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Disease and treatment

Viruses help humans in fighting bacteria

Humans are constantly battling microorganisms. We barely manage to develop an antibiotic before bacteria start to develop resistance. Similarly, microorganisms such as bacteria and viruses battle each other. Now researchers have revealed how viruses evade the immune system of bacteria-like organisms called archaea. The research potentially offers new strategies for combating multidrug-resistant strains of bacteria.

When we catch the flu or a cold, our immune system immediately starts to search its archives of previous attacks by similar pathogens. Like us, bacteria store information in their immune system about previous enemies such as viruses. Just as bacteria do to us, viruses develop countermeasures to evade the immune system of bacteria. Danish researchers have now discovered such a countermeasure that viruses launch against a group of single-celled organisms called archaea.

“Almost all archaea contain the CRISPR-Cas immune system, which enables them to remember and eliminate viruses. Nevertheless, we discovered viruses that could evade the CRISPR weapon that archaea use. We found out that, when we removed the CRISPR weapon, the virus also deleted its anti-CRISPR weapon. This led us to discover how viruses manage this battle. We can use this knowledge to develop novel alternative methods for combating multidrug-resistant bacteria, such as bacteriophage therapy, in which bacterial viruses are used to combat bacteria,” explains a main author, Xu Peng, Associate Professor, Department of Biology, University of Copenhagen.

Countering CRISPR

The researchers have studied archaea for many years. When archaea were first discovered in the 1970s, they were called archaebacteria, but today scientists know that they differ considerably from bacteria and, in many ways, resemble eukaryotes, such as animals. This fact and the fact that they can thrive in extreme environments such as in geysers and under ice caps make them very interesting to study.

“Like bacteria, archaea constantly battle archaeal viruses. And to a greater extent than bacteria, archaea also have an adaptive immune system – CRISPR – that helps them win this battle. But discovering how archaeal viruses actually survive the battle against archaea has been unsuccessful. However, we suspected that this requires the help of some form of protein that can inhibit CRISPR.”

Ninety percent of all archaea have a CRISPR-Cas immune system that protects them from virus attacks. Using CRISPR, the archaea are able to cut and save tiny fragments of the genome from the viruses that attack. When another virus attacks, the system can recognize the foreign virus and then gets the Cas enzymes to cut the viral DNA into pieces. But viruses have evolved (or invented) smart ways of evading this.

“We have discovered an anti-CRISPR protein, AcrID1, that inhibits one CRISPR system in archaea. This means that, although the archaea still recognize the viruses, they cannot eliminate them. We do not yet know how the protein inhibits the CRISPR system. The AcrID1 protein may prevent CRISPR from binding to the genome of a virus – or the protein may just prevent the Cas enzyme from cutting the virus DNA into pieces.”

Revealing how the virus does the trick

This new discovery is very important for basic understanding of how CRISPR works, but the research may also turn out to have important applications. The CRISPR-Cas system is already being used today as an effective gene technology tool based on its ability to cut and initiate specific gene sequences because Cas9 itself does not replace the sequences. The discovery of anti-CRISPR proteins (Acrs) in the viruses means that a possible on-off switch may have been found.

“The new anti-CRISPR-proteins may end up being incredibly important because we currently only have very few effective methods to turn off the very effective gene technology tool, CRISPR. These proteins seem to be much more effective for this purpose than the ones previously used.”

The new knowledge can also be used in the increasingly serious battle against multidrug-resistant bacteria. For example, researchers are testing bacteriophage therapy against multidrug-resistant bacteria by using the viruses’ ability to attack bacteria. Anti-CRISPR proteins will be able to strengthen the viruses’ ability to out-manoeuvre multidrug-resistant bacteria.

“One key to solving this problem is to get to know the bacteria as well as possible, including their strengths and weaknesses. The study provides an important overview of how to bypass the otherwise effective defences of bacteria. If we can reveal the viruses’ tricks, we might be able to weaken the bacteria enough so that they die – or we can stress their immune system enough so they become more receptive to existing methods of elimination,” explains co-author Ditlev Egeskov Brodersen, Associate Professor, Department of Molecular Biology and Genetics, Aarhus University.

A way out of the crisis of multidrug-resistant bacteria

Ditlev Egeskov Brodersen and colleagues focus on understanding the fundamental molecular mechanisms governing microbial survival by elucidating the three-dimensional structure of the molecular components involved. Determining how microorganisms respond to lack of nutrients, antibiotics and other changes in their environment can be used to develop new antimicrobial drugs.

“Microorganisms can adapt extremely efficiently. Humans and bacteria will therefore continue to constantly battle one another. However, just as microorganisms adapt to human weapons – our immune system and the antibiotics we use – we need to understand these microorganisms and their defence mechanism: in this instance, their CRISPR immune system.”

Recent research has revealed that the immune systems of bacteria are much more advanced than previously thought. This applies to both CRISPR-Cas and the toxin-antitoxin systems, in which microorganisms exposed to an antibiotic can release a toxin that virtually puts them in hibernation. They also contain antitoxins that they release when the danger has passed.

“We face a sophisticated opponent. In the past year alone, seven new defence systems located in the CRISPR-Cas area of the bacterial genomes have been identified. This is scary, but it increases the potential to attack the bacteria on several fronts. Combining weapons is presumably the most effective method of countering the present crisis of multidrug-resistant bacteria, in which increasing numbers of people die from bacterial infections that could previously be treated with antibiotics.

Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity” was published in Nature Microbiology. The Novo Nordisk Foundation awarded Ditlev Egeskov Brodersen, Associate Professor, Department of Molecular Biology and Genetics, Aarhus University, a grant in 2017 for the project Understanding the Functional and Evolutionary Links between Microbial CRISPR-Cas and Toxin-antitoxin Systems.

Xu Peng
Associate professor
CRISPR virus-plasmid defence-regulatory system Almost all archaeal chromosomes and some conjugative plasmids contain one or more clusters of short regularly inter-spaced repeats (CRISPR) some of which constitute over 100 repeat-spacer units. These have been implicated in inhibiting propagation of viruses and plasmids in archaea (and in many bacteria) via an intermediate RNA mechanism (Tang et al., 2002; Tang et al., 2005; Mojica et al., 2005). Our laboratory has identified the protein which specifically binds to crenarchaeal repeats (Peng et al., 2003) and the processing products of the cluster-encoded transcripts from each DNA strand (Lillestøl et al., 2006). We are currently exploiting bioinformatic approaches (Vestergaard et al., 2008; Shah et al., 2008) and genetic experiments, to understand the dynamic interactions between chromosomal clusters and extra-chromosomal elements.
Ditlev Egeskov Brodersen
Associate Professor
Microbial survival mechanisms We are interested in uncovering fundamental, molecular mechanisms underlying central survival mechanisms in both bacteria and archaea with the aim of understanding how microorganisms respond to nutritional stress, antibiotics, and other changes in their environment. Knowledge of these mechanisms can be used to develop new antimicrobial drugs. We use classical biochemistry as well as hybrid methods in structural biology (x-ray crystallography, electron microscopy, and small-angle x-ray scattering) in our work. Current projects: 1) Mechanism of activation and activity of bacterial toxin-antitoxin systems (VapBC, RelBE, HicAB etc.), including the mechanism of RNA cleavage. 2) Understanding how phosphonate compounds are utilised as sources of phosphorous via the carbon-phosphorus lyase pathway in E. coli. 3)Understanding the interplay between toxin-antitoxin systems and CRISPR-Cas immunity in bacteria and archaea. 4)Regulation of (p)ppGpp synthesis and the effects of the alarmone during stress in bacteria.