Bacterial, archaeal and viral‐like rhodopsins from the <scp>R</scp>ed <scp>S</scp>ea

Philosof, Alon; Béjà, Oded

doi:10.1111/1758-2229.12037

Cited by 57 publications

(54 citation statements)

References 60 publications

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“…Pelagibacter"-related populations, PR genes were among the most highly expressed transcripts. Expression of SAR11 and SAR86 clade PR genes has also been detected in the Red Sea (103).…”

Section: Environmental Rhodopsin Gene Expression Analysesmentioning

confidence: 97%

“…Consistent with these findings, PCR screening showed that PRs in SAR11 isolates from the Oregon coast were either green-or blue-tuned, while all isolates from the Sargasso Sea had blue-tuned rhodopsins (102). In comparison, among a total of 117 PRs from the North Sea affiliated with Proteobacteria and Bacteroidetes, nearly all PRs (97%) were green-tuned (93), while a majority (71%) of bacterial and archaeal rhodopsins in the Red Sea surface waters were putatively blue-tuned (103).…”

Section: Biogeography Of Rhodopsin Spectral Tuningmentioning

confidence: 99%

“…Analysis of conserved amino acids for rhodopsin functioning indicated that these were sensory rhodopsins, thus potentially affecting, for example, phototaxis of infected photosynthetic protists, such as Phaeocystis (156). Such virus-associated rhodopsins have also been found in Red Sea metagenomes (103). Taking these findings together, future analyses of the way in which rhodopsin-and chlorophyll-based systems for gathering light energy are coordinated promise to provide fascinating novel insights into the factors that control the ecology of marine planktonic microorganisms under different environmental conditions.…”

Section: Proton-pumping Rhodopsins In Chlorophyll-containing Microbesmentioning

confidence: 99%

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Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Pinhassi

DeLong

Béjà

et al. 2016

Microbiol Mol Biol Rev

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175

172

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SUMMARYThe recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of “heterotrophic” bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.

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“…Pelagibacter"-related populations, PR genes were among the most highly expressed transcripts. Expression of SAR11 and SAR86 clade PR genes has also been detected in the Red Sea (103).…”

Section: Environmental Rhodopsin Gene Expression Analysesmentioning

confidence: 97%

Section: Biogeography Of Rhodopsin Spectral Tuningmentioning

confidence: 99%

Section: Proton-pumping Rhodopsins In Chlorophyll-containing Microbesmentioning

confidence: 99%

See 1 more Smart Citation

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

Pinhassi

DeLong

Béjà

et al. 2016

Microbiol Mol Biol Rev

Self Cite

175

172

View full text Add to dashboard Cite

show abstract

“…Subsequent research, particularly using large-scale metagenomic analyses, revealed a high prevalence of viral-encoded auxiliary metabolic genes (AMGs) often encoding critical, rate-limiting steps of host metabolism. AMGs include genes involved in photosystem I, the pentose phosphate pathway, phosphate acquisition, sulfur metabolism, and sphingolipid, rhodopsin and DNA/RNA processing (see [7,[11][12][13][14] and references therein). Metagenomic analyses strongly support the notion that viral auxiliary genes promote viral replication through both degradation of host DNA and RNA as well as a shift in the host metabolism towards nucleotide biosynthesis [15].…”

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confidence: 99%

Cyanophages: Starving the Host to Recruit Resources

Kaplan

2016

Current Biology

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“…Microbial rhodopsins function as light-driven (retinal-based) ion pumps, cation channels, or light sensors in various microorganisms [see Heberle et al 's Retinal Proteins-You can teach an old dog new tricks (1)], are found in all three domains of life (2-4), and were recently reported in viruses as well (5,6). The first discovered microbial rhodopsin, the light-driven proton pump bacteriorhodopsin (BR), was identified in halophilic (high-salt loving) archaea more than 40 y ago (in 1971).…”

mentioning

confidence: 99%