Newly described antiviral defense system in bacteria breaks down infections by chemically modifying the mRNA

Like humans and other complex multicellular organisms, single-celled bacteria can get sick and fight viral infections. A bacterial virus is caused by a bacteriophage, or simply phage, which is one of the most widespread life forms on Earth. Phages and bacteria are in a constant battle. The virus tries to bypass the bacteria's defenses, and the bacteria try to find new ways to protect themselves.

These anti-phage defense systems are carefully controlled and judiciously managed – they are dormant but always ready to attack.

Recently published open access research in Nature from the Laub Lab in the Biology Department at MIT has characterized an anti-phage defense system in bacteria, CmdTAC. CmdTAC prevents viral infection by altering the single-stranded genetic code used to produce proteins called messenger RNA.

This defense system detects a phage infection at a stage where the viral phage has already hijacked the host's machinery for its own purposes. Faced with annihilation, the unfortunate bacterium activates a defense system that stops translation, prevents the formation of new proteins and aborts the infection – but dooms itself in the process.

“When bacteria are in a group, they resemble a multicellular organism that is not connected to each other. It is an evolutionarily advantageous strategy for a cell to kill itself to save another identical cell,” says Christopher Vassallo, postdoctoral researcher and co-author of the study. “You could say it’s like self-sacrifice: one cell dies to protect the other cells.”

The enzyme responsible for changing mRNA is called ADP-ribosyltransferase. Researchers have characterized hundreds of these enzymes – although some are known to target DNA or RNA, all but a handful are known to target proteins. This is the first time these enzymes have targeted mRNA within cells.

Expanding the understanding of anti-phage defense

Co-first author and graduate student Christopher Doering notes that only in the last decade have researchers begun to appreciate the breadth of diversity and complexity of anti-phage defense systems. For example, CRISPR gene editing, a technique used in everything from medicine to agriculture, is based on research into the bacterial anti-phage defense system CRISPR-Cas9.

CmdTAC is a subset of a widespread anti-phage defense mechanism called the toxin-antitoxin system. A TA system is just that: a toxin capable of killing or altering the cell's processes, rendered inert by an associated antitoxin.

Although these TA systems can be identified – when the toxin is expressed alone, it kills the cell or inhibits its growth; When the toxin and antitoxin are co-expressed, the toxin is neutralized – characterizing the cascade of circumstances that activates these systems requires extensive effort. However, in recent years, many TA systems have been shown to serve as anti-phage defenses.

To understand a viral defense system, two general questions must be answered: How do bacteria recognize an infection and how do they respond?

Detect infection

CmdTAC is a TA system with an additional element, and the three components generally exist in a stable complex: the toxic CmdT, the antitoxin CmdA, and an additional component called the chaperone, CmdC.

When the phage's protective capsid protein is present, CmdC dissociates from CmdT and CmdA and instead interacts with the phage capsid protein. In the model outlined in the work, the chaperone CmdC is therefore the system's sensor, responsible for detecting when an infection occurs. Structural proteins such as the capsid, which protects the phage genome, are a common trigger because they are abundant and essential to the phage.

By uncoupling CmdC, the neutralizing antitoxin CmdA is degraded, thereby releasing the toxin CmdT, which can exert its lethal effect.

Toxicity on the loose

Guided by computational tools, the researchers knew that CmdT was likely an ADP-ribosyltransferase due to its similarity to other enzymes. As the name suggests, the enzyme transfers an ADP-ribose to its target.

To determine whether CmdT interacted with specific sequences or positions, they tested a mixture of short sequences of single-stranded RNA. RNA has four bases: A, U, G and C, and there is evidence that the enzyme recognizes GA sequences.

CmdT modification of GA sequences in mRNA blocks their translation. Stopping the production of new proteins aborts the infection and prevents the phage from spreading beyond the host and infecting other bacteria.

“Not only is it a new type of bacterial immune system, but the enzyme involved also does something that has never been seen before: ADP-ribsolation of mRNA,” says Vassallo.

Although the paper describes the basics of the anti-phage defense system, it is unclear how CmdC interacts with the capsid protein and how chemical modification of GA sequences prevents translation.

Beyond bacteria

More broadly, research into anti-phage defenses is consistent with the Laub lab's overall goal of understanding how bacteria function and evolve, but these findings could have broader implications beyond bacteria.

Senior author Michael Laub, Salvador E. Luria Professor and researcher at the Howard Hughes Medical Institute, says ADP-ribosyltransferase has homologues in eukaryotes, including human cells. They are not well studied and are not one of the Laub lab's research subjects, but they are known to be upregulated in response to viral infection.

“There are so many different – ​​and cool – mechanisms that organisms use to defend themselves against viral infections,” says Laub. “The idea that there might be some similarity between the way bacteria and humans defend themselves is a tantalizing possibility.”

This story is republished with permission from MIT News (web.mit.edu/newsoffice/), a popular website that reports news about MIT research, innovation and teaching.