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Article ; Online: Quantitative proteomic analyses reveal the impact of nitrogen starvation on the proteome of the model diatom Phaeodactylum tricornutum.

Lupette, Josselin / Tardif, Marianne / Brugière, Sabine / Couté, Yohann / Salvaing, Juliette / Maréchal, Eric

2022 Volume 22, Issue 22, Page(s) e2200155

Abstract: Diatoms are one of the largest groups in phytoplankton biodiversity. Understanding their response to nitrogen variations, present from micromolar to near-zero levels in oceans and fresh waters, is essential to comprehend their ecological success. ... ...

Abstract	Diatoms are one of the largest groups in phytoplankton biodiversity. Understanding their response to nitrogen variations, present from micromolar to near-zero levels in oceans and fresh waters, is essential to comprehend their ecological success. Nitrogen starvation is used in biotechnological processes, to trigger the remodeling of carbon metabolism in the direction of fatty acids and triacylglycerol synthesis. We evaluated whole proteome changes in Phaeodactylum tricornutum after 7 days of cultivation with 5.5-mM nitrate (+N) or without any nitrogen source (-N). On a total of 3768 proteins detected in biological replicates, our analysis pointed to 384 differentially abundant proteins (DAP). Analysis of proteins of lower abundance in -N revealed an arrest of amino acid and protein syntheses, a remodeling of nitrogen metabolism, and a decrease of the proteasome abundance suggesting a decline in unselective whole-proteome decay. Analysis of proteins of higher abundance revealed the setting up of a general nitrogen scavenging system dependent on deaminases. The increase of a plastid palmitoyl-ACP desaturase appeared as a hallmark of carbon metabolism rewiring in the direction of fatty acid and triacylglycerol synthesis. This dataset is also valuable to select gene candidates for improved biotechnological properties.
MeSH term(s)	Diatoms/genetics ; Diatoms/metabolism ; Proteome/metabolism ; Nitrogen/metabolism ; Proteomics ; Carbon/metabolism ; Fatty Acids/metabolism ; Triglycerides
Chemical Substances	Proteome ; Nitrogen (N762921K75) ; Carbon (7440-44-0) ; Fatty Acids ; Triglycerides
Language	English
Publishing date	2022-10-09
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200155
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Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Pseudomonas aeruginosa

Janet-Maitre, Manon / Job, Viviana / Bour, Maxime / Robert-Genthon, Mylène / Brugière, Sabine / Triponney, Pauline / Cobessi, David / Couté, Yohann / Jeannot, Katy / Attrée, Ina

mBio

2024 Volume 15, Issue 3, Page(s) e0221123

Abstract: Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic ... ...

Abstract	Due to the rising incidence of antibiotic-resistant infections, the last-line antibiotics, polymyxins, have resurged in the clinics in parallel with new bacterial strategies of escape. The Gram-negative opportunistic pathogen
MeSH term(s)	Polymyxins/pharmacology ; Polymyxin B/pharmacology ; Pseudomonas aeruginosa/metabolism ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Lipopolysaccharides/metabolism ; Microbial Sensitivity Tests
Chemical Substances	Polymyxins ; Polymyxin B (J2VZ07J96K) ; Bacterial Proteins ; Anti-Bacterial Agents ; Lipopolysaccharides
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.02211-23
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Article: Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte alga

Lacroux, Julien / Atteia, Ariane / Brugière, Sabine / Couté, Yohann / Vallon, Olivier / Steyer, Jean-Philippe / van Lis, Robert

Frontiers in microbiology

2022 Volume 13, Page(s) 1029828

Abstract: Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but ... ...

Abstract	Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but butyrate is poorly assimilated and can inhibit growth above 1 gC.L
Language	English
Publishing date	2022-10-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.1029828
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Article: Hybrid cluster proteins in a photosynthetic microalga

van Lis, Robert / Brugière, Sabine / Baffert, Carole / Couté, Yohann / Nitschke, Wolfgang / Atteia, Ariane

FEBS journal. 2020 Feb., v. 287, no. 4

2020

Abstract: Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron‐sulfur‐oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and ... ...

