Category Archives: Academic productions

Article: Scientific reports

Posted on by

Highly Efficient CYP167A1 (EpoK) dependent Epothilone B Formation and Production of 7-Ketone Epothilone D as a New Epothilone Derivative. F Kern, T K. F. Dier, Y Khatri , K M. Ewen, JPJacquot, DA. Volmer, R Bernhardt. Scientific Reports | 5:14881 | DOI: 10.1038/srep14881

Abstract

Since their discovery in the soil bacterium Sorangium cellulosum, epothilones have emerged as a valuable substance class with promising anti-tumor activity. Because of their benefits in the treatment of cancer and neurodegenerative diseases, epothilones are targets for drug design and pharmaceutical research. The final step of their biosynthesis – a cytochrome P450 mediated epoxidation of epothilone C/D to A/B by CYP167A1 (EpoK) – needs significant improvement, in particular regarding the efficiency of its redox partners. Therefore, we have investigated the ability of various hetero- and homologous redox partners to transfer electrons to EpoK. Hereby, a new hybrid system was established with conversion rates eleven times higher and Vmax of more than seven orders of magnitudes higher as compared with the previously described spinach redox chain. This hybrid system is the most efficient redox chain for EpoK described to date. Furthermore, P450s from Soce56 were identified which are able to convert epothilone D to 14-OH, 21-OH, 26-OH epothilone D and 7-ketone epothilone D. The latter one represents a novel epothilone derivative and is a suitable candidate for pharmacological tests. The results revealed myxobacterial P450s from S. cellulosum Soce56 as promising candidates for protein engineering for biotechnological production of epothilone

derivatives.

Article: Plos one

Posted on by

Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing

M Diouf, V Roy, P Mora, S Frechault, T Lefebvre, V Hervé, … PLoS ONE 10 (10), e0140014

Abstract

Previous surveys of the gut microbiota of termites have been limited to the worker caste. Termite gut microbiota has been well documented over the last decades and consists mainly of lineages specific to the gut microbiome which are maintained across generations. Despite this intimate relationship, little is known of how symbionts are transmitted to each generation of the host, especially in higher termites where proctodeal feeding has never been reported. The bacterial succession across life stages of the wood-feeding higher termite Nasutitermes arborum was characterized by 16S rRNA gene deep sequencing. The microbial community in the eggs, mainly affiliated to Proteobacteria and Actinobacteria, was markedly different from the communities in the following developmental stages. In the first instar and last instar larvae and worker caste termites, Proteobacteria and Actinobacteria were less abundant than Firmicutes, Bacteroidetes, Spirochaetes, Fibrobacteres and the candidate phylum TG3 from the last instar larvae. Most of the representatives of these phyla (except Firmicutes) were identified as termite-gut specific lineages, although their relative abundances differed. The most salient difference between last instar larvae and worker caste termites was the very high proportion of Spirochaetes, most of which were affiliated to the Treponema Ic, Ia and If subclusters, in workers. The results suggest that termite symbionts are not transmitted from mother to offspring but become established by a gradual process allowing the offspring to have access to the bulk of the microbiota prior to the emergence of workers, and, therefore, presumably through social exchanges with nursing workers.

Article: Cellular microbiology

Posted on by

Rust fungal effectors mimic host transit peptides to translocate into chloroplasts. B Petre, C Lorrain, D Saunders, S Duplessis, S Kamoun. Cellular Microbiology, DOI: 10.1111/cmi.12530

Abstract

Parasite effector proteins target various host cell compartments to alter host processes and promote infection. How effectors cross membrane-rich interfaces to reach these compartments is a major question in effector biology. Growing evidence suggests that effectors use molecular mimicry to subvert host cell machinery for protein sorting. We recently identified CTP1 (chloroplast-targeted protein 1), a candidate effector from the poplar leaf rust fungus Melampsora larici-populina that carries a predicted transit peptide and accumulates in chloroplasts and mitochondria. Here, we show that the CTP1 transit peptide is necessary and sufficient for accumulation in the stroma of chloroplasts. CTP1 is part of a Melampsora-specific family of polymorphic secreted proteins. Two members of that family, CTP2 and CTP3, also translocate in chloroplasts in a N-terminal signal-dependent manner. CTP1, CTP2 and CTP3 are cleaved when they accumulate in chloroplasts, while they remain intact when they do not translocate into chloroplasts. Our findings reveal that fungi have evolved effector proteins that mimic plant-specific sorting signals to traffic within plant cells.

