Formation of hydroxylamine on dust grains via ammonia oxidation

The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH$_2$OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH$_2$OH is considered a likely target of detection with ALMA. We report on an experimental investigation of the formation of hydroxylamine on an amorphous silicate surface via the oxidation of ammonia. The experimental data are then fed into a simulation of the formation of NH$_2$OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH$_2$OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH$_3$. Suggestions of conditions for future observations are provided.Comment: 9 pages, 9 figure

Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum

Clostridium autoethanogenum, the bacterial model for biological conversion of waste gases into biofuels, grows under extreme carbon-monoxide (CO) concentrations. The strictly anaerobic bacterium derives its entire cellular energy and carbon from this poisonous gas, therefore requiring efficient molecular machineries for CO-conversion. Here, we structurally and biochemically characterized the key enzyme of the CO-converting metabolism: the CO-dehydrogenase/Acetyl-CoA synthase (CODH/ACS). We obtained crystal structures of natively isolated complexes from fructose-grown and CO-grown C. autoethanogenum cultures. Both contain the same isoforms and if the overall structure adopts the classic alpha(2)beta(2) architecture, comparable to the model enzyme from Moorella thermoacetica, the ACS binds a different position on the CODH core. The structural characterization of a proteolyzed complex and the conservation of the binding interface in close homologs rejected the possibility of a crystallization artefact. Therefore, the internal CO-channeling system, critical to transfer CO generated at the C-cluster to the ACS active site, drastically differs in the complex from C. autoethanogenum. The 1.9-angstrom structure of the CODH alone provides an accurate picture of the new CO-routes, leading to the ACS core and reaching the surface. Increased gas accessibility would allow the simultaneous CO-oxidation and acetyl-CoA production. Biochemical experiments showed higher flexibility of the ACS subunit from C. autoethanogenum compared to M. thermoacetica, albeit monitoring similar CO-oxidation and formation rates. These results show a reshuffling of internal CO-tunnels during evolution of these Firmicutes, putatively leading to a bidirectional complex that ensure a high flux of CO-conversion toward energy conservation, acting as the main cellular powerplant

A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea

Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society

CO2-Fixation Strategies in Energy Extremophiles: What Can We Learn From Acetogens?

Domestication of CO2-fixation became a worldwide priority enhanced by the will to convert this greenhouse gas into fuels and valuable chemicals. Because of its high stability, CO2-activation/fixation represents a true challenge for chemists. Autotrophic microbial communities, however, perform these reactions under standard temperature and pressure. Recent discoveries shine light on autotrophic acetogenic bacteria and hydrogenotrophic methanogens, as these anaerobes use a particularly efficient CO2-capture system to fulfill their carbon and energy needs. While other autotrophs assimilate CO2 via carboxylation followed by a reduction, acetogens and methanogens do the opposite. They first generate formate and CO by CO2-reduction, which are subsequently fixed to funnel the carbon toward their central metabolism. Yet their CO2-reduction pathways, with acetate or methane as end-products, constrain them to thrive at the "thermodynamic limits of Life". Despite this energy restriction acetogens and methanogens are growing at unexpected fast rates. To overcome the thermodynamic barrier of CO2-reduction they apply different ingenious chemical tricks such as the use of flavin-based electron-bifurcation or coupled reactions. This mini-review summarizes the current knowledge gathered on the CO2-fixation strategies among acetogens. While extensive biochemical characterization of the acetogenic formate-generating machineries has been done, there is no structural data available. Based on their shared mechanistic similarities, we apply the structural information obtained from hydrogenotrophic methanogens to highlight common features, as well as the specific differences of their CO2-fixation systems. We discuss the consequences of their CO2-reduction strategies on the evolution of Life, their wide distribution and their impact in biotechnological applications

Molecular modelling of the heat capacity and anisotropic thermal expansion of nanoporous hydroxyapatite

International audienceHydroxyapatite, which is the main mineral phase of mammalian bone, occurs in the form of small bricks of colloidal size organized in a way that leaves room to micro-and mesopores. These pores are filled with an electrolyte and confined fluids are recognized for manifesting different dynamical and structural behaviors when compared to bulk fluids. Research on other nanoporous materials reported that confinement may have repercussions on the effective the thermal properties of these materials. Understanding the physical origin of thermal expansion and heat capacity as a function of the hydroxyapatite porosity is, therefore, crucial to predict the thermo-mechanical behavior of bone. Molecular dynamics simulations of hydroxyapatite nanopores (2 nm  ≤  H  ≤  16 nm, where H is the size of the nanopore) in contact with liquid water have been used to determine the effect nanoporosity and water confinement on the heat capacity and thermal expansion of this important biomaterial. At temperatures corresponding to in vivo conditions, the thermal expansion of water confined in nanopores smaller than 6 nm was is solid-like but becomes liquid-like in larger nanopores. The heat capacity of confined water exhibits a maximum at pore sizes of approximately 7 nm. An up-scaling strategy taking into account the anomalous behaviour of nanoconfined water is then proposed to determine the effective heat capacity and the effective heat of hydroxyapatite expansion as a function of its porosity, and to predict regions of variability, compared with the bulk, in the thermal properties of porous hydroxyapatite

Anomalous water and ion dynamics in hydroxyapatite mesopores

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When virulence originates from non-agricultural hosts: New insights into plant breeding

Monogenic plant resistance breakdown is a model for testing evolution in action in pathogens. As a rule, plant pathologists argue that virulence – the allele that allows pathogens to overcome resistance – is due to a new mutation at the avirulence locus within the native/endemic population that infects susceptible crops. In this article, we develop an alternative and neglected scenario where a given virulence pre-exists in a non-agricultural host and might be accidentally released or introduced on the matching resistant cultivar in the field. The main difference between the two scenarios is the divergence time expected between the avirulent and the virulent populations. As a consequence, population genetic approaches such as genome scans and Approximate Bayesian Computation methods allow explicit testing of the two scenarios by timing the divergence. This review then explores the fundamental implications of this alternative scenario for plant breeding, including the invasion of virulence or the evolution of more aggressive hybrids, and proposes concrete solutions to achieve a sustainable resistance

Three-Scale Multiphysics Modeling of Transport Phenomena within Cortical Bone

Bone tissue can adapt its properties and geometry to its physical environment. This ability is a key point in the osteointegration of bone implants since it controls the tissue remodeling in the vicinity of the treated site. Since interstitial fluid and ionic transport taking place in the fluid compartments of bone plays a major role in the mechanotransduction of bone remodeling, this theoretical study presents a three-scale model of the multiphysical transport phenomena taking place within the vasculature porosity and the lacunocanalicular network of cortical bone. These two porosity levels exchange mass and ions through the permeable outer wall of the Haversian-Volkmann canals. Thus, coupled equations of electrochemohydraulic transport are derived from the nanoscale of the canaliculi toward the cortical tissue, considering the intermediate scale of the intraosteonal tissue. In particular, the Onsager reciprocity relations that govern the coupled transport are checked

Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen

Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs