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A new paper co-authored by an international team of scientists, among them UvA PhD candidate Charlotte Vavourakis, shows how the team expressed microbial retinal pigments called xenorhodopsins in various model systems to study their structure and function. Some properties of this unique family of rhodopsins make these proteins very attractive for optogenetics.

Hummock Salt Lake
A salt lake in Siberia colored pink because of blooming pigment-rich microbes. Photo: Gerard Muyzer

Microbial rhodopsins are retinal pigments that are related to the retinal pigments in our own human eyes. After their first discovery in salt-loving Archaea, it became clear that many more microbes have one or even a few rhodopsins. Depending on the specific type of rhodopsin, microbes can pump protons or ions (sodium and chloride) out and into the cell upon light activation of the retinal. This action can be used for example to generate energy or direct movement relative to a light source. Xenorhodopsins are a class of rhodopsins that in contrast to all other known membrane proton pumps, seem to pump protons into the cell. The biological function of this proton-pumping direction remains still unclear.

From metagenomics to the function of novel proteins

PhD Candidate Charlotte Vavourakis (IBED-FAME) contributed to the study, led by Valentin Gordeliy from the Université Grenoble Alpes, by providing one of the rhodopsins gene sequences after entangling Nanohaloarchaea, a group of archaea, genomes from soda lake metagenomes. Metagenomics aims to directly sequence all the DNA recovered from various environments ranging from the deep sea to animal guts, and reconstruct genomes of microbes without growing them first in the laboratory. This methodological shortcut enabled by next-generation sequence technologies has truly transformed our knowledge of the microbial diversity over the past few years. Charlotte Vavourakis explains: ‘With gene sequences alone it is possible to reconstruct novel proteins of interest and study their function in biological model systems.’


The discovery of rhodopsins is at the base of a relatively young scientific field called optogenetics, where photoreceptor proteins such as rhodopsins are used to tightly control the activity of genetically engineered cells with light in living tissue or even behaving animals. Optogenetics is mainly used in neuroscience to study neural networks where very precise and fast control of neurons is paramount. In this study, researchers showed that the novel xenorhodopsins can be effectively expressed in rat neuronal brain cells to trigger action potentials in a light-controlled manner.

Publication details

Shevchenko, V., Mager, T., Kovalev K., Polovinkin, V., Alekseev, A., Juettner, J., Chizhov, I., Bamann, C., Vavourakis, C., Ghai, R., Gushchin, I., Borshchevskiy, V., Rogachev, A., Melnikov, I., Popov, A., Balandin, T., Rodriguez-Valera, F., Manstein, D. J., Bueldt, G., Bamberg, E. and Gordeliy, V. (2017). Inward H+ pump xenorhodopsin: mechanism and alternative optogenetic approach. Science Advances Vol 3, no. 9. DOI: 10.1126/sciadv.1603187

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