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Funding Information: We gratefully acknowledge the contribution of Marielle Bauzan for the cultures in syntrophy and Yann Denis for transcriptomic facilities and Grant Zane (Judy Wall laboratory) for providing us the GZ3621Orp ::mini‐Tn5 strain. The authors are also grateful to Emilien Etienne and the EPR facilities available at the national EPR network RENARD (IR CNRS 3443) and the Aix‐Marseille University EPR center. We also thank Martine Company for technical assistance, Katia Villion for her help on the project during its school program, Béatrice Py and Bruno Guigliarelli for insightful discussions. The French National Research Agency (ANR) funded this research project (ANR‐12‐ISV8‐0003‐01). The project leading to this publication has received funding from the Excellence Initiative of Aix‐Marseille University—A*MIDEX, a French “Investissements d'Avenir” programme and is part of the Institute of Microbiologies and Biotechnology—IM2B (AMX‐19‐IET‐006). This work was supported by Fundação para a Ciência e Tecnologia (FCT) (grant to SRP, FCT‐ANR/BBB‐MET/0023/2012) and by the Belgian Federal Science Policy Office (Belspo) (IAP7/44, iPROS project). SRP was also supported by the Applied Molecular Biosciences Unit‐UCIBIO financed by national funds from FCT (UIDP/04378/2020 and UIDB/04378/2020). This article is based upon work from COST Action CA15133, supported by COST (European Cooperation in Science and Technology). Made available in DSpace on 2021-11-29T23:39:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07 publishersversion published

36 páginas, 6 figuras, 4 tablas., Using plant essential oils (EOs) contributes to the growing number of natural plants’ applications in livestock. Scientific data supporting the efficacy of EOs as anti-inflammatory, antibacterial and antioxidant molecules accumulates over time; however, the cumulative evidence is not always sufficient. EOs antioxidant properties have been investigated mainly from human perspectives. Still, so far, our review is the first to combine the beneficial supporting properties of EOs in a One Health approach and as an animal product quality enhancer, opening new possibilities for their utilization in the livestock and nutrition sectors. We aim to compile the currently available data on the main anti-inflammatory effects of EOs, whether encapsulated or not, with a focus on mammary gland inflammation. We will also review the EOs’ antioxidant activities when given in the diet or as a food preservative to counteract oxidative stress. We emphasize EOs’ in vitro and in vivo ruminal microbiota and mechanisms of action to promote animal health and performance. Given the concept of DOHaD (Developmental Origin of Health and Diseases), supplementing animals with EOs in early life opens new perspectives in the nutrition sector. However, effective evaluation of the significant safety components is required before extending their use to livestock and veterinary medicine., This research was funded under H2020-PRIMA 2018—Section 2.

International audience; Hazelnuts (Corylus avellanaL.) have an important role in human nutrition and health. However, they are a common cause of food allergy. Due to hazelnut varietal diversity, variety-dependent differences in the IgE-binding properties may be suspected, which could allow therapeutic strategies based on the use of hypoallergenic varieties to induce desensitization. In a proteogenomic approach, we aimed to evaluate the allergenic potential of a genetically diverse set of hazelnuts (n = 13 varieties). Minor differences were found at the level of genes encoding important allergens, namely Cor a 8, Cor a 9, and Cor a 14. Nevertheless, IgE-reactivity was similar for all varieties using sera from seven allergic individuals. The predominant IgE-reactive proteins were Cor a 9 (100%) and Cor a 1.04 (60%), with the former being the most frequently identified by a two-dimensional gel electrophoresis (2-DE)-based proteomic approach. Therefore, it seems that the conventional exclusion diet will hold its ground for the time being.

