Proteomics is the study of cellular proteins and their functions. It’s a relatively new science but a productive one, yielding insights into maladies like tumors, cancers, and renal disease. Proteomic analysis is becoming an essential tool in the study of human health.
Now, a team of scientists has extended proteomics to the study of ocean health.
In a recent paper published in Science, the team described how they identified and measured proteins in the ocean to determine the responses of single-celled organisms to their environment. Proteomics is bringing a new perspective to the understanding of ocean ecosystems.
Proteomics of the Pacific
The proteome is the entire set of proteins that an organism produces or acts upon. Unlike a genome, a proteome can change with time and with the conditions that an organism encounters. Varying factors like health or disease state, type and stage of tissue development, and the presence of drugs can alter protein types and concentrations. Understanding organism responses, therefore, requires the proteome scientist to evaluate protein at different times and under different conditions.
The new study demonstrated that proteomic techniques can be applied to ocean environments to identify the presence and quantities of proteins in the ocean.
The science team planned a data collection route along a 2,500 mile path between Hawaii and Samoa. The route was designed to ensure water sampling from regions with different concentrations of marine nutrients such as iron, phosphorus, and nitrogen.
The scientists examined their samples back in the lab, focusing on proteins produced by the abundant Prochlorococcus, bacteria that rely on photosynthesis to generate at least half of all atmospheric oxygen.
“Just as you’d analyze proteins in a blood test to get information on what’s happening inside your body, proteomics gives us a new way to learn what’s happening in ocean ecosystems, especially under multiple stresses and over large regions,” said Saito.
Their results showed what factors were controlling metabolism and growth in Prochlorococcus and how the microbes responded to different conditions in different parts of the ocean.
In waters with low nitrogen concentrations, for example, the scientists found high levels of a protein that transports urea, a particular form of nitrogen. In areas where iron was deficient, they found an abundance of proteins that helped to transport that scarce nutrient. In areas where the microbes were starved for both nutrients, protein concentrations revealed which processes the microbes used to compensate for multiple environmental stresses.
The study demonstrated that protein measurements can be used to identify and map ecosystem changes in the ocean.
“Instead of just measuring what species are in the ocean, now we can look inside those organisms and see what biochemical reactions they’re performing in the face of various ocean conditions,” said Saito.
Already, however, the science team is looking to more extensive studies with more comprehensive returns.
“We measured about 20 biomarkers that indicate metabolism,” said Saito. “But we can scale up that capacity to measure many more simultaneously.”
The team is also planning to augment their investigations with the use of ocean-going robots. The goal is to build a proteomic data resource that can diagnose the inner workings of ocean ecosystems and help to understand how they respond to global change.
“It’s a potentially powerful tool we can use to reveal the inner biochemical workings of organisms in ocean ecosystems–and to start diagnosing how the oceans are responding to pollution, climate change and other shifts.” Ambitious agenda.
Proteomic methods used to diagnose human health are leading to better medical interventions. The recent study in Science shows that proteomics can also diagnose essential features of ocean health. Whether the insights of proteomics will also lead to better ocean interventions is, however, still an open question.