Light-powering Escherichia coli with proteorhodopsin

Department of Physics, University of California, Berkeley, CA 94720, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 03/2007; 104(7):2408-12. DOI: 10.1073/pnas.0611035104
Source: PubMed

ABSTRACT Proteorhodopsin (PR) is a light-powered proton pump identified by community sequencing of ocean samples. Previous studies have established the ecological distribution and enzymatic activity of PR, but its role in powering cells and participation in ocean energy fluxes remains unclear. Here, we show that when cellular respiration is inhibited by depleting oxygen or by the respiratory poison azide, Escherichia coli cells expressing PR become light-powered. Illumination of these cells with light coinciding with PR's absorption spectrum creates a proton motive force (pmf) that turns the flagellar motor, yielding cells that swim when illuminated with green light. By measuring the pmf of individual illuminated cells, we quantify the coupling between light-driven and respiratory proton currents, estimate the Michaelis-Menten constant (Km) of PR (10(3) photons per second/nm2), and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions. Moreover, sunlight-illuminated PR+ cells are less sensitive to azide than PR- cells, consistent with PR+ cells possessing an alternative means of maintaining cellular pmf and, thus, viability. Proteorhodopsin allows Escherichia coli cells to withstand environmental respiration challenges by harvesting light energy.

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    • "In heterotrophic bacteria, the physiological functions suggested for PR include enhanced survival or growth under starvation conditions (Lami et al., 2009; Gómez-Consarnau et al., 2010; Steindler et al., 2011; Akram et al., 2013) and powering of cell motility (Walter et al., 2007), among others (Fuhrman et al., 2008). Along these lines, PR in cyanobacteria might play a role in nutrient acquisition when photosynthetic activities are limited by bioavailable nutrients such as nitrogen (Van Mooy and Devol, 2008) or iron (Mann and Chisholm, 2000). "
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    ABSTRACT: Uncovering the metabolic capabilities of microbes is key to understanding global energy flux and nutrient transformations. Since the vast majority of environmental microorganisms are uncultured, metagenomics has become an important tool to genotype the microbial community. This study uses a recently developed computational method to confidently assign metagenomic reads to microbial clades without the requirement of metagenome assembly by comparing the evolutionary pattern of nucleotide sequences at non-synonymous sites between metagenomic and orthologous reference genes. We found evidence for new, ecologically relevant metabolic pathways in several lineages of surface ocean bacterioplankton using the Global Ocean Survey (GOS) metagenomic data, including assimilatory sulfate reduction and alkaline phosphatase capabilities in the alphaproteobacterial SAR11 clade, and proteorhodopsin-like genes in the cyanobacterial genus Prochlorococcus. These findings raise new hypotheses about microbial roles in energy flux and organic matter transformation in the ocean.
    Environmental Microbiology Reports 10/2013; 5(5):686-696. DOI:10.1111/1758-2229.12068 · 3.26 Impact Factor
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    • "AND4, another PR-containing strain, exhibited longer survival during starvation than its corresponding PR deletion mutant (Gomez-Consarnau et al. 2010). When expressed in E. coli, a PR from the SAR-86 clade of the Gammaproteobacteria promotes proton-motive force that turns the flagellar motor during light illumination (Walter et al. 2007). Several lines of evidence suggest that the PR in DSW-6 should be a functional equivalent of other PRs and may play similar roles to contribute to the growth or survival of the bacterium in oligotrophic environments. "
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    ABSTRACT: Rhodopsin-containing marine microbes such as those in the class Flavobacteria play a pivotal role in the biogeochemical cycle of the euphotic zone . Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins is important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in marine oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of cytophaga, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.
    Genome Biology and Evolution 01/2013; 5(1). DOI:10.1093/gbe/evs134 · 4.53 Impact Factor
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    • "Proteorhodopsin studies have, in fact, radically revised previous knowledge of the nature and FEMS Microbiol Rev 35 (2011) 1082–1099 c 2011 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved prevalence of light utilization in ocean waters (DeLong, 2005; Martinez et al., 2007), even though a great deal remains to be understood about the physiological functions and fitness benefits of these proteins (Giovannoni et al., 2005; G ´ omez-Consarnau et al., 2007, 2010; Stingl et al., 2007; Walter et al., 2007; Fuhrman et al., 2008 "
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    ABSTRACT: The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields.
    FEMS microbiology reviews 05/2011; 35(6):1082-99. DOI:10.1111/j.1574-6976.2011.00281.x · 13.81 Impact Factor
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