Bacterial immunity (Introduction)
by David Turell 
, Wednesday, February 11, 2015, 14:39 (3366 days ago)
Special complex techniques:-https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/-This is the sentience dhw's favorite researchers talk about. All in the bacteria's genetic tool kit and all done at a molecular level automatically. To me this is anything but God-given, being too complexly specified to be the result of chance: -"Koonin knew that microbes are not passive victims of virus attacks. They have several lines of defense. Koonin thought that CRISPR and Cas enzymes provide one more. In Koonin's hypothesis, bacteria use Cas enzymes to grab fragments of viral DNA. They then insert the virus fragments into their own CRISPR sequences. Later, when another virus comes along, the bacteria can use the CRISPR sequence as a cheat sheet to recognize the invader-"To test Koonin's hypothesis, Barrangou and his colleagues infected the milk-fermenting microbe Streptococcus thermophilus with two strains of viruses. The viruses killed many of the bacteria, but some survived. When those resistant bacteria multiplied, their descendants turned out to be resistant too. Some genetic change had occurred. Barrangou and his colleagues found that the bacteria had stuffed DNA fragments from the two viruses into their spacers. When the scientists chopped out the new spacers, the bacteria lost their resistance.-"As Wiedenheft, Doudna and their colleagues figured out the structure of Cas enzymes, they began to see how the molecules worked together as a system. When a virus invades a microbe, the host cell grabs a little of the virus's genetic material, cuts open its own DNA, and inserts the piece of virus DNA into a spacer.-"As the CRISPR region fills with virus DNA, it becomes a molecular most-wanted gallery, representing the enemies the microbe has encountered. The microbe can then use this viral DNA to turn Cas enzymes into precision-guided weapons. The microbe copies the genetic material in each spacer into an RNA molecule. Cas enzymes then take up one of the RNA molecules and cradle it. Together, the viral RNA and the Cas enzymes drift through the cell. If they encounter genetic material from a virus that matches the CRISPR RNA, the RNA latches on tightly. The Cas enzymes then chop the DNA in two, preventing the virus from replicating.-"As CRISPR's biology emerged, it began to make other microbial defenses look downright primitive. Using CRISPR, microbes could, in effect, program their enzymes to seek out any short sequence of DNA and attack it exclusively."
Bacterial immunity; more on CAS enzymes
by David Turell , Friday, November 30, 2018, 00:05 (1979 days ago) @ David Turell
This is part of the CRISPR enzyme system that scientists have converted to use for slicing up DNA and tailoring it for study. This study shows how bacteria use it for immune protection:
https://phys.org/news/2018-11-shape-shifting-protein-bacteria-invaders.html
"The study, published in Molecular Cell, shows that the protein Cas10 is usually harmless, but transforms into an enzymatic assassin when confronted with foreign genetic material.
"One way that bacteria protect themselves is through the use of CRISPRs, or clustered regularly interspaced short palindromic repeats, and associated Cas proteins. These systems not only fend off pathogens, but also memorize them: when a bacterium is attacked, it copies and stores a section of the invader's DNA. This genetic sequence, called a spacer, helps the bacterium identify the invader next time it strikes. Once a trespasser is detected, Cas enzymes dissolve its DNA.
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"In 2017, Marraffini and his colleagues showed that Type III systems have the unique ability to target not just a single invader sequence, but variations on a genetic theme. This means that even if a virus mutates, CRISPR-Cas can still identify and destroy its DNA.
"'For other systems, you have a single mutation in the target sequence and immunity is usually lost," says Liu. "But type III systems, which use the Cas10 enzyme, can be effective even when the target has multiple mutations."
"Compared to enzymes in other CRISPR types, Cas10 fires at relatively wide variety of targets; yet, it manages to avoid harming a bacteria's own DNA. How, Liu wondered, do type III complexes discriminate between self and other?
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"The researchers found that when Cas10 was exposed to an invader's RNA, the enzyme's structure took on new shapes. And, Liu says, as Cas10 cycles through various conformations, it intermittently enters active states, which imbue the enzyme with DNA-dissolving powers.
"By contrast, when then Cas10 encountered "self" RNA, the enzyme became locked in an inactive position, which prohibited any dicing and slicing of DNA. These results, says Liu, explain how type III systems avoid self-destructive behavior.