Abstract	Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron‐sulfur‐oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox‐titrated samples. Both proteins contain a [4Fe‐4S]‐cluster as well as a [4Fe‐2O‐2S]‐hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry‐based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S‐nitrosylation in bacteria.
Keywords	Chlamydomonas reinhardtii ; Desulfovibrio ; Escherichia coli ; S-nitrosylation ; electron paramagnetic resonance spectroscopy ; eukaryotic cells ; genes ; hybrids ; immunoblotting ; mass spectrometry ; metalloproteins ; microalgae ; models ; nitrates ; photosynthesis ; phylogeny ; proteomics
Language	English
Dates of publication	2020-02
Size	p. 721-735.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15025
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Article ; Online: Phylogenetic and functional diversity of aldehyde-alcohol dehydrogenases in microalgae.

van Lis, Robert / Couté, Yohann / Brugière, Sabine / Tourasse, Nicolas J / Laurent, Benoist / Nitschke, Wolfgang / Vallon, Olivier / Atteia, Ariane

Plant molecular biology

2021 Volume 105, Issue 4-5, Page(s) 497–511

Abstract: Key message: The study shows the biochemical and enzymatic divergence between the two aldehyde-alcohol dehydrogenases of the alga Polytomella sp., shedding light on novel aspects of the enzyme evolution amid unicellular eukaryotes. Aldehyde-alcohol ... ...

Abstract	Key message: The study shows the biochemical and enzymatic divergence between the two aldehyde-alcohol dehydrogenases of the alga Polytomella sp., shedding light on novel aspects of the enzyme evolution amid unicellular eukaryotes. Aldehyde-alcohol dehydrogenases (ADHEs) are large metalloenzymes that typically perform the two-step reduction of acetyl-CoA into ethanol. These enzymes consist of an N-terminal acetylating aldehyde dehydrogenase domain (ALDH) and a C-terminal alcohol dehydrogenase (ADH) domain. ADHEs are present in various bacterial phyla as well as in some unicellular eukaryotes. Here we focus on ADHEs in microalgae, a diverse and polyphyletic group of plastid-bearing unicellular eukaryotes. Genome survey shows the uneven distribution of the ADHE gene among free-living algae, and the presence of two distinct genes in various species. We show that the non-photosynthetic Chlorophyte alga Polytomella sp. SAG 198.80 harbors two genes for ADHE-like enzymes with divergent C-terminal ADH domains. Immunoblots indicate that both ADHEs accumulate in Polytomella cells growing aerobically on acetate or ethanol. ADHE1 of ~ 105-kDa is found in particulate fractions, whereas ADHE2 of ~ 95-kDa is mostly soluble. The study of the recombinant enzymes revealed that ADHE1 has both the ALDH and ADH activities, while ADHE2 has only the ALDH activity. Phylogeny shows that the divergence occurred close to the root of the Polytomella genus within a clade formed by the majority of the Chlorophyte ADHE sequences, next to the cyanobacterial clade. The potential diversification of function in Polytomella spp. unveiled here likely took place after the loss of photosynthesis. Overall, our study provides a glimpse at the complex evolutionary history of the ADHE in microalgae which includes (i) acquisition via different gene donors, (ii) gene duplication and (iii) independent evolution of one of the two enzymatic domains.
MeSH term(s)	Alcohol Dehydrogenase/classification ; Alcohol Dehydrogenase/genetics ; Alcohol Dehydrogenase/metabolism ; Aldehyde Dehydrogenase/classification ; Aldehyde Dehydrogenase/genetics ; Aldehyde Dehydrogenase/metabolism ; Algal Proteins/genetics ; Algal Proteins/metabolism ; Amino Acid Sequence ; Chlorophyta/enzymology ; Chlorophyta/genetics ; Genetic Variation ; Mass Spectrometry/methods ; Microalgae/enzymology ; Microalgae/genetics ; Phylogeny ; Proteomics/methods ; Sequence Analysis, DNA/methods ; Sequence Homology, Amino Acid
Chemical Substances	Algal Proteins ; Alcohol Dehydrogenase (EC 1.1.1.1) ; Aldehyde Dehydrogenase (EC 1.2.1.3)
Language	English
Publishing date	2021-01-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	778032-1
ISSN	1573-5028 ; 0167-4412
ISSN (online)	1573-5028
ISSN	0167-4412
DOI	10.1007/s11103-020-01105-9
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Article ; Online: Plastidial and cytosolic thiol reductases participate in the control of stomatal functioning.

Montillet, Jean-Luc / Rondet, Damien / Brugière, Sabine / Henri, Patricia / Rumeau, Dominique / Reichheld, Jean-Philippe / Couté, Yohann / Leonhardt, Nathalie / Rey, Pascal

Plant, cell & environment

2021 Volume 44, Issue 5, Page(s) 1417–1435

Abstract: Stomatal movements via the control of gas exchanges determine plant growth in relation to environmental stimuli through a complex signalling network involving reactive oxygen species that lead to post-translational modifications of Cys and Met residues, ... ...

