Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity

Flores‐Uribe, José; Hevroni, Gur; Ghai, Rohit; Pushkarev, Alina; Inoue, Kazuhide; Kandori, Hideki; Béjà, Oded

doi:10.1111/1758-2229.12730

Cited by 32 publications

(39 citation statements)

References 35 publications

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“…The host of the unique protein A0A0L0D8K8 is a eukaryote Thecamonastrahens. Importantly, the sequences belong to both gram-positive and gram-negative bacteria, which is inconsistent with the previously made conclusion (26). Fig.…”

Section: Resultscontrasting

confidence: 89%

“…The analysis of the presence/absence of HeRs in monoderm and diderm representatives of the Tara Oceans and 25 freshwater lakes metagenomes led to the conclusion that HeRs were absent in diderms, confirming their absence in cultured Proteobacteria. Judging by a specific semipermeability of outer membranes of diderms, the authors proposed a role of HeRs in lightdriven transport of amphiphilic molecules (26). However, the structures of 48С12 do not support such function for HeRs.…”

Section: Discussionmentioning

confidence: 99%

“…The function of HeRs is not yet known (25,26). Moreover, the structural data on HeRs are limited to the very recently reported…”

mentioning

confidence: 99%

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High-resolution structural insights into the heliorhodopsin family

Kovalev

Volkov

Astashkin

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

162

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Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR’s extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.

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Section: Resultscontrasting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

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High-resolution structural insights into the heliorhodopsin family

Kovalev

Volkov

Astashkin

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

162

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“…The host of the unique protein A0A0L0D8K8 is eukaryotic Thecamonas trahens. Importantly, the sequences belong to both gram-positive and gram-negative bacteria, which is inconsistent to previously made conclusion 22 .…”

Section: Structure-based Bioinformatic Analysis Of Heliorhodopsinscontrasting

confidence: 99%

“…The function and structure of these heliorhodopsins are not yet known 21,22 . Here we present high resolution crystallographic structures of a HeR (48C12), discovered in an actinobacterial fosmid from freshwater lake Kinneret 20 , corresponding to two states of the protein both solved at 1.5 Å resolution.…”

Section: Introductionmentioning

confidence: 99%

High Resolution Structural Insights into Heliorhodopsin Family

Kovalev

Volkov

Astashkin

et al. 2019

Preprint

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Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), was recently discovered. In opposite to the known rhodopsins their N-termini face the cytoplasm. HeRs structure and function remain unknown. We present structures of two HeR-48C12 states at 1.5 Å showing its remarkable difference from all known rhodopsins. Its internal extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity ('active site'), surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH a planar triangle molecule (acetate) is present in the 'active site' which demonstrated its ability to maintain such anions as carbonate or nitrate. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement into fundamental redox biological processes.

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Planktonic microbial communities from microbialite‐bearing lakes sampled along a salinity‐alkalinity gradient

Iniesto

Moreira

Benzerara³

et al. 2022

Limnology & Oceanography

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Continental freshwater systems are particularly vulnerable to environmental variation. Climate changeinduced desertification and the anthropogenic exploitation of hydric resources result in the progressive evaporation and salinization of inland water bodies in many areas of the globe. However, how this process impacts microbial communities and their activities in biogeochemical cycles is poorly known. Here, we take a space-fortime substitution approach and characterize the prokaryotic and eukaryotic microbial communities of two planktonic cell-size fractions (0.2-5 μm and 5-30 μm) from lakes of diverse trophic levels sampled along a salinity-alkalinity gradient located in the Trans-Mexican Volcanic Belt (TMVB). We applied a 16S/18S rRNA gene metabarcoding strategy to determine the microbial community composition of 54 samples from 12 different lakes, from the low-salinity lake Zirahuén to the hypersaline residual ponds of Rinc on de Parangueo. Except for systems at both extremes of the salinity gradient, most lakes along the evaporation trend bear actively forming microbialites, which harbor microbial communities clearly distinct from those of plankton. Several lakes were sampled in winter and late spring and the crater lakes Alchichica and Atexcac were sampled across the water column. Physicochemical parameters related to salinity-alkalinity were the most influential drivers of microbial community structure whereas trophic status, depth, or season were less important. Our results suggest that climate change and anthropogenic-induced hydric deficit could significantly affect microbial communities, potentially altering ecosystem functioning.

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Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity

Cited by 32 publications

References 35 publications

High-resolution structural insights into the heliorhodopsin family

High-resolution structural insights into the heliorhodopsin family

High Resolution Structural Insights into Heliorhodopsin Family

Planktonic microbial communities from microbialite‐bearing lakes sampled along a salinity‐alkalinity gradient

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