Monterey Bay Aquarium Research Institute
Celebrating our 20th Anniversary

Proteorhodopsin discovery—A new photopigment in oceanic bacteria

Celebrating 20 years

One of the exciting breakthroughs at MBARI in 2000 was the discovery of a new light-absorbing pigment in oceanic bacteria. This finding demonstrated the possibility that a whole new class of microorganisms was capable of harnessing sunlight in the ocean

"We've uniquely applied new advances in genomic technology to our studies of oceanic microbes and it has led us to unexpected results," said lead researcher Ed DeLong. "We now have the techniques to address some important ecological questions about the role of these microorganisms in the ocean."

DeLong focuses his research on oceanic picoplankton—microscopic bacteria that are 0.2 to 2 micrometers in diameter. These microbes are challenging to study because many of them cannot be grown in the laboratory. However, by analyzing their genetic material, biologists have started to identify prominent groups of microbes in the ocean, as well as to map their distribution and abundance.

Proteorhodopsin illustration
Model of the energy generating mechanism in marine bacteria. When sunlight strikes a rhodopsin molecule (1), it changes its configuration such that a proton is expelled from the cell (2). The chemical potential causes the proton to flow back into the cell (3), thus generating energy (4) in the form of adenosine triphosphate (5).

Even after identifying many new marine microbes, scientists couldn’t tell how they obtained food, or what roles they played in marine ecosystems. DeLong and postdoctoral associate Oded Béjà devised new methods to analyze the genomes of the uncultivated microbes, allowing the researchers to identify the functions of specific genes, and to predict their ecological significance.

For their research DeLong’s team collected oceanic bacteria from Monterey Bay. The MBARI researchers isolated large genome fragments and, with colleagues at Amersham Pharmacia Biotech (Sunnyvale, CA), determined some of the sequences of genes that were common in the picoplankton DNA. These sequences were assembled and analyzed at MBARI to reveal the  hypothetical functions of those genes.

This analysis revealed a new pigment never before found in bacteria. This pigment was similar to a light-absorbing pigment called rhodopsin that is associated with vision in animals. The bacterial gene sequence suggested that this new photopigment might enable the oceanic microbes to obtain energy for from sunlight.

MBARI researchers used recombinant DNA technology to express and test the function of the gene that coded for the new pigment. As predicted, when exposed to light, the photopigment moved ions across the bacteria’s cell membrane, showing that it could generate energy by absorbing light. This process is much simpler than the process of photosynthesis used by plants and algae.

Because the new photopigment was relatively easy to manipulate and mass produce, DeLong’s team applied for and received a patent on using this pigment (which they named proteorhodopsin) to convert light energy into useful forms of biochemical or electric energy.

DeLong and his colleagues were excited by the many implications of this research, especially the fact that they had demonstrated how useful genomics could be in characterizing naturally-occurring but unculturable microbes. Their research suggested that rhodopsin-like photopigments were more taxonomically widespread than previously thought, and revealed a new type of light-driven energy generation in ocean microbes.

MBARI contributors to proteorhodopsin project: Oded Béjà, Lynne Christianson, Ed DeLong, Chris Preston, Marcelino Suzuki, Jose de la Torre


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