The French National Research Agency (ANR) funded this research project (ANR-12-ISV8-0003-01). This work was supported by Fundacao para a Ciencia e Tecnologia (FCT) (grant to SRP, FCT-ANR/BBB-MET/0023/2012, and to CC, SFRH/BD/87898/2012) and by the Belgian Federal Science Policy Office (Belspo) (grant to BD, IAP7/44, iPROS project). Unidade de Ciencias Biomoleculares Aplicadas-UCIBIO was financed by national funds from FCT/MEC (UID/Multi/04378/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007728). This article is based upon work from COST Action CA15133, supported by COST (European Cooperation in Science and Technology). Despite recent advances in understanding the biogenesis of iron-sulfur (Fe-S) proteins, most studies focused on aerobic bacteria as model organisms. Accordingly, multiple players have been proposed to participate in the Fe-S delivery step to apo-target proteins, but critical gaps exist in the knowledge of Fe-S proteins biogenesis in anaerobic organisms. Mrp/NBP35 ATP-binding proteins are a subclass of the soluble P-loop containing nucleoside triphosphate hydrolase superfamily (P-loop NTPase) known to bind and transfer Fe-S clusters in vitro. Here, we report investigations of a novel atypical two-domain Mrp/NBP35 ATP-binding protein named MrpORP associating a P-loop NTPase domain with a dinitrogenase iron-molybdenum cofactor biosynthesis domain (Di-Nase). Characterization of full length MrpORP, as well as of its two domains, showed that both domains bind Fe-S clusters. We provide in vitro evidence that the P-loop NTPase domain of the MrpORP can efficiently transfer its Fe-S cluster to apo-target proteins of the ORange Protein (ORP) complex, suggesting that this novel protein is involved in the maturation of these Fe-S proteins. Last, we showed for the first time, by fluorescence microscopy imaging a polar localization of a Mrp/NBP35 protein. publishersversion published

Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 ( orp2 ) and DVU2107-DVU2108-DVU2109 ( orp1 ) form two divergent operons transcribed by the σ 54 -RNA polymerase. We further demonstrate that the σ 54 -dependent transcriptional regulator DVU2106, located between orp1 and orp2 , collaborates with σ 54 -RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the σ 70 -RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.

International audience; A novel metalloprotein containing a unique [S2MoS2CuS2MoS2](3-) cluster, designated as Orange Protein (ORP), was isolated for the first time from Desulfovibrio gigas, a sulphate reducer. The orp operon is conserved in almost all sequenced Desulfovibrio genomes and in other anaerobic bacteria, however, so far D. gigas ORP had been the only ORP characterized in the literature. In this work, the purification of another ORP isolated form Desulfovibrio alaskensis G20 is reported. The native protein is monomeric (12443.8 +/- A 0.1 Da by ESI-MS) and contains also a MoCu cluster with characteristic absorption bands at 337 and 480 nm, assigned to S-Mo charge transfer bands. Desulfovibrio alaskensis G20 recombinant protein was obtained in the apo-form from E. coli. Cluster reconstitution studies and UV-visible titrations with tetrathiomolybdate of the apo-ORP incubated with Cu ions indicate that the cluster is incorporated in a protein metal-assisted synthetic mode and the protein favors the 2Mo:1Cu stoichiometry. In Desulfovibrio alaskensis G20, the orp genes are encoded by a polycistronic unit composed of six genes whereas in Desulfovibrio vulgaris Hildenborough the same genes are organized into two divergent operons, although the composition in genes is similar. The gene expression of ORP (Dde\₃198) increased 6.6 +/- A 0.5 times when molybdate was added to the growth medium but was not affected by Cu(II) addition, suggesting an involvement in molybdenum metabolism directly or indirectly in these anaerobic bacteria.

The isolation and characterization of a new metalloprotein containing Cu and Fe atoms is reported. The as-isolated Cu-Fe protein shows an UV-visible spectrum with absorption bands at 320 nm, 409 nm and 615 nm. Molecular mass of the native protein along with denaturating electrophoresis and mass spectrometry data show that this protein is a multimer consisting of 14+/-1 subunits of 15254.3+/-7.6 Da. Mössbauer spectroscopy data of the as-isolated Cu-Fe protein is consistent with the presence of [2Fe-2S](2+) centers. Data interpretation of the dithionite reduced protein suggest that the metallic cluster could be constituted by two ferromagnetically coupled [2Fe-2S](+) spin delocalized pairs. The biochemical properties of the Cu-Fe protein are similar to the recently reported molybdenum resistance associated protein from Desulfovibrio, D. alaskensis. Furthermore, a BLAST search from the DNA deduced amino acid sequence shows that the Cu-Fe protein has homology with proteins annotated as zinc resistance associated proteins from Desulfovibrio, D. alaskensis, D. vulgaris Hildenborough, D. piger ATCC 29098. These facts suggest a possible role of the Cu-Fe protein in metal tolerance.