"'We don't want Cas10 to go around randomly cleaving DNA. Its activity has to be regulated," he says. "And it appears that the enzyme is operative only when it is unlocked from its inactive configuration."
Read more at: https://phys.org/news/2018-11-shape-shifting-protein-bacteria-invaders.html#jCp
"The researchers also found that when Cas10 was exposed to mutated enemy RNA, the enzyme could bend into only a limited number active shapes. And as the malleability of Cas10 decreased, so did the strength of the bacterium's immune response.
"These findings suggest that a robust immune response depends on Cas10's ability to move around: When the enzyme can shimmy freely, it spends more time in an active state, and thus more time degrading dangerous DNA. Still, Liu notes, even when the enzyme loses some of its flexibility, it does not entirely forfeit its ability to injure invaders."
Comment: If this process of a shape-altering enzyme was fully known, it would help answer the dhw/David debate about automaticity in cells: does the CAS10 simply react on its own in changing its form or can a directive process be found. That directive process can also be automatic or shown to be an independent control. At some point as layers are plied off the answer will appear.
Read more at: https://phys.org/news/2018-11-shape-shifting-protein-bacteria-invaders.html#jCp
Read more at: https://phys.org/news/2018-11-shape-shifting-protein-bacteria-invaders.html#jCp
Bacterial immunity using CRISPR system
by David Turell , Saturday, June 01, 2019, 20:31 (1795 days ago) @ David Turell
Further definition of the mechanism:
https://www.sciencedaily.com/releases/2019/05/190530160647.htm
"In a new study, described in Nature, Rockefeller scientists showed that microbes under viral attack turn their defenses not only on their enemies, but also on themselves. This drastic measure, the researchers found, doesn't kill the bacteria, but rather sends them into a dormant state that prevents the infection from spreading.
"Among bacteria, viruses called bacteriophages are public enemy number one.
These pathogens propagate by injecting their genome into unsuspecting microbes, eventually causing their host cell to rupture, at which point progeny phage is released to infect other members of a bacterial colony.
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"Microbes have at their disposal many different CRISPR systems, one of which caught the attention of Luciano Marraffini due to its unique strategy for fending off intruders. Whereas most Cas enzymes destroy viral DNA, this particular enzyme, Cas13, works by cleaving RNA.
"'Since Cas13 targets RNA, it was initially thought to have evolved to impede phages with RNA genomes. The problem is, RNA phages exceedingly rare," he says. "So we wanted to see whether it might have evolved to serve a different function."
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"Through a series of experiments, the researchers found that Cas13 helps bacteria, ironically, by hindering them. That is, the enzyme cuts up bits of host RNA, sending the bacteria into a dormant state -- a kind resting phase in which the microbes remain alive but don't grow. This strategy works, says Meeske, because viruses need host RNA to replicate.
"'Phages are parasites: They don't have all the elements needed for their propagation, so they rely on the host," he explains. "And if the host cell isn't making those elements, the phage cannot propagate."
"The researchers also found that Cas13 kills viruses more thoroughly than other Cas enzymes. Standard CRISPR-Cas systems are highly specific, cutting up bits of DNA that match a precise genetic sequence. And while this specificity can be an asset, it also comes with a big drawback: If a virus mutates, CRISPR cannot recognize the invader, and the phage escapes scot-free.
"'If a phage has a single point mutation in its target sequence, then usually the virus is invisible to Cas and the infection will succeed," says Marraffini. "But with Cas13 we didn't see any escaper mutants."
"The researchers attribute this superb virus-fighting power to the fact that cell dormancy does not target one particular virus, but rather makes it impossible for any phage -- including mutants -- to propagate. And while an indefinite nap may not seem like much of a life for a microbe, Meeske notes that the real benefit of Cas13 lies not at the level of the individual, but of the bacterial community as a whole.
"'The phage has one shot to deliver its genetic payload and replicate," he says. "So if they inject their genome into a host that turns out to be inhospitable, the infection stops there. The phage loses, and the bacterial colony wins.'"
Comment: Like all other complex protective defense mechanisms, assuming bacteriophages developed at the same time as bacteria, such a complex system, in which the bacteria attacks itself, had to be carefully designed, limiting change to just enough for dormancy, and the ability to revive.