Abstract	Stomatal movements via the control of gas exchanges determine plant growth in relation to environmental stimuli through a complex signalling network involving reactive oxygen species that lead to post-translational modifications of Cys and Met residues, and alter protein activity and/or conformation. Thiol-reductases (TRs), which include thioredoxins, glutaredoxins (GRXs) and peroxiredoxins (PRXs), participate in signalling pathways through the control of Cys redox status in client proteins. Their involvement in stomatal functioning remains poorly characterized. By performing a mass spectrometry-based proteomic analysis, we show that numerous thiol reductases, like PRXs, are highly abundant in guard cells. When investigating various Arabidopsis mutants impaired in the expression of TR genes, no change in stomatal density and index was noticed. In optimal growth conditions, a line deficient in cytosolic NADPH-thioredoxin reductases displayed higher stomatal conductance and lower leaf temperature evaluated by thermal infrared imaging. In contrast, lines deficient in plastidial 2-CysPRXs or type-II GRXs exhibited compared to WT reduced conductance and warmer leaves in optimal conditions, and enhanced stomatal closure in epidermal peels treated with abscisic acid or hydrogen peroxide. Altogether, these data strongly support the contribution of thiol redox switches within the signalling network regulating guard cell movements and stomatal functioning.
MeSH term(s)	Abscisic Acid/metabolism ; Arabidopsis/enzymology ; Arabidopsis/physiology ; Cytosol/metabolism ; Gene Expression Regulation, Plant ; Gene Ontology ; Hydrogen Peroxide/metabolism ; Models, Biological ; Mutation/genetics ; Oxidoreductases/metabolism ; Phenotype ; Plant Stomata/cytology ; Plant Stomata/physiology ; Plastids/metabolism ; Transcriptome/genetics
Chemical Substances	Abscisic Acid (72S9A8J5GW) ; Hydrogen Peroxide (BBX060AN9V) ; Oxidoreductases (EC 1.-)
Language	English
Publishing date	2021-03-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.14013
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Article ; Online: Hybrid cluster proteins in a photosynthetic microalga.

van Lis, Robert / Brugière, Sabine / Baffert, Carole / Couté, Yohann / Nitschke, Wolfgang / Atteia, Ariane

The FEBS journal

2019 Volume 287, Issue 4, Page(s) 721–735

Abstract: Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and ... ...

Abstract	Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.
MeSH term(s)	Algal Proteins/chemistry ; Algal Proteins/genetics ; Algal Proteins/metabolism ; Binding Sites ; Chlamydomonas reinhardtii/chemistry ; Chlamydomonas reinhardtii/classification ; Chlamydomonas reinhardtii/genetics ; Chlamydomonas reinhardtii/metabolism ; Cloning, Molecular ; Desulfovibrio/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Evolution, Molecular ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Iron-Sulfur Proteins/chemistry ; Iron-Sulfur Proteins/genetics ; Iron-Sulfur Proteins/metabolism ; Microalgae/chemistry ; Microalgae/genetics ; Microalgae/metabolism ; Models, Molecular ; Multigene Family ; Nitrates/metabolism ; Photosynthesis/physiology ; Phylogeny ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Structural Homology, Protein
Chemical Substances	Algal Proteins ; Iron-Sulfur Proteins ; Nitrates ; Recombinant Proteins
Language	English
Publishing date	2019-08-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15025
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Article: Phylogenetic and functional diversity of aldehyde-alcohol dehydrogenases in microalgae

van Lis, Robert / Couté, Yohann / Brugière, Sabine / Tourasse, Nicolas J / Laurent, Benoist / Nitschke, Wolfgang / Vallon, Olivier / Atteia, Ariane

Plant molecular biology. 2021 Mar., v. 105, no. 4-5

2021

Abstract: KEY MESSAGE: The study shows the biochemical and enzymatic divergence between the two aldehyde-alcohol dehydrogenases of the alga Polytomella sp., shedding light on novel aspects of the enzyme evolution amid unicellular eukaryotes. Aldehyde-alcohol ... ...

