Functional metagenomic screen reveals new and diverse microbial rhodopsins

The ISME Journal
Alina Pushkarev, Oded Béjà

Abstract

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.

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Citations

Aug 31, 2016·Journal of the American Chemical Society·E Siva Subramaniam IyerSanford Ruhman
Apr 29, 2018·Applied and Environmental Microbiology·Julia A MarescaBarbara J Campbell
Mar 30, 2018·Frontiers in Microbiology·Alina PushkarevOded Béjà
Aug 31, 2020·Critical Reviews in Biotechnology·Zaiwei ManZhiqiang Cai
Dec 17, 2020·MSystems·Mario López-PérezFrancisco Rodriguez-Valera
Apr 3, 2020·Journal of Microbiology and Biotechnology·Soon-Kyeong KwonJihyun F Kim
Jun 3, 2020·Journal of Microbiology and Biotechnology·Soon-Kyeong KwonJihyun F Kim
Aug 4, 2021·Annual Review of Microbiology·Andrey RozenbergOded Béjà
Nov 26, 2021·Journal of Cell Science·Takashi Nagata, Keiichi Inoue

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