Bacterial immunity using self-destruction
by David Turell , Friday, January 10, 2020, 21:55 (1572 days ago) @ David Turell
Hit by a bacteriophage a bacterium self-distructs:
https://phys.org/news/2020-01-team-bacteria-self-destruct-viral-infections.html
"Researchers at University of California San Diego School of Medicine have discovered how a new immune system works to protect bacteria from bacteriophages (phages), viruses that specifically infect bacteria. This new system is unusual in that it works by abortive infection—the infected bacterial cell self-destructs to keep the infection from spreading to other cells.
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"One aspect of meiosis that particularly interests them is how a specific protein family, called HORMA proteins, help maintain the stability of the genome during this specialized cell division. But when a 2015 study published by National Institutes of Health bioinformaticians predicted that some bacteria might also produce HORMA proteins, and that these proteins might be involved in a new kind of immune system, Corbett was intrigued.
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"'Almost 75,000 different bacteria have had their genomes sequenced. Of those, Corbett said this new defense system is found in approximately 10 percent. His team cloned the system, now called CBASS, into a laboratory strain of E. coli that is usually sensitive to phage infection. "We were thrilled to find that CBASS provided nearly absolute immunity to phages," Corbett said.
"Digging deeper, the team went on to unravel a number of biochemical and structural details about the CBASS defense system, which contains several proteins. They found that the HORMA proteins sense the infection, then stimulate a second protein to synthesize a second messenger molecule. This molecule in turn activates a nuclease enzyme that destroys the bacterium's own genome, killing the cell and also keeping the phage from replicating and infecting other cells."
Comment: This presents a reproductive problem. It is logical to have cells take one for the group, but if they kill themselves, how do they reproduce new copies? The response might be some bacteria have the ability but pass it on by not being infected and killed. Fine but how did they learn the process if they never met the challenge? Looks designed to me.
Bacterial immunity: inhibiting phages
by David Turell , Saturday, April 27, 2024, 20:35 (3 days ago) @ David Turell
A new study of the molecules at work:
https://phys.org/news/2024-04-common-bacterial-defense-viral-infection.html
"In a new study, a team from The Ohio State University has reported on the molecular assembly of one of the most common anti-phage systems—from the family of proteins called Gabija—that is estimated to be used by at least 8.5%, and up to 18%, of all bacteria species on Earth.
"Researchers found that one protein appears to have the power to fend off a phage, but when it binds to a partner protein, the resulting complex is highly adept at snipping the genome of an invading phage to render it unable to replicate.
"'We think the two proteins need to form the complex to play a role in phage prevention, but we also believe one protein alone does have some anti-phage function," said Zhangfei Shen, co-lead author of the study and a postdoctoral scholar in biological chemistry and pharmacology at Ohio State's College of Medicine. "The full role of the second protein needs to be further studied."
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"The two proteins that make up this defense system are called Gabija A and Gabija B, or GajA and GajB for short.
"Researchers used cryo-electron microscopy to determine the biochemical structures of GajA and GajB individually and of what is called a supramolecular complex, GajAB, created when the two bind to form a cluster consisting of four molecules from each protein.
"In experiments using Bacillus cereus bacteria as a model, researchers observed the activity of the complex in the presence of phages to gain insight into how the defense system works.
"Though GajA alone showed signs of activity that could disable a phage's DNA, the complex it formed with GajB was much more effective at ensuring phages would not be able take over the bacterial cell.
"'That's the mysterious part," Yang said. "GajA alone is sufficient to cleave the phage nucleus, but it also does form the complex with GajB when we incubate them together. Our hypothesis is that GajA recognizes the phage's genomic sequence, but GajB enhances that recognition and helps to cut the phage DNA."
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"'We only know GajB helps enhance GajA activity, but we don't yet know how it works because we only see about 50% of it on the complex," Shen said.
"One of their hypotheses is that GajB may influence the concentration level of an energy source, the nucleotide ATP (adenosine triphosphate), in the cellular environment—specifically, by driving ATP down upon detection of the phage's presence. That would have the dual effect of expanding GajA's phage DNA-disabling activity and stealing energy that a phage would need to start replicating, Yang said."
Comment: this follows closely on Shapiro's work. Not that bacteria modify DNA in this case, but they have other mechanism to protect themselves as free living single cells. Remember the CRISPR mechanism to edit DNA is part of the bacterial defense system and we stole it for our use.