Article: Plos one

Posted on by

The GSTome Reflects the Chemical Environment of White-Rot Fungi. A Deroy, F Saiag, Z Kebbi-Benkeder, N Touahri, A Hecker, … PloS one 10 (10), e0137083

Abstract

White-rot fungi possess the unique ability to degrade and mineralize all the different components of wood. In other respects, wood durability, among other factors, is due to the presence of extractives that are potential antimicrobial molecules. To cope with these molecules, wood decay fungi have developed a complex detoxification network including glutathione transferases (GST). The interactions between GSTs from two white-rot fungi, Trametes versicolor and Phanerochaete chrysosporium, and an environmental library of wood extracts have been studied. The results demonstrate that the specificity of these interactions is closely related to the chemical composition of the extracts in accordance with the tree species and their localization inside the wood (sapwood vs heartwood vs knotwood). These data suggest that the fungal GSTome could reflect the chemical environment encountered by these fungi during wood degradation and could be a way to study their adaptation to their way of life

Article: Forest Ecology and Management

Posted on by

Pre-existing forests as sources of pathogens? The emergence of Armillaria ostoyae in a recently planted pine forest F Labbé, B Marcais, JL Dupouey, T Bélouard, X Capdevielle, D Piou, …. Forest Ecology and Management 357, 248-258

Abstract

Fungi are among the principal causal agents of emerging plant diseases, which are a matter of worldwide concern. Changes in land use, such as the expansion of cultivated areas, are implicated in the emergence of fungal diseases, but have been less often reported for native species plantations. In the maritime pine (Pinus pinaster) forest of the Landes de Gascogne (south-western France), pine mortality due to the root rot fungus Armillaria ostoyae (Basidiomycete) has been increasing over the last 30 years. The first cases of this disease occurred in 1920 only few years after a period of rapid major change to the landscape. During the second half of the 19th century the landscape was transformed from marshes to the largest monospecific maritime pine plantation forest in Europe. We carried out two surveys (0.24 and 1 million hectares) of Armillaria root rot disease in the Landes area, to investigate the spatial distribution of pathogen damage and to determine the role of historical factors in the establishment of this pattern. For the two surveys, spatial analyses and generalised linear models revealed a significant effect on the current geographical distribution of A. ostoyae disease of the proportion of pre-existing forest in the vicinity of afforested areas and a significant effect of the proximity of the first forests planted in the coastal dunes. These results suggest that A. ostoyae was commonly distributed in pre-existing forest areas, and that most of these fragments acted as source for the colonisation of newly planted forests. Better predictions on the risk of establishment of new disease foci in this forest area can be achieved from these results.

Article: Microbial Ecology

Posted on by

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences. M Jeanbille, M Buée, C Bach, A Cébron, P Frey-Klett, MP Turpault, S Uroz. Microbial Ecology, 1-12.

Abstract

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Article: Annals of Forest Science

Posted on by

Total phenolic and lignin contents, phytochemical screening, antioxidant and fungal inhibition properties of the heartwood extractives of ten Congo Basin tree species. S Mounguengui, JBS Tchinda, MK Ndikontar, S Dumarçay, C Attéké, … Annals of Forest Science, 1-10

Abstract

Content and type of extractives vary considerably among woody species in the Congo Basin tropical forest. They influence the natural durability of wood with respect to fungal and insect degradation. Species containing higher amounts of extractives and Klason lignin were generally less susceptible to fungal colonization. Phenolic extractives with large anti-fungal and high antioxidant activities were the main chemical family of compounds extracted from the tested species, which suggests a potential chemical valorization of these extractives.

Article: Fungal Genetics and Biology

Posted on by

Evolutionary divergence of Ure2pA glutathione transferases in wood degrading fungiT Roret, A Thuillier, F Favier, E Gelhaye, C Didierjean, M Morel-Rouhier Fungal Genetics and Biology

Abstract

The intracellular systems of detoxification are crucial for the survival of wood degrading fungi. Within these systems, glutathione transferases could play a major role since this family of enzymes is specifically extended in lignolytic fungi. In particular the Ure2p class represents one third of the total GST number in Phanerochaete chrysosporium. These proteins have been phylogenetically split into two subclasses called Ure2pA and Ure2pB. Ure2pB can be classified as Nu GSTs because of shared structural and functional features with previously characterized bacterial isoforms. Ure2pA can rather be qualified as Nu-like GSTs since they exhibit a number of differences. Ure2pA possess a classical transferase activity, a more divergent catalytic site and a higher structural flexibility for some of them, compared to Nu GSTs. The characterization of four members of this Ure2pA subclass (PcUre2pA4, PcUre2pA5, PcUre2pA6 and PcUre2pA8) revealed specific functional and structural features, suggesting that these enzymes have rapidly evolved and differentiated, probably to adapt to the complex chemical environment associated with wood decomposition.

Article: Applied Soil Ecology

Posted on by

Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe. RE Creamer, SE Hannula, JP Van Leeuwen, D Stone, M Rutgers, …

Applied Soil Ecology

Abstract

Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators.

Article: Genome announcements

Posted on by

Draft Genome Sequence of Burkholderia sp. Strain PML1 (12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability. S Uroz, P Oger Genome announcements 3 (4), e00798-15

ABSTRACT

We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France).