Biology subjects

Oger, P. M.

Publications and source records attributed to Oger, P. M..

8 recordsLinked to original sources

bioRxiv2026

Coumarin-based blue excitable probe for functional screening of dehalogenase activity

In the enzymatic toolbox of depollution, hydrolytic dehalogenases are of particular interest for the bioremediation of organohalogenated compounds. To better identify and characterize these enzymes, it is important to develop appropriate sensing methods. Fluorescent probes for dehalogenase detection have been developed in the past years, however, to this date none were available for application using the common FITC parameters (i.e. excitation laser at 488 nm). To address this limitation, we herein report a new fluorescent probe, COU4-Cl, excitable in the violet (405 nm) and blue (488 nm) wavelengths adapted for the detection and characterization of haloalkane dehalogenases. Its applicability is discussed and evaluated in comparison to the previously described COU2-Cl probe only excitable in the violet (405 nm). This study shows the advantages and complementarity of the two probes, and further demonstrate their application for the discrimination of dehalogenase activity in whole cell assays.

biochemistry↗

bioRxiv2026

Thermococcales pangenome uncovers new genera and modular evolution.

The order Thermococcales is unusual among Archaea in being known primarily from hundreds of lab-cultured isolates rather than metagenome-assembled genomes. Such cultivation is powerful for comparative genomics, allowing access to complete closed genomes rather than fragmented assemblies. We analysed 122 complete genomes, comprising all publicly available type species plus 67 new isolates, as a single pangenome. A combination of genome-scale metrics resolved 70 species across five genus-level clades, two proposed here as the new genera Oleococcus and Piezococcus, in addition to the canonical Pyrococcus, Palaeococcus, and Thermococcus. Only 6.1% of the 21,490 gene families are persistent, yet these contribute over half the genes in any genome. We observe that accessory functions, such as amino-acid biosynthesis, often behave modularly, being gained and lost as intact cassettes from genus-specific chromosomal loci. Combined with 114 mobile genetic elements, 72 of which are integrated in the chromosome at conserved tRNA genes, we find that Thermococcales genomes accommodate rapid horizontal turnover through a constrained chromosomal architecture.

genomics↗

bioRxiv2025

Bilayer-forming lipids enhance archaeal monolayer membrane stability

Archaeal membranes exhibit remarkable stability under extreme environmental conditions, a feature attributed to their unique lipid composition. While it is widely accepted that tetraether lipids confer structural integrity by forming monolayers, the role of bilayer-forming diether lipids in membrane stability remains unclear. Here, we demonstrate that the incorporation of diethers into archaeal-like lipid assemblies enhances membrane organization and adaptability under thermal stress. Using neutron diffraction, we show that membranes composed of mixed diethers and tetraethers exhibit greater structural order and stability compared to pure lipid systems. Contrary to expectations, monolayer-forming tetraethers alone display increased variability in lamellar spacing under fluctuating temperature and humidity, whereas mixed lipid membranes maintain a consistent architecture. Furthermore, neutron scattering length density profiles reveal an unexpected density feature at the bilayer midplane, challenging conventional models of archaeal monolayer organization. These findings suggest that molecular diversity of lipid molecules, rather than tetraether dominance, plays a critical role in membrane auto assembly, stability and adaptability. Our results provide new insights into archaeal membrane adaptation strategies, with implications for the development of bioinspired, robust synthetic membranes for industrial and biomedical applications.

biophysics↗

bioRxiv2024

Bradyrhizobium hardenbergiae sp. nov., isolated from Hardenbergia violacea in Australia, represents a novel basal lineage of the B. elkanii supergroup

Bradyrhizobia are widespread across the Australian continent, where they are essential to Australian ecosystems by helping legumes to compensate nutrient deficiencies and low fertility of Australian soils. Among the Bradyrhizobium genospecies identified during a survey of Australian native rhizobia communities in 1994-1995, genospecies L appeared to be only distantly related to any Bradyrhizobium lineages known at the time. We take advantage of the recent sequencing of the genome of strain BDV5419, the original strain corresponding to Bradyrhizobium genospecies L, to re-assess this lineage taxonomic status. We characterized further strain BDV5419 based on morpho-physiological traits and determined its phylogenetic relationships with the type strains of the 88 currently known Bradyrhizobium species based on sequence comparisons of SSU rRNA genes and complete genomes. The digital DNA-DNA hybridization relatedness with any type strain was less than 33% and both SSU rRNA gene and genome phylogenies confirmed that this strain does not belong to any formerly described species within the Bradyrhizobium genus. Whereas its position within the lineage encompassing the B. elkanii and B. jicamae supergroups is unresolved in the SSU rDNA phylogeny, strain BDV5419 appears to be one of most basal lineages of the B. elkanii supergroup in the genome comparison. All data thus support the description of the novel species Bradyrhizobium hardenbergiae sp. nov. which type strain is BDV5419T (= CFBP 9111T = LMG 32897T), isolated from a nodule of Hardenbergia violaceae in Black Mountain Nature Reserve, in Canberra, ACT, Australia.

microbiology↗

bioRxiv2022

Unravelling the mechanisms of adaptation to high pressure in proteins

Life is thought to have appeared in the depth of the sea, under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here we show the molecular bases of these mechanisms through a neutron scattering study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein-water dynamics and the elimination of cavities in the protein core. This is achieved by an enrichment of acidic residues on the protein surface and by the use of bulkier hydrophobic residues in the core. These findings will be the starting point in the search of a complete genomic model explaining high pressure adaptation.

biophysics↗

bioRxiv2022

High temperature molecular motions within a model protomembrane architecture

Modern phospholipid membranes are known to be in a functional, physiological state, corresponding to the liquid crystalline phase, only under very precise external conditions. The phase is characterised by specific lipid motions, which seem mandatory to permit sufficient flexibility and stability for the membrane. It can be assumed that similar principles hold for proto-membranes at the origin of life although they were likely composed of simpler, single chain fatty acids and alcohols. In the present study we investigated molecular motions of four types of model membranes to shed light on the variations of dynamics and structure as a function of temperature as protocells might have existed close to hot vents. We find a clear hierarchy among the flexibilities of the samples, where some structural parameters seem to depend on the lipids used while others do not.

biophysics↗

bioRxiv2021

The exploration of Thermococcus barophilus lipidome reveals the widest variety of phosphoglycolipids in Thermococcales.

One of the most distinctive characteristics of Archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures Archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other Archaea.

microbiology↗

bioRxiv2021

Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

Microbes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the core lipid composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the core lipid composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea. Significance statementWe describe here the membrane adaptive strategies the hyperthermophilic, neutrophilic, and marine model archaeon Pyrococcus furiosus implements in response to one of the largest sets of environmental stressors tested to date, including temperature, pH, salinity, presence/absence of elemental sulfur, carbon source, and genetic background. In contrast to the other archaea investigated so far, which response mainly involves the modulation of their diether/tetraether ratio and/or of their average number of cyclopentane rings, P. furiosus regulates its monoalkyl (so called H-shaped) to dialkyl tetraether ratio. Our study thus provides for the first time evidence of adaptive functions of archaeal monoalkyl tetraethers towards low temperature and pH and high salinity.

microbiology↗