A new research in Zagazig University offers insight into the dynamics of phage genomes and some phage-host interactions and regulation, hoping to use phages to combat a broadly-spread lethal and persistent strain of land pathogenic bacteria.
The research wants to use bacteriophages – found in soil, air, water and everywhere around us – to decrease the virulence of this land pathogen, known as Ralstonia solanacearum, which typically infects a variety of crops, devastating them.
Bacteriophages are already cropping up as possible alternatives to antibiotics due to rising antibiotic resistance.
What are bacteriophages?
More colloquially known as phages, these viral organisms that infect bacteria are essential to life. Perhaps the best description of how they function comes from Microbial ecologist Forest Rohwer. ”[The phages] float about, awaiting a microbial encounter, then attach themselves to their preferred targets using a remarkable array of equipment—arms like grappling hooks, tails like hypodermic needles, fibres like teeth—each of which is perfectly adapted to bind to, and then sneak genetic material through, the bacterial membrane,” he tells The New Yorker. “Once inside the cell, some phages replicate at speed, destroying the host by bursting out of it, like a fungus dispersing its spores. Others are parasitic, integrating their DNA with that of their host. Sometimes they even provide it a benefit of some kind.”
Two lines diverged in a lab
It is this benefit that Ahmed Askora, the researcher from Zagazig, speaks of when he tells me that he is trying to turn a phage from a killer to a friend.
Studying two lines of phage strains, Askora says he has found that one line of the bacteriophages harbours what he calls a “repressor” gene, in other words, a phage-encoded regulator that somehow affects the expression of host genes involved in bacterium Ralstonia’s virulence. In short, it suppresses the “toxic gene” when the DNA of the parasite, the phage, and its host, the bacteria, are integrated.
And that’s a first, he says.
But first, let’s talk Ralstonia
The notorious Ralstonia is a sort of grassroots predator; it invades plants through roots or vascular bundles and replicates inside, with the wilting working its way up. It can colonise an entire water system, contaminating it and eventually causing the death of said plants.
The bacterial wilt, caused by Ralstonia, affects around 200 plant species over the world.
According to Askora, the US spends heavily to control the disease using pesticides, antibiotics and disinfectants, and the virulence also affects crops in the Middle East, including principle crops like potatoes, eggplants and tomatoes. Egypt in particular is in crisis, he says, and is short on resources to fight the disease.
But it just so happens that Egypt is the only country in the Arab world, Askora claims, who’s studying the bacteriophage genomes and their effect on the virulence of Ralstonia in an attempt to nip its offensive in the bud.
… A sneaky invader
Ralstonia‘s invasion strategies, on the molecular level, have been scrutinised before. A study published this month in Cell showed that Ralstonia uses a decoy in which it injects specific pathogen molecules or “effectors” into host cells to block its immune defenses.
Among these effectors is a type of protein that blocks transcription factors responsible for regulating the expression of defense-related genes, neutralising them, then allowing the invasion to “clean up.”
Some plant species have improved their arsenal against this, but if anything, this recent research shows that new immune receptors in the plant cells need to be developed to better intercept virulence factors of pathogens, such as Ralstonia, which cause wide scale agricultural losses.
But there are many ways to fight the same enemy
Phages are widely spread and exist in different strains of pathogenic bacteria. They might evolve rapidly and play roles in the introduction of new genes into their hosts.
Askora wants to use this dynamic to manipulate the pathogenic bacteria itself – in simpler terms, put it in therapy, where the plant’s bacteria, with the help of its parasite’s DNA, would be able to repress its own poisonous genes.
Askora’s experiment involves isolating specific filamentous bacteriophages from the soil, where the affected plants live. The bacteriophages – an obligate parasite that needs its host in order to survive and complete its lifecycle – has to be tested against the pathogenic bacteria in vitro, and then added to said bacteria to see if it can kill it.
This is to begin with.
Most bacteriophages include some virulent genes; when the bacteriophage infects the bacteria, the phage transfers this gene to the bacteria through a process called “integration,” where the genomic DNA of the phage is integrated into the genomic DNA of the bacteria.
The phage changes the transcription of the bacterial genes, resulting in genes that are toxic when activated.
But Askora found a specific gene in that second line of phages that does the opposite of this; it causes loss of virulence in Ralstonia – “the first discovery of its kind in the world,” he boasts repeatedly.
“Phages sometimes help host bacteria infect plants by enhancing bacterial virulence, and they sometimes interrupt bacterial infection of plants by repressing host genes involved in virulence,” reads the study published last week in the open-source journal Frontiers of Genetics. “Such contradictory effects of these phages largely depend on the phage state.”
The research is done collaboratively with Japanese researcher Takashi Yamada whose lab has the specific technology that can isolate and test the phages, something that’s not available in Zagazig University.
It’s not final, future trials should reveal more
“We need more and more experiments to confirm this phenomenon,” says Askora as an afterthought, “There are many questions; is it a stable phenomenon? Do we need to modify some genes? The idea is to extract the repressor gene, amplify this gene in the phage, then we will clone it or insert it into a specific vector then transform this vector to a highly virulent bacteria, then see what happens when we do this.”
Askora hopes that with further trials he and his research partner can develop a global application of such repressor. “We want to make it wide scale,” he says.