Bacteria are constantly attacked by bacteriophages, which are viruses that specifically target bacteria, aiming to take over their cellular machinery and force them to produce more bacteriophages. However, a new study reveals how bacteria have developed an ingenious immunity defence mechanism that destroys bacteriophages as soon as they enter.
Life as a bacterium is anything but simple. In their microscopic world, they are neither alone nor safe. Bacteria are continually assaulted by bacteriophages attempting to penetrate and seize control from within.
Fortunately, bacteria have various immunity mechanisms that defend them from bacteriophages.One of these is called Zorya, named after a Slavic feminine personification of dawn, possibly a goddess. Researchers have studied this defence system in great detail, unveiling how it helps bacteria to evade the ever-present threat of bacteriophages.
This discovery may have implications that transcend the survival of bacteria.
“Improving insight into bacterial immunity mechanisms could enhance understanding of how to defend beneficial bacteria when they serve important purposes, such as producing molecules useful to industry. Moreover, this knowledge might by potentially applied in ways we have yet to envision,” explains a researcher behind the study, Nicholas Taylor, Associate Professor and Group Leader, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark.
The research has been published in Nature.
Comprehensive microscale studies
Bacteria have developed several mechanisms to defend themselves against bacteriophages. Perhaps the most well known is CRISPR-Cas, which has been commercially adapted into the world’s most useful molecular tool for cutting DNA. Thousands of laboratories worldwide use CRISPR-Cas daily.
Zorya is another immunity mechanism, but researchers did not fully understand how it functions. The new study aimed to address this gap by using a broad arsenal of techniques to investigate proteins within cells.
These methods included cryoelectron microscopy – freezing proteins and examining their structure at extremely high resolution – and mutagenesis, which involves altering the genes that form Zorya. The researchers also used fluorescence microscopy to obtain insight into structures within cells and functional studies to explore how the components of the molecular immunity mechanism interact.
Zorya comprises four proteins
The researchers found that Zorya comprises four proteins: ZorA, ZorB, ZorC and ZorD. ZorA and ZorB have the same structure as previously identified motor proteins, MotA and MotB, which power the flagellum: a long tail, powered by a molecular motor that enables bacteria to move.
This discovery suggested that ZorA and ZorB likely also form a molecular motor, and this study confirmed this hypothesis. However, ZorA and ZorB do not create a motor that drives an external flagellum. Instead, they generate a long tail that extends into the cell’s cytoplasm.
To investigate further, the researchers introduced the genes coding for all components of the Zorya system into a bacterium lacking this immunity mechanism. They observed that a bacteriophage breaching the cell surface – similar to a mosquito piercing human skin – activates Zorya.
The activation of Zorya resembles a missile defence system being triggered when a foreign missile enters airspace.
ZorA, located near the entry site, detects the presence of the bacteriophage, prompting ZorA to rotate around ZorB. This process forms a rotating tail that extends into the cytoplasm. The interaction between ZorA and ZorB sends a signal to recruit ZorC and ZorD to the site.
ZorC and ZorD cut DNA into pieces
ZorC and ZorD rapidly arrive at the site where ZorA and ZorB have detected the bacteriophage’s breach of the cell membrane, where the bacteriophage has begun injecting its DNA into the bacterium.
The DNA introduced by the bacteriophage is lethal to bacteria, since the bacterial molecular machinery that converts DNA into proteins cannot differentiate between the bacterium’s own DNA and that of the bacteriophage.
As a result, once the bacteriophage’s DNA interacts with these molecular systems, the bacterium starts producing the components needed to assemble new bacteriophages.
This process continues until the bacterium becomes so overwhelmed with bacteriophage components that it bursts, releasing new bacteriophages.
Recruited to the rescue
However, this can be averted if ZorC and ZorD are recruited in time. They have a critical role by binding to the ZorAB complex. Together, they degrade the DNA introduced by the bacteriophage, effectively neutralising the threat.
ZorD carries out this function, and ZorC appears to have a crucial role in anchoring ZorD to the ZorAB complex and ensuring that it is activated.
“This mechanism prevents these proteins from degrading the bacterium’s own DNA, which otherwise freely floats within the cell. For several years, we have known that Zorya protects bacteria against bacteriophages, but now we understand how it operates,” says Nicholas Taylor.
He further notes that Zorya enables the bacteria to survive. Many other immunity mechanisms defending against bacteriophage attacks result in the bacteria sacrificing themselves (apoptosis) to prevent the infection from spreading.
In addition, this immunity mechanism is effective against numerous types of bacteriophages.
“This study represents a major step forward in understanding bacterial immunity mechanisms. Future research will likely delve deeper into the molecular details of Zorya and investigate its potential applications in fields such as medicine and biotechnology,” concludes Nicholas Taylor.
