As the number of antibiotic-resistant bacteria increases around the world, rendering conventional antibiotics ineffective, specific viruses may offer a solution.
Viruses called bacteriophages or phages target bacteria but cannot infect humans or other higher organisms. Phages inject their DNA into a bacterial cell, multiply to large numbers using the host’s resources, and then break out to infect more nearby bacteria.
Essentially, they are naturally occurring, self-replicating and specific antibiotics. Discovered more than 100 years ago, their use against bacteria has been largely sidelined in favor of antibiotics.
Our new research focused on a specific protein used by phages to bypass bacteria’s natural defenses. We found that this protein has an essential control function by binding to DNA and RNA.
This increased understanding is an important step toward using phages against bacterial pathogens in human health or agriculture.
Bacterial defense systems
There are obstacles to using phages to target bacteria. Just as our bodies have immune systems to fight viruses, bacteria have also developed defenses against phage infection.
One such defence is “clustered regularly interspaced short palindromic repeats”, or CRISPR, now better known for its applications in medicine and biotechnology. CRISPR systems normally act as “molecular scissors” by cutting DNA into pieces, whether in a lab-based setting or in nature, inside bacteria to destroy a phage.
Imagine you want to use a phage against an antibiotic-resistant bacterial infection. The only obstacle standing in the way of that phage killing the bacterium and eradicating the infection might be the bacterium’s CRISPR defenses, making the phage useless as an antimicrobial.
This is where it becomes important to know as much as possible about phage counter-defenses. We are investigating so-called anti-CRISPRs: proteins or other molecules that phages use to stop CRISPR.
Bacteria that have CRISPR can prevent the phage from infecting them. But if the phage has the right anti-CRISPR, it can neutralise this defence and kill the bacteria.
The Importance of Anti-CRISPR
Our recent research focused on how the anti-CRISPR response is controlled.
When faced with powerful CRISPR defenses, phages automatically want to produce large amounts of anti-CRISPR to increase their chances of circumventing CRISPR immunity. But excessive production of anti-CRISPR inhibits phage replication and is ultimately toxic. This is why control is important.
To achieve this control, phages have another protein: an anti-CRISPR-associated (or ACA) protein, which is often found alongside anti-CRISPR.
The ACA proteins act as regulators of the phage’s defense. They ensure that the initial burst of anti-CRISPR production that inactivates CRISPR is then rapidly reduced to a low level. This way, the phage can allocate energy to where it is needed most: its replication and, ultimately, release from the cell.
We found that this regulation occurs at multiple levels. For any protein to be produced, the gene sequence in DNA must first be transcribed into messenger-RNA. It is then decoded, or translated, into a protein.
Many regulatory proteins act by inhibiting the first step (transcription into messenger-RNA), others by inhibiting the second step (translation into protein). Either way, the regulator often acts as a kind of “road block” by binding to DNA or RNA.
Surprisingly and unexpectedly, the Aca protein we examined performs both functions – although its structure suggests that it is simply a transcriptional regulator (a protein that controls the translation of DNA into RNA), which is very similar to proteins that have been investigated for decades.
We also investigated why this extra strict control at two levels is necessary. Again, it seems to be all about the dosage of anti-CRISPR, especially when the phage replicates its DNA in the bacterial cell. This replication will inevitably lead to the production of messenger-RNA, even in the presence of transcriptional control.
Therefore, it seems that additional regulation is needed to rein in anti-CRISPR production. This comes back to the toxicity of excessive production of this counter-defense protein, the harm caused by “too much of a good thing.”
Sophisticated Controls
What does this research mean in a broader sense? We now know a lot about how to use anti-CRISPR. It needs to be precisely controlled to make the phage successful in its battle against the host bacterium.
This is important not only in nature but also in the case of the use of phages as alternative antimicrobials.
Knowing every detail about something as obscure as an anti-CRISPR-related protein could make a huge difference between a phage’s success or defeat — and life or death not just for the phage, but for the person infected with antibiotic-resistant bacteria.
Nils Birkholz, Postdoctoral Fellow in Molecular Microbiology, University of Otago
This article is republished from The Conversation under a Creative Commons license. Read the original article.
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