Salmon 'molecular switches' open a new way to tackle SRS
Chilean scientists suggest that transposable elements play a key role in the immune response and could become early biomarkers of infection and targets for genetic selection.
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A paradigm shift in the understanding of piscirickettsiosis, also known as salmonid rickettsial septicaemia (SRS), is beginning to take shape in salmon farming. This is the view of Dr Francisca Madrid, a researcher at the University of Santiago, Chile, and one of the authors of a newly published study whose findings point to a key player in the salmon immune response that has been underestimated until now: transposable elements.
According to Madrid, the research stems from the need to rethink the scientific approach to one of the main bacterial diseases affecting salmon in Chile. It is also increasingly prevalent in other salmon producing regions.
“For years we focused almost exclusively on protein-coding genes, but that leaves out more than half of the salmon genome. We posed a disruptive hypothesis: what if the key to mitigating piscirickettsiosis lies not in that small percentage of traditional genes, but in the 54% of the genome that classical science had historically simplistically categorised as 'junk DNA' or evolutionary remnants? We wanted to be the first to decipher the dynamics of this hidden 'mobilome' in the face of a real bacterial challenge,” the expert explains.
From 'junk DNA' to key regulators
Transposable elements (or transposons) are dynamic DNA sequences capable of being activated and moving within the genome. Far from being inert material, the study describes them as true “emergency molecular switches”.
“When salmon face a critical threat, such as the entry of a bacterium, these elements are massively 'switched on' to activate, coordinate, and amplify the salmon's alarms and immune defences,” the researcher explains.
The study identified the activation of more than 4,500 transposable elements during infection, in a highly organised pattern. In particular, it highlights specific families such as TcMar-like DNA transposons, whose activation is synchronised with key genes involved in metabolism and immunity.
It’s not just about selecting fish that have the defence gene, but about ensuring they have the optimal activation mechanism to turn it on in time.
“We identified an almost perfect synchronisation (positive co-expression) between these elements and the most important genes responsible for the salmon's metabolic and immune processes. Furthermore, we discovered that the activated regions are replete with binding sites for immune transcription factors. This tells us that they act as true command platforms that orchestrate and enhance the biological response against the pathogen,” emphasises Madrid.
One of the most relevant findings is that 84% of the transposable elements increase their activity in infected fish, generating a clear “molecular signature” that distinguishes healthy individuals from sick ones.
This behaviour opens the door to practical applications in the field. “These elements are extremely sensitive to the first signs of cellular stress, so they could be activated before clinical symptoms appear. This would allow for the development of much more accurate early diagnostic tools,” says the researcher from USACh.
New frontier in genetic improvement
The potential impact also extends to genetic selection programmes. Currently, the industry focuses on conventional genes, but this study proposes broadening the focus to include the mechanisms that regulate their activation.
“It’s not just about selecting fish that have the defence gene, but about ensuring they have the optimal activation mechanism to turn it on in time. This introduces a completely new criterion of immunometabolic resilience for the industry,” explains Madrid.
According to the researcher, incorporating these elements into breeding programmes would allow the selection of fish with more efficient immune responses to SRS.
The next steps aim to validate these findings under production conditions and advance their practical application. Among the most promising avenues is the development of functional diets or additives capable of modulating the activation of these elements at the epigenetic level.
“The potential for developing new commercial and on-the-ground health management strategies is immense. One example is the development of functional diets or additives specifically designed to modulate chromatin and optimise the activation of these transposable elements,” Madrid concludes.