The mechanisms of radiationless decay involved in the photodissociation of formaldehyde into H-2 and CO have been investigated using complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics in the S-1, T-1, and S-0 states. A commonly accepted scheme involves Fermi Golden Rule internal conversion from S-1 followed by dissociation of vibrationally hot H2CO in S-0. We recently proposed a novel mechanism [M. Araujo et al., J. Phys. Chem. A 112, 7489 (2008)] whereby internal conversion and dissociation take place in concert through a seam of conical intersection between S-1 and S-0 after the system has passed through an S-1 transition barrier. The relevance of this mechanism depends on the efficiency of tunneling in S-1. At lower energy, an alternative scheme to internal conversion involves intersystem crossing via T-1 to regenerate the reactant before the S-0 barrier to dissociation. We propose here a previously unidentified mechanism leading directly to H-2 and CO products via T-1. This channel opens at medium energies, near or above the T-1 barrier to dissociation and still lower than the S-1 barrier, thus making T-1 a possible shortcut to molecular dissociation. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3242082]

Membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617 can be solubilized in either of two ways that will ultimately determine the presence or absence of the small (Iota) subunit. The enzyme complex (NarGHI) is composed of three subunits with molecular masses of 130, 65, and 20 kDa. This enzyme contains approximately 14 Fe, 0.8 Mo, and 1.3 molybdopterin guanine dinucleotides per enzyme molecule. Curiously, one heme b and 0.4 heme c per enzyme molecule have been detected. These hemes were potentiometrically characterized by optical spectroscopy at pH 7.6 and two noninteracting species were identified with respective midpoint potentials at Em=+197 mV (heme c) and -4.5 mV (heme b). Variable-temperature (4-120 K) X-band electron paramagnetic resonance (EPR) studies performed on both as-isolated and dithionite-reduced nitrate reductase showed, respectively, an EPR signal characteristic of a [3Fe-4S]+ cluster and overlapping signals associated with at least three types of [4Fe-4S]+ centers. EPR of the as-isolated enzyme shows two distinct pH-dependent Mo(V) signals with hyperfine coupling to a solvent-exchangeable proton. These signals, called "low-pH" and "high-pH," changed to a pH-independent Mo(V) signal upon nitrate or nitrite addition. Nitrate addition to dithionite-reduced samples at pH 6 and 7.6 yields some of the EPR signals described above and a new rhombic signal that has no hyperfine structure. The relationship between the distinct EPR-active Mo(V) species and their plausible structures is discussed on the basis of the structural information available to date for closely related membrane-bound nitrate reductases.

Two proteins were purified and preliminarily characterized from the soluble extract of cells (310 g, wet weight) of the aminolytic and peptidolytic sulfate-reducing bacterium Desulfovibrio (D.) aminophilus DSM 12254. The iron-sulfur flavoenzyme adenylylsulfate (adenosine 5'-phosphosulfate, APS) reductase, a key enzyme in the microbial dissimilatory sulfate reduction, has been purified in three chromatographic steps (DEAE-Biogel A, Source 15, and Superdex 200 columns). It contains two different subunits with molecular masses of 75 and 18 kDa. The fraction after the last purification step had a purity index (A(278nm) / A(388nm)) of 5.34, which was used for further EPR spectroscopic studies. The D. aminophilus APS reductase is very similar to the homologous enzymes isolated from D. gigas and D. desulfuricans ATCC 27774. A tetraheme cytochrome c(3) (His-heme iron-His) has been purified in three chromatographic steps (DEAE- Biogel A, Source 15, and Biogel-HTP columns) and preliminarily characterized. It has a purity index ([A(553nm) - A(570nm)](red) / A(280nm)) of 2.9 and a molecular mass of around 15 kDa, and its spectroscopic characterization (NMR and EPR) has been carried out. This hemoprotein presents similarities with the tetraheme cytochrome c(3) from Desulfomicrobium (Des.) norvegicum (NMR spectra, and N-terminal amino acid sequence).

