Many deep-sea species have never been seen or collected before. Nevertheless, we can learn a great deal by studying them with next-generation laboratory equipment and methods like optical oxygen microsensors, high-pressure instruments, genome-scale sequencing, protein purification, and gene cloning and expression. For the DEEPC project, MBARI Scientist Steve Haddock and collaborator Erik Thuesen, of The Evergreen State College, and their teams, are applying these tools to learn how ctenophores (comb jellies) adapt to a broad range of temperatures and pressures.

Some ctenophores live in the warm temperatures and lower pressures of the shallow waters, while others live in the cold temperatures and high pressures of the deep sea. Proteins tend to be sensitive to extreme temperature and pressure, so our DEEPC project asks: How do the proteins in both deep- and shallow-dwelling species function efficiently under such dramatically different conditions?

Years ago, when biologists wanted to characterize a particular protein, they might need to collect thousands of individual animals to obtain enough material for experiments. Now, by analyzing an animal’s “transcriptome.” we can learn a lot about the capabilities of a species using just a small amount of material from a single organism.

The transcriptome is the portion of the genome that an organism is using as blueprints to make proteins. Each gene in a transcriptome, then, reveals the sequence of a protein. Using computational methods, we can compare these protein sequences across a variety of organisms.

For our DEEPC project, graduate students Jacob Winnikoff and Tiffany Bachtel are using transcriptomes and biochemical experiments to compare the metabolic enzymes of deep and shallow ctenophores.

Combined with traditional biochemistry, transcriptomes let them detect subtle differences in the structure of these essential proteins that affect their temperature and pressure tolerance.

Long after the DEEPC project is complete, the transcriptomes themselves will remain useful. We can revisit the data anytime, for example, to compare photoproteins, which are responsible for making bioluminescence. We can also compare sequences of multiple proteins simultaneously, to learn about the evolutionary relationships and diversity of many species. By applying new tools to old questions, we can unlock more of the mysteries of life in the deep ocean.