I observed that after adding this antibiotic the bacterial number began decreasing, so the bacteria undergo lysis, how? Why the terminations of protein synthesis cause disintegrating the bacteria?

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