Abstract	KEY MESSAGE: The study shows the biochemical and enzymatic divergence between the two aldehyde-alcohol dehydrogenases of the alga Polytomella sp., shedding light on novel aspects of the enzyme evolution amid unicellular eukaryotes. Aldehyde-alcohol dehydrogenases (ADHEs) are large metalloenzymes that typically perform the two-step reduction of acetyl-CoA into ethanol. These enzymes consist of an N-terminal acetylating aldehyde dehydrogenase domain (ALDH) and a C-terminal alcohol dehydrogenase (ADH) domain. ADHEs are present in various bacterial phyla as well as in some unicellular eukaryotes. Here we focus on ADHEs in microalgae, a diverse and polyphyletic group of plastid-bearing unicellular eukaryotes. Genome survey shows the uneven distribution of the ADHE gene among free-living algae, and the presence of two distinct genes in various species. We show that the non-photosynthetic Chlorophyte alga Polytomella sp. SAG 198.80 harbors two genes for ADHE-like enzymes with divergent C-terminal ADH domains. Immunoblots indicate that both ADHEs accumulate in Polytomella cells growing aerobically on acetate or ethanol. ADHE1 of ~ 105-kDa is found in particulate fractions, whereas ADHE2 of ~ 95-kDa is mostly soluble. The study of the recombinant enzymes revealed that ADHE1 has both the ALDH and ADH activities, while ADHE2 has only the ALDH activity. Phylogeny shows that the divergence occurred close to the root of the Polytomella genus within a clade formed by the majority of the Chlorophyte ADHE sequences, next to the cyanobacterial clade. The potential diversification of function in Polytomella spp. unveiled here likely took place after the loss of photosynthesis. Overall, our study provides a glimpse at the complex evolutionary history of the ADHE in microalgae which includes (i) acquisition via different gene donors, (ii) gene duplication and (iii) independent evolution of one of the two enzymatic domains.
Keywords	acetates ; acetyl coenzyme A ; alcohol dehydrogenase ; aldehyde dehydrogenase ; ethanol ; eukaryotic cells ; functional diversity ; gene duplication ; genes ; microalgae ; molecular biology ; photosynthesis ; polyphyly ; surveys
Language	English
Dates of publication	2021-03
Size	p. 497-511.
Publishing place	Springer Netherlands
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	778032-1
ISSN	1573-5028 ; 0167-4412
ISSN (online)	1573-5028
ISSN	0167-4412
DOI	10.1007/s11103-020-01105-9
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Article ; Online: Proteomics Evidence of a Systemic Response to Desiccation in the Resurrection Plant

Mladenov, Petko / Zasheva, Diana / Planchon, Sébastien / Leclercq, Céline C / Falconet, Denis / Moyet, Lucas / Brugière, Sabine / Moyankova, Daniela / Tchorbadjieva, Magdalena / Ferro, Myriam / Rolland, Norbert / Renaut, Jenny / Djilianov, Dimitar / Deng, Xin

International journal of molecular sciences

2022 Volume 23, Issue 15

Abstract: Global warming and drought stress are expected to have a negative impact on agricultural productivity. Desiccation-tolerant species, which are able to tolerate the almost complete desiccation of their vegetative tissues, are appropriate models to study ... ...

Abstract	Global warming and drought stress are expected to have a negative impact on agricultural productivity. Desiccation-tolerant species, which are able to tolerate the almost complete desiccation of their vegetative tissues, are appropriate models to study extreme drought tolerance and identify novel approaches to improve the resistance of crops to drought stress. In the present study, to better understand what makes resurrection plants extremely tolerant to drought, we performed transmission electron microscopy and integrative large-scale proteomics, including organellar and phosphorylation proteomics, and combined these investigations with previously published transcriptomic and metabolomics data from the resurrection plant
MeSH term(s)	Craterostigma/genetics ; Desiccation ; Droughts ; Lamiales ; Proteomics
Language	English
Publishing date	2022-07-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23158520
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Article ; Online: The hexosamine pathway and coat complex II promote malignant adaptation to nutrient scarcity.

Dragic, Helena / Barthelaix, Audrey / Duret, Cédric / Le Goupil, Simon / Laprade, Hadrien / Martin, Sophie / Brugière, Sabine / Couté, Yohann / Machon, Christelle / Guitton, Jerome / Rudewicz, Justine / Hofman, Paul / Lebecque, Serge / Chaveroux, Cedric / Ferraro-Peyret, Carole / Renno, Toufic / Manié, Serge N

Life science alliance

2022 Volume 5, Issue 7

Abstract: The glucose-requiring hexosamine biosynthetic pathway (HBP), which produces UDP-N-acetylglucosamine for glycosylation reactions, promotes lung adenocarcinoma (LUAD) progression. However, lung tumor cells often reside in low-nutrient microenvironments, ... ...

Abstract	The glucose-requiring hexosamine biosynthetic pathway (HBP), which produces UDP-N-acetylglucosamine for glycosylation reactions, promotes lung adenocarcinoma (LUAD) progression. However, lung tumor cells often reside in low-nutrient microenvironments, and whether the HBP is involved in the adaptation of LUAD to nutrient stress is unknown. Here, we show that the HBP and the coat complex II (COPII) play a key role in cell survival during glucose shortage. HBP up-regulation withstood low glucose-induced production of proteins bearing truncated
MeSH term(s)	ErbB Receptors/genetics ; Glucose/metabolism ; Glycosylation ; Hexosamines/metabolism ; Humans ; Nutrients
Chemical Substances	Hexosamines ; ErbB Receptors (EC 2.7.10.1) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202101334
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