The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes

Vernette, Caroline; Lecubin, Julien; Sánchez, Pablo; Acinas, Silvia G.; Babin, Marcel; Bork, Peer; Boss, Emmanuel; Bowler, Chris; Cochrane, Guy; Vargas, Colomban de; Gorsky, Gabriel; Guidi, Lionel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Kandels‐Lewis, Stefanie; Karp‐Boss, Lee; Karsenti, Eric; Not, Fabrice; Ogata, Hiroyuki; Poulton, Nicole; Pesant, Stéphane; Sardet, Christian; Speich, Sabrina; Stemmann, Lars; Sullivan, Matthew B.; Sunagawa, Shinichi; Wincker, Patrick; Delmont, Tom O.; Pelletier, Éric; Lescot, Magali

doi:10.1093/nar/gkac420

Cited by 49 publications

(45 citation statements)

References 30 publications

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“…The KAA0157615 protein of Cafeteria burkhardae strain BVI was found using NCBI BLASTP against the nonredundant (NR) protein database. The metagenomic MATOU-v2.141421879_4, MATOU-v2.32008995_3, MATOU-v2.119411731_5, and TARA_MED_95_MAG_00407_000000002956 proteins were found using BLASTP in the Ocean Gene Atlas ( https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/ ) ( 45 , 46 ). MATOU-v2.141421879_4, MATOU-v2.32008995_3, and MATOU-v2.119411731_5 were extracted from the Marine Atlas of Tara Ocean Unigenes (MATOU [ 47 ]) data set, while TARA_MED_95_MAG_00407_000000002956 was found in Tara Oceans Single-Cell and Metagenome Assembled Genomes (EUK-SMAGs [ 48 ]) data set.…”

Section: Methodsmentioning

confidence: 99%

Structural Foundations of Potassium Selectivity in Channelrhodopsins

Govorunova

Sineshchekov

Brown

et al. 2022

mBio

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Recently discovered microbial light-gated ion channels (channelrhodopsins) with a higher permeability for K + than for Na + (potassium-selective channelrhodopsins [kalium channelrhodopsins, or KCRs]) demonstrate an alternative K + selectivity mechanism, unrelated to well-characterized “selectivity filters” of voltage- and ligand-gated K + channels. KCRs can be used for optogenetic inhibition of neuronal firing and potentially for the development of gene therapies to treat neurological and cardiovascular disorders.

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Section: Methodsmentioning

confidence: 99%

Structural Foundations of Potassium Selectivity in Channelrhodopsins

Govorunova

Sineshchekov

Brown

et al. 2022

mBio

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“…KAA0157615 protein of Cafeteria burkhardae strain BVI was found using NCBI BLASTP against the Non-redundant (NR) protein database. Metagenomic MATOU-v2.141421879_4, MATOU-v2.32008995_3, MATOU-v2.119411731_5, and TARA_MED_95_MAG_00407_000000002956 proteins were found using BLASTP in the Ocean Gene Atlas (https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/) (43, 44). The MATOU-v2.141421879_4, MATOU-v2.32008995_3, and MATOU-v2.119411731_5 were extracted from the Marine Atlas of Tara Ocean Unigenes (MATOU; (45)) dataset, while TARA_MED_95_MAG_00407_000000002956 was found in Tara Oceans Single-Cell and Metagenome Assembled Genomes (EUK-SMAGs;(46)) dataset.…”

Section: Methodsmentioning

confidence: 99%

Structural foundations of potassium selectivity in channelrhodopsins

Govorunova

Sineshchekov

Brown

et al. 2022

Preprint

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Kalium channelrhodopsins (KCRs) are light-gated K+ channels recently found in the stramenopile protist Hyphochytrium catenoides. When expressed in neurons, KCRs enable high-precision optical inhibition of spiking (optogenetic silencing). KCRs are capable of discriminating K+ from Na+ without the conventional K+-selectivity filter found in classical K+ channels. The genome of H. catenoides also encodes a third paralog that is more permeable for Na+ than for K+. To identify structural motifs responsible for the unusual K+ selectivity of KCRs, we systematically analyzed a series of chimeras and mutants of this protein. We found that mutations of three critical residues in the paralog convert its Na+ selective channel into a K+ selective one. Our characterization of homologous proteins from other protists (Colponema vietnamica, Cafeteria burkhardae and Chromera velia) and metagenomic samples confirmed the importance of these residues for K+ selectivity. We also show that Trp102 and Asp116, conserved in all three H. catenoides orthologs, are necessary, although not sufficient, for K+ selectivity. Our results provide the foundation for further engineering of KCRs for optogenetic needs.

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“…The copyright holder for this preprint this version posted December 1, 2022. ; https://doi.org/10.1101/2022.12.01.518734 doi: bioRxiv preprint Oceans dataset, a collection of pan-oceanic plankton metagenomes and metatranscriptomes (15). When using the DL sequence from Symbiodinium (Sym-Alma) as query (which is more similar to other DLHs, as compared to Alma1, see Dataset S1) high abundance of eukaryotic DLHs was detected in both metagenomes and metatranscriptomes databases (Marine Atlas of Tara Ocean Unigenes, MATOU (31); Fig.…”

Section: Global Biogeographic Distribution Of Dmsp Lyase Homologs In ...mentioning

confidence: 99%

“…The copyright holder for this preprint this version posted December 1, 2022. ; https://doi.org/10.1101/2022.12.01.518734 doi: bioRxiv preprint 4 widespread than previously thought, as it is encoded by known algal taxa as haptophytes and dinoflagellates, but also by chlorophytes, pelagophyte and diatoms, which were conventionally considered to lack DL. By exploring the Tara Oceans gene dataset (15), we demonstrate that DLH mRNA expression is occurring in diverse oceanic provinces, predominantly by dinoflagellates.…”

Section: Introductionmentioning

confidence: 99%

“…Our findings show that the DL enzyme is more taxonomically widespread than previously thought, as it is encoded by known algal taxa as haptophytes and dinoflagellates, but also by chlorophytes, pelagophyte and diatoms, which were conventionally considered to lack DL. By exploring the Tara Oceans gene dataset(15), we demonstrate that DLH mRNA expression is occurring in diverse oceanic provinces, predominantly by dinoflagellates. Haptophytes and diatoms DLHs are enriched in specific ‘hotspots’, with correlation to nutrient availability.…”

Section: Introductionmentioning

confidence: 99%

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Phylogeny and biogeography of the algal DMS-releasing enzyme

Shemi

Ben-Dor

Rotkopf

et al. 2022

Preprint

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Phytoplankton produce the volatile dimethyl sulfide (DMS), an important infochemical, which is emitted to the atmosphere and affecting the global climate. Albeit the enzymatic source for DMS in eukaryotes was elucidated, namely a DMSP lyase (DL) called Alma1, we still lack basic knowledge regarding its taxonomy and biogeographic distribution. We defined unique sequence motifs which enable the identification of DL homologs (DLHs) in model systems and environmental populations. We used these motifs to predict DLHs in diverse algae by analyzing hundreds of genomic and transcriptomic sequences from model systems under stress conditions and environmental samples. Our findings show that the DL enzyme is more taxonomically widespread than previously thought, as it is encoded by known algal taxa as haptophytes and dinoflagellates, but also by chlorophytes, pelagophytes and diatoms, which were conventionally considered to lack the DL enzyme. By exploring the Tara Oceans database, we showed that DLHs are widespread across the oceans and are predominantly expressed by dinoflagellates. Certain dinoflagellate DLHs were differentially expressed between the euphotic and mesopelagic zones, suggesting a functional specialization and an involvement in the metabolic plasticity of mixotrophic dinoflagellates. In specific regions such as the Southern Ocean, DLH expression by haptophytes and diatoms was correlated with environmental drivers such as nutrient availability. The expanded repertoire of putative DL enzymes from diverse microbial origins and geographic niches suggests new potential players in the marine sulfur cycle and provides a foundation to study the cellular function in marine microbes.

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The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes

Cited by 49 publications

References 30 publications

Structural Foundations of Potassium Selectivity in Channelrhodopsins

Structural Foundations of Potassium Selectivity in Channelrhodopsins

Structural foundations of potassium selectivity in channelrhodopsins

Phylogeny and biogeography of the algal DMS-releasing enzyme

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