Dissimilatory nitrate and nitrite ammonification by sulphate-reducing bacteria

International audience; Sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. HmcA is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. We report the crystal structure of HmcA isolated from the periplasm of Desulfovibrio gigas. Crystals were grown using polyethylene glycol 8K and zinc acetate, and diffracted beyond 2.1 A resolution. A multiple-wavelength anomalous dispersion experiment at the iron absorption edge enabled us to obtain good-quality phases for structure solution and model building. DgHmcA has a V-shape architecture, already observed in HmcA isolated from Desulfovibrio vulgaris Hildenborough. The presence of an oligosaccharide molecule covalently bound to an Asn residue was observed in the electron density maps of DgHmcA and confirmed by mass spectrometry. Three modified monosaccharides appear at the highly hydrophobic vertex, possibly acting as an anchor of the protein to the cytoplasmic membrane.

Cytochrome c nitrite reductase is a multicenter enzyme that uses a five-coordinated heme to perform the six-electron reduction of nitrite to ammonium. In the sulfate reducing bacterium Desulfovibrio desulfuricans ATCC 27774, the enzyme is purified as a NrfA2NrfH complex that houses 14 hemes. The number of closely-spaced hemes in this enzyme and the magnetic interactions between them make it very difficult to study the active site by using traditional spectroscopic approaches such as EPR or UV–Vis. Here, we use both catalytic and non-catalytic protein film voltammetry to simply and unambiguously determine the reduction potential of the catalytic heme over a wide range of pH and we demonstrate that proton transfer is coupled to electron transfer at the active site.

International audience

Key determinants for the development of an allergic response to an otherwise ‘harmless’ food protein involve different factors like the predisposition of the individual, the timing, the dose, the route of exposure, the intrinsic properties of the allergen, the food matrix (e.g. lipids) and the allergen modification by food processing. Various physicochemical parameters can have an impact on the allergenicity of animal proteins. Following our previous review on how physicochemical parameters shape plant protein allergenicity, the same analysis was proceeded here for animal allergens., We found that each parameter can have variable effects, ranging on an axis from allergenicity enhancement to resolution, depending on its nature and the allergen. While glycosylation and phosphorylation are common, both are not universal traits of animal allergens. High molecular structures can favour allergenicity, but structural loss and uncovering hidden epitopes can also have a similar impact. We discovered that there are important knowledge gaps in regard to physicochemical parameters shaping protein allergenicity both from animal and plant origin, mainly because the comparability of the data is poor. Future biomolecular studies of exhaustive, standardised design together with strong validation part in the clinical context, together with data integration model systems will be needed to unravel causal relationships between physicochemical properties and the basis of protein allergenicity., The authors highly appreciate the support from the COST Office. This article is based upon work from COST Action FA1402, supported by COST (European Cooperation in Science and Technology, www.cost.eu). This work was also supported by Fundação para a Ciência e Tecnologia under the Partnership Agreement UIDB 50006/2020 and by the projects AlleRiskAssess—PTDC/BAA-AGR/31720/2017. C.V. is grateful to FCT grant (PD/BD/114576/2016) financed by POPH-QREN (subsidised by FSE and MCTES). J.C. acknowledges FCT for the research contract (SFRH/BPD/102404/2014). T.C.V. is grateful to the Ministry of Education, Science and Technological Development of the Republic of Serbia through grant number OI172024. P.M.R. and D.S. are grateful to FCT through project UIDB/04326/2020 and Mar2020 16-02-01-FMP-0014—“ALLYFISH”. J.K. and A.K. acknowledge PRIDE program grants (PRIDE/11012546/NEXTIMMUNE). J.K. also acknowledges FNR (Fonds National de la Recherche) and the PMC (Personalised Medicine Consortium).