Subcellular localisation of Medicago truncatula 9/13-hydroperoxide lyase reveals a new localisation pattern and activation mechanism for CYP74C enzymes

<p>Abstract</p> <p>Background</p> <p>Hydroperoxide lyase (HPL) is a key enzyme in plant oxylipin metabolism that catalyses the cleavage of polyunsaturated fatty acid hydroperoxides produced by the action of lipoxygenase (LOX) to volatile aldehydes and oxo acids. The synthesis of these volatile aldehydes is rapidly induced in plant tissues upon mechanical wounding and insect or pathogen attack. Together with their direct defence role towards different pathogens, these compounds are believed to play an important role in signalling within and between plants, and in the molecular cross-talk between plants and other organisms surrounding them. We have recently described the targeting of a seed 9-HPL to microsomes and putative lipid bodies and were interested to compare the localisation patterns of both a 13-HPL and a 9/13-HPL from <it>Medicago truncatula</it>, which were known to be expressed in leaves and roots, respectively.</p> <p>Results</p> <p>To study the subcellular localisation of plant 9/13-HPLs, a set of YFP-tagged chimeric constructs were prepared using two <it>M. truncatula </it>HPL cDNAs and the localisation of the corresponding chimeras were verified by confocal microscopy in tobacco protoplasts and leaves. Results reported here indicated a distribution of <it>M</it>.<it>truncatula </it>9/13-HPL (HPLF) between cytosol and lipid droplets (LD) whereas, as expected, <it>M</it>.<it>truncatula </it>13-HPL (HPLE) was targeted to plastids. Notably, such endocellular localisation has not yet been reported previously for any 9/13-HPL. To verify a possible physiological significance of such association, purified recombinant HPLF was used in activation experiments with purified seed lipid bodies. Our results showed that lipid bodies can fully activate HPLF.</p> <p>Conclusion</p> <p>We provide evidence for the first CYP74C enzyme, to be targeted to cytosol and LD. We also showed by sedimentation and kinetic analyses that the association with LD or lipid bodies can result in the protein conformational changes required for full activation of the enzyme. This activation mechanism, which supports previous <it>in vitro </it>work with synthetic detergent micelle, fits well with a mechanism for regulating the rate of release of volatile aldehydes that is observed soon after wounding or tissue disruption.</p

Follistatin, a Novel Biomarker for Malignant Gliomas

Molecular biomarkers are commonly used for the management of several types of malignant tumours in routine clinical practice. However, this is not the case for malignant gliomas. Cytokines and Angiogenesis factors are potential candidates due to their intrinsic role in tumourigenesis. Pre- and post-operative serum from 36 malignant glioma patients and 36 controls was analysed using the Bio-Plex Pro Angiogenesis and Cytokines Assay (Bio-Rad, USA). Amongst the molecules tested, the serum concentration of follistatin was significantly higher in patients than in controls. Moreover, the serum concentration of follistatin of the patients postoperatively was significantly reduced compared to that preoperatively. Factors such as age and gender did not affect the concentrations of follistatin measured in the serum of patients pre- and post-operatively as well as healthy controls. This is the first report of follistatin as potential biomarker for the detection of malignant gliomas

Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes

This study reports the ability of one hyperthermophile and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. A. pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in A. pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with observations made on A. fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions.This research was financially supported by Shell Global Solutions International BV. Research of AJMS is supported by ERC grant (project 323009) and the Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO). Sequencing data for strain NMP have been submitted to the European Nucleotide Archive (ENA) under accession number PRJEB8377. Mass spectrometry proteomics data and database search results have been deposited to the ProteomeXchange Consortium (Vizcaino et al., 2014) via the PRIDE partner repository with the dataset identifier PXD001683 and DOI 0.6019/PXD001683

Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure

Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments

Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure

Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments

The gateway pDEST17 expression vector encodes

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Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms

International audienceSulfite-reducing and sulfate-reducing microorganisms (SRM) play important roles in anoxic environments, linking the sulfur and carbon cycles. With climate warming, the distribution of anoxic habitats conductive to dissimilatory SRM is expanding. Consequently, we hypothesize that novel SRM are likely to emerge from the rare biosphere triggered by environmental changes. Using the dsrB gene as a molecular marker of sulfite-reducers and sulfate-reducers, we analyzed the diversity, community composition, and abundance of SRM in 200 samples representing 14 different ecosystems, including marine and freshwater environments, oil reservoirs, and engineered infrastructure. Up to 167,397 species-level OTUs affiliated with 47 different families were identified. Up to 96% of these can be considered as "rare biosphere SRM". One third of the dsrB genes identified belonged to uncharacterized lineages. The dsrB sequences exhibited a strong pattern of selection in different ecosystems. These results expand our knowledge of the biodiversity and distribution of SRM, with implications for carbon and sulfur cycling in anoxic ecosystems

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry