Deep purple functional metagenomics

Abundant, novel rhodopsins detected in microbes and viruses

Go to the profile of Oded Béjà
Jun 20, 2018
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The paper in Nature is here:


Currently, only two types of phototrophic strategies are known to exist on Earth, chlorophyll-based (oxygenic and anoxygenic photosynthesis) and retinal-based (rhodopsin phototrophy). In an attempt to find new forms of phototrophy, we recently developed a functional metagenomics screen to enable the detection of environmental fosmid clones (in Escherichia coli) that produce proton gradients upon illumination. Using this functional screen with a marine library, we were able to find some already known proteorhodopsins, and as expected most came from Proteobacteria (Pushkarev and Béjà, 2016). 

Leading author Alina Pushkarev concentrating water from Lake Kinneret (September 2015) in order to construct the fosmid library used to detect the first heliorhodopsin

The second library screened was from a freshwater lake (Lake Kinneret / the Sea of Galilee). This time we were also scoring positive clones by color. One 96-well-plate, #48, gave a single clone with a distinct deep purple color (see insight in the figure below). This color was observed only when retinal was added, so we were expecting a known microbial rhodopsin. To our surprise, and actually disbelief at first, no rhodopsin gene was observed in the sequence obtained from this clone (a 32 kb insert). As we were flying blind, Tnmutagenesis screening was used to detect the gene responsible for the purple color. This gene turned out to code for a 7 trans-membrane helices (TM) protein with a lysine in the 7th TM and inverted membrane topology compared to any known rhodopsins. In addition, this protein had less than 15% identity to known microbial rhodopsins, the reason it was not detected in BLAST searches as a rhodopsin. The detection of this new protein enabled us to find a whole portfolio of novel rhodopsins, heliorhodopsins, in archaea, bacteria, algae and even in viruses (Pushkarev, Inoue, et al. 2018).

We are now in the process of sequencing and analyzing a dozen more colored clones from the same library. 

Screening fosmid libraries in our robotic setup. Insight- E. coli expressing a heliorhodopsin with (right) and without (left) retinal

The paper in Nature is here:

Go to the profile of Oded Béjà

Oded Béjà

Professor, Biology, Technion


Go to the profile of Ricardo Cavicchioli
Ricardo Cavicchioli about 1 month ago

Definitely worthy of 'smoke on the water'!