A team of researchers from the Laboratory of Genomics and Genetics of Biological Interactions (LG²IB) at the University of Chile and INTA, led by Rodrigo Pulgar, PhD, has successfully identified and characterized for the first time the complete kinome of Atlantic salmon (Salmo salar). The kinome includes the total set of protein kinases encoded in an organism's genome. These enzymes are crucial, as they phosphorylate other proteins to amplify and transduce cellular signals, thus enabling the response to environmental triggers.
The study, “Genome-wide prediction and gene expression profiling of the Atlantic Salmon Kinome,” (https://doi.org/10.1016/j.aquaculture.2025.743033) published in the journal Aquaculture, was conducted by doctoral students Francisca Vera and Felipe Galdames, under the guidance of PhDs Christian Hödar and Rodrigo Pulgar. Using a predictive bioinformatics strategy at the genomic and proteomic scale, the team identified 1,157 typical eukaryotic kinases (ePKs) and 137 atypical kinases (aPKs), revealing that this kinome is the largest described to date in any animal species, including humans. The researchers also performed a global gene expression analysis using public RNA-Seq data, which revealed that each salmon tissue has a specific transcriptional profile for these proteins.
The study focused on the expression patterns of kinases in muscle, due the economic relevance of muscle development in salmon farming. Interestingly, the most highly expressed kinases in this tissue are involved in key processes such as muscle differentiation and calcium signaling, suggesting a fundamental role in regulating skeletal muscle growth. The work also demonstrated that, despite the evolutionary divergence between salmon and humans, a large number of these kinases are highly conserved between the two species. This similarity opens the possibility for innovative translational applications, such as the use of kinase inhibitor drugs already approved for humans in studies with salmon. It also enables the use of advanced tools such as phosphoproteomics and CRISPR/Cas9 gene editing to investigate the role of these enzymes in muscle development in both salmon and humans. Thus, this research not only advances basic knowledge of fish biology, but also offers significant applied potential for aquaculture and biomedicine to optimize muscle development and growth.
This work is the outcome of a productive collaboration that integrates human capital formation and competitive funding. It is the primary objective of the FONDECYT Regular Project led by Prof. Rodrigo Pulgar, entitled “Disclosing the phosphorylation landscape of the host-pathogen interaction between Piscirickettsia salmonis and Atlantic salmon.” It was also part of Francisca Vera's doctoral research unit in the Doctorate Program in Silvoagricultural and Veterinary Sciences at the University of Chile, and was Felipe Galdames' thesis seminar to obtain his degree in Molecular Biotechnology Engineering, under the joint supervision of professors Christian Hödar and Rodrigo Pulgar.
Here, Professor Rodrigo Pulgar discusses some important aspects of this work:
"While the complete mapping of the salmon kinome (the set of all its kinases) is a fundamental milestone in itself, there are two most significant findings. First, we discovered that salmon have the largest kinome reported in the animal kingdom, even larger than that of humans. Second, despite this difference in size, we found that these enzymes are highly conserved at the evolutionary level between the two species, which opens up the possibility of using what is known in humans to apply it to salmon, and in turn using salmon as a model for biomedical study," he explains.
– Why is it important that salmon has the largest reported kinome? Why hadn’t it been studied before?
-Their size can be explained by a complete duplication of their genome that occurred about 100 million years ago. However, the crucial thing is not only that they have more genes, but that they have retained such a large number of kinases. This suggests that this genetic redundancy gives them a biological advantage: a broader repertoire of cellular responses to adapt to changes in their environment, such as variations in temperature or pathogenic challenges.
As for why this had not been studied before, I believe there are two main reasons. First, despite its commercial importance, salmon is not a traditional model species in molecular biology, which presents greater technical challenges. Second, the high-quality reference genome necessary for such a study has only been available for the last four years. Our research was made possible by this essential resource.
– How could these findings help improve aquaculture salmon production?
-These findings pave the way for direct biotechnological applications. By knowing the identity and expression profile of kinases associated with key processes such as muscle growth, disease resistance, and stress adaptation, we can design strategies to modulate them.
This can be achieved through nutritional, pharmacological, or genetic tools to, for example:
- Enhance muscle development and improve production efficiency.
- Increase resistance to pathogens such as Piscirickettsia salmonis.
- Improve adaptation to changing climatic conditions.
– What's next step in research after characterizing the kinome?
-The next step is functional validation: figuring out the specific role of specific kinases in the phenotypes we're interested in. The big advantage we have is evolutionary conservation with humans. This lets us use kinase inhibitor drugs that are already approved in human medicine to test their effect in salmon systems. Besides, we have already successfully implemented CRISPR/Cas9 technology in salmon cells to edit these genes. We are currently combining these tools (drugs and gene editing) with phosphoproteomics analysis to study the role of selected kinases in the response to intracellular infections and to unravel the signaling pathways they control.
Reference: F. Vera-Tamargo, F. Galdames-Contreras, C. Hödar, R. Pulgar, Genome-wide prediction and gene expression profiling of the Atlantic Salmon Kinome, Aquaculture, Volume 611, 2026, 743033, ISSN 0044-8486, https://doi.org/10.1016/j.aquaculture.2025.743033.
Keywords: Atlantic salmon; Protein kinases; Kinome;Transcriptional expression; Muscle development
