A multi-drug resistant strain of Staphylococcus aureus (MRSA) has been studied by an international team of researchers, including those from UNSW’s School of Biotechnology & Biomolecular Sciences, who used the promising new tool CLASH to capture hundreds of hitherto unknown mechanisms of gene regulation.
The mRNA of S served as the foundation for the 500 processes discovered by the new technology. These recently discovered mRNAs were regulating other genes in S, despite typically only acting as instructions for manufacturing proteins. Through direct interactions, aureus controls the bacteria’s genetic makeup and tolerance to antibiotics.
These RNAs included one that thickens the bacterial cell wall, a modification that is frequently observed in clinical MRSA strains that are resistant to last-line antibiotics and may help uncover novel targets for antibiotic therapy. Nature Communications has published their work.
“Before our study, only three other mRNAs had been shown to regulate bacterial RNA,” says co-author Associate Professor Jai Tree. “It’s relatively rare. But looking at our CLASH data was the real surprise. We found that in Staphylococcus aureus, there was evidence for 543 regulatory mRNAs interactions. This is a shift from our current understanding of gene regulation in bacteria.”
Due to a lack of techniques for comprehensively collecting RNA interactions, this adaptive system in S. aureus has gone unnoticed. Similar strategies in other pathogenic bacteria depend on the presence of specific proteins; these proteins don’t appear to be active in S. aureus.
The regulatory mRNAs in S. aureus have abandoned the chef and started setting the pace and producing their own dishes if mRNA is like copied pages from a recipe book.
“When a gene (DNA) is transcribed into RNA, a little bit of extra sequence is transcribed from either side like the aglets of a shoelace these are termed the ‘untranslated regions’ or UTRs,” says A/Prof Tree. “It’s these UTRs of mRNAs in S. aureus that are performing a regulatory role.
“And where a typical UTR is 40 to 50 bases long, we found that around one-third of the UTRs in S. aureus are 100 bases long which is long. This likely adds an entirely new layer of gene regulation.”
Before our study, only three other mRNAs had been shown to regulate bacterial RNA. It’s relatively rare. But looking at our CLASH data was the real surprise. We found that in Staphylococcus aureus, there was evidence for 543 regulatory mRNAs interactions. This is a shift from our current understanding of gene regulation in bacteria.
Associate Professor Jai Tree
The specific strain of S. aureus employed in this investigation was isolated from a patient with MRSA septicemia who received 42 days of treatment with vancomycin, our “last-line of defense” and most potent antibiotic.
The researchers used CLASH to analyze this strain in order to determine how they were evolving vancomycin tolerance because S. aureus do not naturally acquire vancmycin tolerance from other S. aureus but rather through a series of mutations.
“One of the mRNA UTRs we discovered was a regulatory RNA that promotes an enzyme involved in cell wall thickening. It’s this thickening that is consistent with vancomycin-tolerant S. aureus,” says A/Prof Tree.
“We found evidence of over 500 mRNA-mRNA interactions occuring in S. aureus information uncovered by CLASH that allows us to ascribe functions to many regulatory RNAs in S. aureus often for the first time.”
“The ‘superbug’, multi-drug resistant Staphylococcus aureus, is a major problem in both healthcare and community settings,” says A/Prof. Tree. “Treatment options for MRSA septicaemia infections that enter the blood are limited to last-line antibiotics, and the treatment of choice is vancomycin.
“Vancomycin is an antibiotic that blocks assembly of a new cell wall in S. aureus. If the bacterium can’t make a new cell wall during division, it explodes. Those S. aureus tolerant to vancomycin have thicker cell walls, likely limiting antibiotic at the site of cell wall synthesis.”
In order to protect our aggressive, “re-sensitizing” resistant S.aureus, one of the mechanisms of vancomycin tolerance in S.aureus was revealed. again to vancomycin for aureus.
“There has been renewed interest in using ‘antisense RNA’ that can be delivered into the bacterial cell, penetrating the cell wall and binding RNAs within the cell. In this way, we might be able to co-administer an antisense RNA with vancomycin the antisense RNA would make MRSA sensitive and the vancomycin would kill the cell,” says A/Prof Tree.
While several mRNAs in S. aureus have been assigned roles, much work has to be done, especially considering the variety of processes behind S. aureus’s tolerance to vancomycin.
“The next steps are to understand if the regulatory RNA we’ve already isolated is required for a broad spectrum of other, clinical strains of vancomycin-tolerant S. aureus. These are genetically heterogenous isolates and one of the difficulties has been the multitude of methods of becoming vancomycin tolerant.”
“So we would like to understand if targeting the regulatory RNA would be a useful approach for many different vancomycin tolerant strains. Although we don’t know exactly what all the mRNAs are doing, our next step is to identify the really important ones.”
