New functionalities of microbial rhodopsins - where bioinformatics meets biophysics

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Many important processes in biology are driven by sunlight. Nature designed several light-sensitive elements used by proteins to catch and utilize its energy. One of these light-sensitive elements is retinal, a form of vitamin A. Retinal-binding proteins are called rhodopsins, which are used by humans and animals to perform one of the most important physiological functions - vision. Microbes, including various bacteria, some viruses, most fungi, and microscopic algae, have rhodopsins as well, but use them for different purposes. Microbial rhodopsins are used as light-driven ion transporters, light-gated ion channels, light-switchable enzymes, and photosensory receptors. Thus, these microbial rhodopsins are very important in bioenergetics and in all kinds of light-regulated microbial processes, including swimming and growth. They also have very interesting applications in neuroscience and biomedicine, via so-called optogenetics, where neurons can be rendered light-sensitive and manipulated by light, serving, for example, as visual prosthetics. Our group works at the intersection of biology, chemistry, and physics, trying to discover, produce, and characterize in depth novel microbial rhodopsins. We will use bioinformatics to look for new microbial rhodopsin genes in the DNA material derived from various environmental sources (so-called metagenomes). We will analyze the genes, and once we find an interesting unusual target, we will make the corresponding novel rhodopsin in bacteria or yeast (in their unmodified and mutated forms). Then we will use cutting-edge biophysical and biochemical techniques, including several kinds of advanced spectroscopy, to understand what these novel rhodopsins do (that is, their physiological functions) and how they do it (that is, the corresponding molecular mechanisms). This research approach has already yielded many novel insights into microbial ecology, evolution, and physiology, and also produced novel optogenetic tools. We are hopeful that our research will contribute to both of these exciting directions.