טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentSabehi Gazalah
SubjectMicrobial Genomics and Ecological Diversity of
Proteorhodopsin in the Mediterranean Sea, Red Sea
and Sargasso Sea
DepartmentDepartment of Biology
Supervisor Professor Oded Beja


Abstract

Proteorhodopsin (PR) proteins are bacterial retinal-binding membrane pigments that function as light driven-proton pumps and mediate a new type of phototrophy in the ocean’s photic zone. At this work, we identified different PR variants from the Red Sea and Mediterranean Sea. These PRs formed new and distinctive groups which could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous PRs that are distributed amongst divergent planktonic microbial taxa. Furthermore, we identify the diversity and depth distribution of `blue absorbing` PRs (BPRs) and `green absorbing` PRs (GPRs) in samples collected from the Sargasso Sea and the Mediterranean Sea in stratified and mixed conditions. No spectral tuning was observed with Sargasso Sea PRs and all diverse PRs collected from different depths absorb in blue. In the Mediterranean Sea, on the other hand, both BPRs and GPRs were retrieved from surface waters while more BPRs were detected in deeper samples. Spectral tuning was observed in different PR families from both the alpha- and gammaproteobacteria as well as in other microbial groups. Differences in PR compositions were also observed within and between the stations sampled. In an effort to characterize uncultured PR-exploiting bacteria, large-insert bacterial artificial chromosome (BAC) libraries from the Mediterranean Sea and Red Sea were constructed and analyzed. PR-carrying bacteria were found to be an important component of the microbial communities in the Mediterranean Sea and the Red Sea, at least 13% of the bacteria in the photic zone were found to possess PR genes. The PR genes were distributed among divergent marine bacterial taxa, including alpha- and gammaproteobacteria, SAR11 and SAR86 groups. GPRs and BPRs were found in the libraries. We confirmed the function of five phylogenetically diverse PR genes. These PRs have fast photocycles typical of retinylidene transporters and encode functional light-driven proton pumps. The BPRs have a fast photocycle and adapted to high light intensities in contrast to BPRs previously isolated from deep waters. At this work we identified the first bacterial dioxygenase involves in retinal biosynthesis. Thus, bacteria possessing PR apoproteins also carry the ability to synthesize the retinal chromophore. Furthermore, we revealed previously unrecognized links between PR genes and different and partly unexpected metabolic traits in some uncultured PR-carrying bacteria. Some of these PR-carrying bacteria are apparently energy scavengers, ideally adapted to oligotrophic marine surface waters by exploiting not only light but possibly also some reduced organic sulfur compounds for energy generation.