Microorganisms like bacteria and fungi can evade treatment by acquiring mutations within the genes targeted by antibiotics or antifungal drugs. These permanent mutations were once regarded as the only method for drug-resistant strains to evolve. Now a new study has shown that microorganisms can use a brief silencing of drug targets known as epimutations to gain the advantages of drug resistance with no commitment.
Though the new mechanism is discovered inside a fungus called Mucor circinelloides, it is likely to be used by other fungi as well as bacteria, viruses along with other organisms to resist treatment with assorted drugs. The finding appears July 27, 2014, in Nature.
“This mechanism provides the organism more flexibility,” said Joseph Heitman, M.D., Ph.D., senior study author and professor and chair of molecular genetics and microbiology at Duke University Med school. “A classic, Mendelian mutation is a more permanent binding decision, like a traditional marriage. These epimutations are reversible, more similar to moving in together. If conditions change, it is easier to revert towards the way things were.”
The epimutations are so transient, actually, the researchers almost disregarded them. Cecelia Wall, a graduate student in Drs. Heitman and Maria Cardenas’ labs, had been searching for mutations that will make the human fungal pathogen M. circinelloides resistant to the antifungal drug FK506 (also known as tacrolimus). This pathogen causes the rare but lethal fungal infection mucormycosis, an emerging infectious disease that predominantly affects individuals with weakened immune systems.
As is typical for many drug resistance experiments, Wall first grew the pathogen in Petri dishes containing the antifungal drug. She found that the few organisms that survived treatment looked different, being smaller and less diffuse than their parent fungi. Wall then isolated those fungi and sequenced the gene FKBP12 the target of FK506 to look for mutations that would confer drug resistance.
However, she couldn’t detect any mutations in about a third from the isolates. What’s more, Wall discovered that most of the mutants kept “disappearing,” looking less like mutants and much more similar to their parents after she took the drug away.
“This is an illustration of something you might find within the laboratory and merely discard,” said Silvia Calo, Ph.D., lead study author and postdoctoral fellow within the Heitman and Cardenas labs. “You look for mutants in a single gene and when you don’t look for a mutation in certain from the isolates, you decide not to work on those anymore and instead concentrate on others. But we wanted to know what happening.”
The researchers started to wonder whether a phenomenon known as RNA interference or RNAi could be the cause of this unstable drug resistance. RNAi uses items of RNA the chemical cousin of DNA to silence specific genes. Though RNAi doesn’t appear in every organism, they knew it had been active in M. circinelloides due to the pioneering work of the collaborators Rosa Ruiz-Vazquez and Santiago Torres-Martinez, with whom Calo trained at the University of Murcia, Spain.
So Calo sought out the existence of small RNAs a signature of RNAi in the drug resistant isolates. She didn’t find small RNAs within the isolates that contained mutations in FKBP12, but she did find them in those lacking mutations. Importantly, Calo found that these small RNAs only silenced the FKBP12 gene and not every other loci within the genome. The outcomes demonstrate that M. circinelloides can develop drug resistance two various ways, either stably through permanent mutations or transiently through reversible epimutations.
“This plasticity enables an organism to reverse epigenetic mutations when selective pressures are relaxed,” said Calo. “Otherwise, silencing a gene when it doesn’t have to be silenced would be a waste of one’s.”
The researchers think these epimutations might be employed in a number of situations, enabling a living thing to adjust to an unfavorable environment and then adapt again when conditions improve. Though they have only shown epimutations in 2 types of M. circinelloides, they have already been approached by a few other researchers who are interested in investigating similar unstable behavior in other organisms like Aspergillus and Neurospora.
“It could be such as the discovery of other molecular phenomena like introns or microRNAs, where everything began with only an example,” said Heitman. “We believe this discovery may turn out to be generalized rapidly.”
