The back up plan

Rhodopsin is a biological pigment found within the retina of animal eyes, and its extreme sensitivity to light enables a level of vision in near-darkness. It has been discovered in a variety of unsuspected places, such as the depths of the Atlantic Ocean, hidden within the naked retina of Rimicaris exoculata, the 'eyeless rift shrimp'. The pigments found within this organism had extremely similar properties to the Rhodopsin within our own eyes, highlighting how rhodopsin-like pigments can occur in areas almost entirely void of light. Photoproteins similar to rhodopsin have also been found within a diversity of marine bacteria, where integral membrane proteins carry out the role of photon-powered proton pumps, facilitating phototrophy  independent of oxygen. Rhodopsin like pigments are found throughout a vast diversity of organisms on our planet, but how did they work their way into the microbial genomes, and are they of any use?

With marine microbes producing an estimated 50% of the earths primary productivity, it seems logical for their to be a 'back up plan' , enabling phototrophy in hypoxic conditions . The discovery of proteorhodopsin came about through metagenomics within marine bacteria. Proteorhodopsins are a family of 50 photoactive retinylidene proteins which use retinal as a chromophore for light-mediated respiration. They were  originally discovered within the Archaean Halo bacterium, and were thought to be unique only to them. Metagenomics however showed that marine microbes also contained a concoction of proteorhodopsins, and thus continued to unravel the story of how they became enscripted within marine microbial genomes.This ultimately lead scientists to the logical conclusion that the spread of these pigments was due to lateral gene transfer. McCanne & Delong(2006) showed how only 6 genes needed to be transferred to enable the successful harvest of protons. With only 6 genes being needed to harvest biochemical energy from light, it was confirmation that lateral gene transfer was the enabling device for marine microbial proteorhodopsins.

Up to 13% of marine microbes inhabiting the photic zone are thought to contain proteorhodopsin, and research lead by Beja et al (2001) indicates that proteorhodopsin levels are adapted to particular ecotypes, with bacteria in surface waters absorbing light maximally at 527 nm (green light), and deeper waters (75m) having a maximum absorption of 490 nm (blue light) It is therefore undisputed now that proteorhodopsins are found within marine microbes, and that they are widely spread throughout the microbial inhabitants of the photic zone via LGT.

However, it is still unknown whether there is a physiological benefit to the acquisition of these light absorbing pigments. In an experiment led by Beju et al (2000) using bioinformatic tools, the gene responsible for encoding the transmembrane domains critically associated with the functioning of rhodopsin, was cloned in Escherichia coli. It was expressed within the E.coli genome as an active protein which successfully  acted as a proton pump. Beju et al (2001) and McCarren & Delong(2007) both highlight how the correct transferal of genes can enable phototrophy via a light-driven photon pump. It wasn't until 2010, when Consarnau et al showed how the presence of proteorhodopsin lead to an increased survival of vibrio strain when starved in sea water exposed to light, rather than starvation in darkness.Yet, there was no difference between the survival of the proteorhodopsin deficient strain, suggesting that more experiments are needed to fathom why so many marine  microbes contain proteorhodopsin, if it serves no advantage.  Although the findings of Consarnou's experiment fail to explain why so many marine microbes contain proteorhodopsin, it is widely held that the ability to harvest biochemical energy acts as a evolutionary back up plan, a so called 'solar recharge'. As our oceans are heterotrophic and patchy, marine microbes containing these light harvesting genes may be at an advantage when in low nutrient waters, or when normal oxidative respiration is inhibited, as they can fall back on their 'solar generators'. However, it is possible that the acquisition of proteorhodopsin in marine microbes is a simple accident enabled by lateral gene transfer, or it could be a brilliant evolutionary adaptation to increase the survival of marine microbes. Until somebody unpicks the truth - we'll have to keep hypothesising.

Béja, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., Jovanovich, S.B., Gates, C.M., Feldman, R.A., Spudich, J.L. and Spudich, E.N., 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science, 289(5486), pp.1902-1906.

Béja, O., Spudich, E.N., Spudich, J.L., Leclerc, M. and DeLong, E.F., 2001. Proteorhodopsin phototrophy in the ocean. Nature, 411(6839), pp.786-789.

Gómez-Consarnau, L., Akram, N., Lindell, K., Pedersen, A., Neutze, R., Milton, D.L., González, J.M. and Pinhassi, J., 2010. Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol, 8(4), p.e1000358.

McCarren, J. and DeLong, E.F., 2007. Proteorhodopsin photosystem gene clusters exhibit co‐evolutionary trends and shared ancestry among diverse marine microbial phyla. Environmental microbiology, 9(4), pp.846-858.

Munn, C., 2011. Marine microbiology. Garland Science.