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The lysis-lysogeny state of bacteriophage lambda is well known. Under certain conditions, the phage will enter the lysogenic state after infection of a bacterium. Then, after a while, the phage switches to the lytic state and breaks the bacterium. I forgot the details but the phage must expressed some proteins toxic to the bacteria, e.g., a protease, to lyse the bacteria.

Here is the question: Did bacteria have any immune strategies to defend themselves in face of these toxic proteins? In mammals, both nucleic acid and protein can induce immunological responses and activate T/B cells. In bacteria, I know that the CRISPR system is an immune strategy to degrade viral nucleic acids, but seemingly not proteins.

So if the CRISPR system has missed cutting the viral DNA, the phage has switched to lytic state and begun to produce toxic proteins, did the host bacteria still have weapons to defend? Obviously, most of the time the bacteria failed and died. However, after billions of years' evolution, how could bacteria just give up in face of the toxic proteins?

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I don't know of any direct defenses available to bacteria once a prophage genome has been integrated. If a prophage has induced and carried out its program to the point that lysis proteins are being produced, it is far too late for the host cell.

However, an indirect defense for the bacteria is to simply survive and replicate faster than its prophages induce. You seem to be thinking about this as a purely antagonistic relationship, but once the viral genome is integrated into the bacteria, their reproductive fitness becomes intertwined. When the host replicates, both genomes are copied, so the phage can produce far more progeny by delaying activation until the host builds up its numbers. Phage that boost the fitness of their lysogenic hosts will be even more successful. Prophage can defend against infection by other viruses, confer antibiotic resistance, or provide toxins against eukaryotes or rival bacteria. After many generations, mutations that destroy the prophage's ability to induce and kill the host cell but preserve the beneficial genes are selected for; bacterial "domestication" of integrated viral genomes appears to be common. A thorough discussion of bacterial/prophage co-evolution could fill a textbook, but is mostly beyond the scope of this question. The links in this answer should provide a good starting point if you'd like to know more.

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  • $\begingroup$ Thanks very much for your inspiring answer! Actually I wanted to seek molecular tools for proteins as CRISPR, the bacteria's immune system against nucleic acids, has been so useful. $\endgroup$
    – Wei Feng
    Oct 27, 2022 at 6:34
  • $\begingroup$ Yes I realize my answer doesn't really address the main part of your question. I don't think there is anything like CRISPR for proteins. $\endgroup$
    – timeskull
    Oct 27, 2022 at 18:37

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