Pushkarev Alina, Béjà Oded
Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
ISME J. 2016 Sep;10(9):2331-5. doi: 10.1038/ismej.2016.7. Epub 2016 Feb 19.
Ion-translocating retinylidene rhodopsins are widely distributed among marine and freshwater microbes. The translocation is light-driven, contributing to the production of biochemical energy in diverse microbes. Until today, most microbial rhodopsins had been detected using bioinformatics based on homology to other rhodopsins. In the past decade, there has been increased interest in microbial rhodopsins in the field of optogenetics since microbial rhodopsins were found to be most useful in vertebrate neuronal systems. Here we report on a functional metagenomic assay for detecting microbial rhodopsins. Using an array of narrow pH electrodes and light-emitting diode illumination, we were able to screen a metagenomic fosmid library to detect diverse marine proteorhodopsins and an actinorhodopsin based solely on proton-pumping activity. Our assay therefore provides a rather simple phenotypic means to enrich our understanding of microbial rhodopsins without any prior knowledge of the genomic content of the environmental entities screened.
离子转运视黄醛视紫红质广泛分布于海洋和淡水微生物中。这种转运由光驱动，有助于多种微生物产生生化能量。直到如今，大多数微生物视紫红质都是通过基于与其他视紫红质的同源性的生物信息学方法检测到的。在过去十年中，由于发现微生物视紫红质在脊椎动物神经系统中最为有用，因此光遗传学领域对微生物视紫红质的兴趣与日俱增。在此，我们报告一种用于检测微生物视紫红质的功能宏基因组学分析方法。通过使用一系列狭窄pH电极和发光二极管照明，我们能够筛选宏基因组fosmid文库，仅基于质子泵浦活性来检测多种海洋视紫质和放线菌视紫红质。因此，我们的分析方法提供了一种相当简单的表型手段，可增进我们对微生物视紫红质的理解，而无需对所筛选环境实体的基因组内容有任何先验知识。
