Ancient Defense: The CRISPR Bacterial Immune System

If a bacterium is exposed to a virus, then it needs a way to recognize and destroy that virus in the future. If the CRISPR system allows the cell to "remember" and target specific viral DNA, then it serves as an adaptive immune system.

If an immune system gathers information from a specific past infection to defend against future attacks, then it is defined as adaptive. If CRISPR saves snippets of viral DNA for future use, then the statement that it is merely innate is false.

If the bacterial genome contains alternating repeats and unique sequences, then the unique sequences represent historical viral infections. If these sequences act as memory markers, then they are identified as spacers.

If the CRISPR locus is an organized genomic region, then it must include the "scissors" (Cas genes), the "scaffold" (repeats), and the "memory" (spacers). If bacteria are prokaryotes, then they lack a nuclear envelope and mitochondria.

If the acquisition phase is the "learning" step, then the cell must gain new information. If it takes a piece of DNA from a virus (a protospacer) and adds it to its own CRISPR array, then it has acquired the information needed for immunity.

If new viral DNA must be physically cut and integrated into the bacterial chromosome, then specialized enzymes are required. If Cas1 and Cas2 form a complex that performs this specific integration, then they are the drivers of acquisition.

If the system needs a way to "read" the spacers to find a matching virus, then it must transcribe them into RNA. If these RNAs serve as guides for the Cas proteins, then they are named CRISPR RNAs, or crRNAs.

If the crRNA guide finds a perfect match in the invading virus, then the attached Cas protein is positioned correctly. If the Cas protein is a nuclease, then it will break the phosphodiester bonds and cleave the viral DNA, stopping the infection.

If the Cas protein needs to avoid cutting its own DNA, then it must look for a signal found only in the virus. If the PAM sequence is found only in the target (virus) and not in the host's CRISPR locus, then the statement that it is in the repeats is false.

If the Cas9 protein requires a Protospacer Adjacent Motif (PAM) to trigger its cutting action, and if the PAM is only present in the viral target but not in the bacterial CRISPR locus, then the host DNA remains safe from self-cleavage.

If the system is an evolutionary response to specific pathogens, then we must identify those pathogens. If the natural enemies of bacteria are viruses that inject DNA into them, then those viruses are bacteriophages.

If the system adds new spacers after each attack, then it improves. If the spacers are in the DNA, then they are inherited by offspring. Since each spacer is unique to a virus, the system is specific and adaptive. Bacteria do not have blood or antibodies.

If genomic surveys show that CRISPR is found in approximately 40/50% of bacteria and 90% of archaea, then it is common but not universal. If it is missing from many species, then the statement that it is in "every" species is false.

If the spacers are all different, then the cell needs a constant "handle" to process them. If the identical repeat sequences allow the cell to recognize where to cut the long RNA into small crRNAs, then they act as structural binding sites.

If the acronym CRISPR identifies the DNA repeats, then the "Cas" part (CRISPR-associated) identifies the functional tools. If these tools perform the enzymatic work of cutting, then they are the Cas proteins.

If Cas genes are often found on mobile genetic elements and spacers match known viruses, then the system evolved through the co-opting of foreign genes. If this process happened over billions of years, then it is a natural evolutionary product.

If a bacterium survives a viral attack and incorporates a new spacer into its DNA, then that DNA is replicated during binary fission. If the daughter cells receive that same DNA, then they inherit the immunity without being exposed to the virus first.

If Cas9 is the effector protein, then it must open the DNA to check the sequence and then make a double-strand break. While it interacts with RNA, it does not synthesize it (handled by RNA polymerase) and does not handle host replication.

If an immune system cannot tell the difference between its own parts and an invader, then it will destroy itself. If the presence of a PAM in the virus identifies it as a threat, then the bacterium has successfully distinguished self from non-self.

If the DNA memory is to be used, then it must be converted into a functional tool. If the cell makes a long RNA copy of the CRISPR array and then chops it into individual crRNAs, then it is "expressing" the immune response.