Project description:The anaerobic plant biomass delignification was questioned till recently despite being a key process for plant cell wall degradation in anaerobic biotopes where plant debris accumulate, the carbon mineralization being the limiting step of the Carbon cycle. Besides no actors were identified till now and no data were available on this processus performed by anaerobic cellulolytic bacteria or even on its existence Using RNAseq, we here report the idenfication of secreted (including cellulosomal) enzymes, especially SGNH hydrolase family members known to be esterases but never described to act on lignin. We also propose based on our genetic, biochemical and bioinformatic approaches, a new role for the SGNHs in the remodeling of lignin to favor the access to polysaccharides by plant polysaccharides degrading proteins, function that could be useful for the design of biotechnological applications.
Project description:Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers often utilize denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen-gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well-described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci. However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to highlight microbial drivers for lignocellulose transformation in woodchip bioreactors with the aim to provide an in-depth characterization of the indigenous microorganisms and their active enzymes. Our findings highlight a microbial community enriched for lignocellulose-degrading denitrifiers with key players from Giesbergeria, Cellulomonas, Azonexus, and UBA5070, including polysaccharide utilization loci from Bacteroidetes. A wide substrate specificity is observed among the many expressed carbohydrate active enzymes (CAZymes), evidencing a swift degradation of lignocellulose, including even enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.
Project description:Plant cell suspension cultures offer a sustainable method for producing valuable secondary metabolites, such as bioactive pentacyclic triterpenes. This study established a high-triterpene-yielding cell suspension culture from the apple cultivar "Cox Orange Pippin." Through transcriptomic analysis and triterpene profiling across growth phases, we uncovered complex regulatory networks that govern biomass production and triterpene biosynthesis. Key biological processes, including cell cycle regulation, cell wall biosynthesis, lipid metabolism, and stress response mechanisms, play pivotal roles in culture dynamics. Differential gene expression linked to these processes revealed how the culture adapts to growth conditions and nutrient availability at each growth phase. Methyl jasmonate elicitation enhanced phenylpropanoid and flavonoid biosynthesis, along with specific triterpene production pathways, highlighting its potential for optimizing secondary metabolite production. Key enzymes, including oxidosqualene cyclase 4 and a putative C-2α hydroxylase, emerged as promising targets for future metabolic engineering of triterpene pathways. This study represents the first in-depth report on the molecular mechanisms underlying plant cell growth in bioreactors, specially focusing on a non-model plant species . These findings reveal key regulatory pathways in biomass accumulation and triterpene production, offering insights to optimize bioreactor cultures for industrial use. The research opens new avenues to enhance triterpene yields via targeted metabolic engineering and innovative bioprocessing strategies, paving the way for efficient large-scale production.
Project description:In this study we examined an anaerobic digester reactor fed with cellulose in order to identify cellulose degrading microorganisms using a culture independent approach. A metagenome was linked to the newly synthesized proteins involved by cellulose, by investigation of labelled proteins (Protein-SIP). The study aims at identifying microorganisms involved in the degradation of plant-based biomass.