Unique structure and function of viral rhodopsins

Bratanov, Dmitry; Kovalev, Kirill; Machtens, Jan‐Philipp; Astashkin, Roman; Chizhov, Igor; Soloviov, Dmytro; Volkov, Dmytro; Polovinkin, Vitaly; Zabelskii, Dmitrii; Mager, Thomas; Gushchin, Ivan; Rokitskaya, Tatyana I.; Antonenko, Yuri N.; Alekseev, Alexey; Shevchenko, Vitaly; Yutin, Natalya; Rosselli, Riccardo; Baeken, Christian; Borshchevskiy, Valentin; Bourenkov, Gleb; Popov, A.; Balandin, Taras; Büldt, Georg; Manstein, Dietmar J.; Rodrı́guez-Valera, Francisco; Fahlke, Christoph; Bamberg, Ernst; Koonin, Eugene V.; Gordeliy, Valentin

doi:10.1038/s41467-019-12718-0

Cited by 69 publications

(45 citation statements)

References 80 publications

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“…Among the members of the rhodopsin family are light-driven proton, anion and cation pumps, light-gated anion and cation channels, and photoreceptors (3,5,14,15). Genomic and metagenomic studies dramatically expanded the world of rhodopsin sequences, some of which were found in unexpected organisms and habitats: for example, sodium-pumping rhodopsins in Flavobacteria (16,17) and the rhodopsins from giant viruses (18)(19)(20). The widely spread presence and importance of pR-based phototrophy in the marine environment (21) were identified.…”

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confidence: 99%

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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mentioning

confidence: 99%

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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“…One of the best examples of the biotechnological harvest of metagenomics has been the retrieval of a vast diversity of retinal proteins (rhodopsins) [56][57][58] critical for the development of optogenetics, a technology with remarkable potential in neurobiology and medicine [59,60]. The photic zone of the ocean is the quintessential habitat to screen for the diversity of rhodopsins and already many have been retrieved by SR assembly metagenomics [61,62]. Remarkably, the largest numbers of rhodopsins (>200 amino acids, clustered at 90 % amino acid identity) were found in the individual LRa (330 rhodopsin genes/Gb assembled) ( Figure 3A).…”

Section: Recovery Of Novel Genesmentioning

confidence: 99%

Long read metagenomics, the next step?

Haro-Moreno

López‐Pérez

Rodrı́guez-Valera

2020

Preprint

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BackgroundThird-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, 2nd generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in allowing assembly of microbes with high microdiversity or retrieving the flexible (adaptive) compartment of prokaryotic genomes.ResultsHere we have used different 3rd generation techniques to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared Oxford Nanopore and PacBio last generation technologies with the classical approach using Illumina short reads followed by assembly. PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. Long reads allow efficient direct retrieval of complete genes (473M/Tb) and operons before assembly, facilitating annotation and compensates the limitations of short reads or short-read assemblies. MetaSPAdes was the most appropriate assembly program when used in combination with short reads. The assemblies of the long reads allow also the reconstruction of much more complete metagenome-assembled genomes, even from microbes with high microdiversity. The flexible genome of reconstructed MAGs is much more complete and allows rescuing more adaptive genes.ConclusionsFor most applications of metagenomics, from community structure analysis to ecosystem functioning, long-reads should be applied whenever possible. Particularly for in-silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be used from raw reads, before a computing-demanding (and potentially artefactual) assembly step.

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“…Preliminary data shows that the presented approach works well also for larger K 10 (40 TM helices) and smaller c 13 (26 TM helices) rings (data not shown). We believe that it can be used for assembly of other protein complexes with encapsulated lipids such as the multidrug exporter AcrB (Qiu et al, 2018) or oligomeric light-driven pumps, microbial rhodopsins (Gushchin and Gordeliy, 2018; Bratanov et al, 2019; Kovalev et al, 2019) as well. As lipids are often critical for correct folding and operation of membrane proteins (Cournia et al, 2015; Hedger and Sansom, 2016; Gupta et al, 2017), reproducing their correct positions in simulations is of utmost importance.…”

Section: Resultsmentioning

confidence: 99%

Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex

Novitskaia

Buslaev

Gushchin

2019

Front. Mol. Biosci.

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Rotor ATPases are large multisubunit membrane protein complexes found in all kingdoms of life. The membrane parts of these ATPases include a ring-like assembly, so-called c-ring, consisting of several subunits c, plugged by a patch of phospholipids. In this report, we use a nature-inspired approach to model the assembly of the spinach (Spinacia oleracea) c14 ring protein-lipid complex, where partially assembled oligomers are pulled toward each other using a biasing potential. The resulting assemblies contain 23 to 26 encapsulated plug lipids, general position of which corresponds well to experimental maps. However, best fit to experimental data is achieved with 15 to 17 lipids inside the c-ring. In all of the simulations, the lipids from one leaflet (loop side of the c subunit) are ordered and static, whereas the lipids from the other leaflet are disordered and dynamic. Spontaneous permeation of water molecules toward Glu61 at the active site is also observed. The presented assembly approach is expected to be generalizable to other protein complexes with encapsulated lipid patches.

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Unique structure and function of viral rhodopsins

Cited by 69 publications

References 80 publications

High-resolution structural insights into the heliorhodopsin family

High-resolution structural insights into the heliorhodopsin family

Long read metagenomics, the next step?

Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex

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