Unveiling the Remarkable Arsenal of Antiphage Defense Systems in Bacteria

Did you know that bacteria have developed incredibly diverse and fascinating defense systems to protect themselves against viruses known as phages? These defense mechanisms, collectively referred to as antiphage defense systems, play a vital role in the survival and evolution of bacteria in a world teeming with viral threats. Phage resistance is caused by one or more of these systems, in which a bacteria becomes resistant to the phage, indicating that it is no longer susceptible to phage infection. In this article, we will explore some of the most intriguing antiphage defense systems that bacteria employ, using vivid scenarios to help us understand. Don’t worry about the complicated science with synonyms and short forms; I’ll try to make it as simple to understand as possible and to make it easier to digest, I have divided it into four groups based on the mode of action and/or pathways.

Group 1: Genetic Guardians (RM and RM-like systems, CRISPR-Cas, pAgo)

Imagine a bustling city, where each building represents a bacterium, and phages roam the streets like stealthy invaders. The first line of defense is the RM system (Restriction-Modification), acting as a security guard stationed at each building’s entrance. This system detects foreign DNA based on specific sequences and chops it up, preventing phage invasion. Similar to the RM system, RM-like systems employ different strategies to recognize and degrade phage DNA.

But what happens when a phage escapes the initial defense? This is where the CRISPR-Cas system steps in. It’s like an intelligent surveillance network that records and remembers previous phage encounters. When a new phage invades, the CRISPR-Cas system utilizes the recorded information to precisely target and destroy the phage’s DNA. Of course, some phages, such as Jumbo phages, have tried to avoid this by using methods such as Chimallin protein.

A powerful weapon used by bacteria to fend off phages is the pAgo (Prokaryotic Argonaute) system. Picture this as a molecular sniper rifle, with pAgo proteins acting as highly accurate marksmen. They bind to phage DNA and precisely cleave it, ensuring the phage’s demise.

Group 2: Multi-Faceted Protectors (AbiZ, stk2, DSR, RexAB, CapRel, PARIS, AVAST/AVs)

In our city scenario, the phages are becoming smarter, finding new ways to infiltrate buildings. Enter Group 2 defense systems, which fight back with diverse strategies. AbiZ (Abortive infection Z), for instance, is like a barricade that prevents phage DNA injection into the bacterial cell, ensuring its survival. More information on abortive infection can be found here.

The stk2 (Serine/threonine protein kinase 2) system acts as a bacterial assassin. It produces toxins that target and kill infected neighboring cells, acting as a sacrificial shield to protect the community.

Another defense mechanism, the DSR (Dormancy survival regulator) system, senses the presence of phages and induces dormancy in the bacterial population. This is like a city-wide lockdown, preventing phage replication until the threat has passed.

The RexAB (Replication exclusion and abortive infection) system is akin to a SWAT team, attacking phages head-on. It hijacks phage replication processes, leading to the production of defective phages.

CapRel (Capsule regulation) is like a city-wide communication network that alerts neighboring cells about a phage attack, allowing them to arm their defenses in advance.

PARIS (Phage-derived Anti-repeat Interference System), an intriguing defense mechanism, selectively degrades phage RNA within infected cells, preventing the production of phage proteins critical for replication.

AVAST/AVs, short for Anti-Virus Associated Silencing Transcripts and Antiviral Small RNAs/Antiviral Small RNAs, are like spies that detect the presence of phage genetic material and initiate a cascade of events to destroy it.

Group 3: Molecular Sentinels (PrrC, ToxIN, RniAB, Retrons, Avcid, dGTpase)

In our city, some buildings are equipped with clever defense mechanisms. PrrC (Phage-related repressor C) is like a Trojan horse, tricking phages into entering the bacterial cell, only to face destruction once inside.

ToxIN is a toxin-antitoxin system that, when activated, prevents phage replication by inhibiting protein synthesis. This target is crucial to lowering the costs to the host because protein synthesis is crucial for the invader (phage) to reproduce.

RniAB (RNA interference antiviral barrier) is like an information assassin, targeting and destroying phage RNA, thereby preventing translation and replication. The effects of this system on the phage, in some way, resemble those of ToxIN, don’t they?

Retrons (Retroelements) are like molecular booby traps. They synthesize special DNA molecules that, when transcribed into RNA, can be reverse-transcribed back into DNA. This process forms a loop structure that interferes with phage replication.

Avcid (Antiviral cell death) is a clever system that detects phage infection and induces cell death, sacrificing the infected cell to protect the bacterial population. Should we label such behavior as suicidal for the community’s protection? It would be similar to an infected person choosing to end their lives by themselves in order to avoid spreading the infection.

dGTpase (deoxyguanosine triphosphatase) is like a garbage disposal system. It recognizes and destroys foreign DNA, preventing phages from integrating their genetic material into the bacterial genome. Simple as that—no phage DNA, no infection. Having the phage’s DNA in the host right away after injection is one of the first crucial steps in establishing an infection. The infection is terminated if the DNA gets disintegrated.

Group 4: Phage Fighters Extraordinaire (CBASS and PYCSAR, Theoris, bGSDM, DarTG, Viperins, Antiviral biosynthesis pathways)

Now, let’s imagine a city facing a relentless wave of phages. The CBASS (Clustered, Regularly Interspaced, Short Palindromic Repeats-Associated Systems) and PYCSAR (Phage-Encoded Yersinia Consortium Abortive Infection and Restriction) systems act as an emergency evacuation plan. They trigger cell death upon phage infection, ensuring that the phage cannot spread to neighboring cells.

Theoris (Theoretical ORF-specific system) is like a city under siege. It produces multiple defense proteins that target different stages of phage infection, overwhelming the invaders.

bGSDM (Bacteriophage Growth Suppression by a DNA Mimic), an intriguing system, detects phage DNA and initiates a process called “genome slicing,” preventing phages from integrating into the bacterial genome.

DarTG (DArwinian Thermostable G-quadruplexes), resembling a phage thief, steals genetic material from infecting phages, incorporating it into the bacterial genome. This allows the bacterium to acquire new defenses and evolve to fight future phage attacks.

Viperins (Virus Inhibitory Proteins Induced by Interferon), analogous to biochemical ninjas, produce molecules that interfere with phage replication and protein synthesis, severely hampering phage survival.

Finally, the antiviral biosynthesis pathways are like factories that produce small molecules with potent antiviral properties. These molecules can directly attack and neutralize phages, providing an effective defense against infection.

Bacteria possess an astonishing array of highly diverse antiphage defense systems. They have evolved these mechanisms over millions of years to protect themselves from the constant threat of phages. By employing strategies ranging from DNA degradation to RNA interference and programmed cell death, bacteria demonstrate their incredible ability to adapt and survive in the face of viral adversaries. These defense systems not only contribute to the resilience of bacterial communities but also inspire scientists to explore their potential applications in fields such as biotechnology and medicine.

References

• Shany Doron et al., Systematic discovery of antiphage defense systems in the microbial pangenome.Science359,eaar4120(2018).DOI:10.1126/science.aar4120 (open source)
• Georjon, H., Bernheim, A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol (2023). https://doi.org/10.1038/s41579-023-00934-x (Not open hence may need subscription)
• Tesson, F., & Bernheim, A. (2023). Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?. Current Opinion in Microbiology, 71, 102238. (Open source)