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ANR funded project

Biotechnologies : biotransformation des ressources biologiques (DS0503)
Edition 2014


BLUE ENZYMES


Discovery of novel enzymes for the valorization of algal biomass

Discovery of novel enzymes for the valorization of algal biomass
Seaweeds represent a huge biomass mainly constituted of polysaccharides. These diverse and complex polymers differ from land plant polysaccharides. Despite promising properties, high value products based on algal poly- and oligo-saccharides remain rare. The main bottleneck for the development of a seaweed-based bioeconomy is the lack of enzymes which can specifically cleave algal polysaccharides or modify their structure, and thus allow the tailoring of their biological properties.

The challenge of the discovery of enzymes for Blue Biotechnology
Commercial enzymes essentially originate from terrestrial organisms which degrade plant biomass and thus are inefficient or inactive on algal biomass. Although few specific enzymes were discovered the last years (mainly due to the efforts of our group), the pathways for the biodegradation of algal polysaccharides remain largely uncharacterized. The most relevant sources of specific enzymes are marine bacteria which feed on seaweeds and thus naturally “crack” algal biomass. Among these microorganisms, marine flavobacteria are recognized as the key players in the recycling of seaweeds. In the context of the emergence of blue biotechnologies in France, the BLUE ENZYMES project aims at discovering novel enzymes from marine flavobacteria involved in the bioconversion of algal polysaccharides.

A multidisciplinary approach for marine bioprospection
To discover novel enzymes specific for algal polysaccharides, we are using a multidisciplinary strategy combining catabolic and transcriptomic profiling, comparative genomics and reconstruction of metabolic networks. The most promising candidate enzymes from marine flavobacteria will be overexpressed in Escherichia coli using a medium throughput approach. After an activity screening step using algal polysaccharides and oligosacccharides, the novel active enzymes will be studied in depth at both the biochemical and structural level.

Results

Since the beginning of the project in February 2015 we have analyzed 41 genomes of marine flavobacteria using the MicroScope annotation plateform (https://www.genoscope.cns.fr/agc/microscope/home/). In our first round of medium-throughput protein expression we have succeeded to obtain 51% of soluble recombinant enzymes (49/96 target-proteins). Characterization of the most promising candidates is currently underway.
The genome of Zobellia galactanivorans, a macroalgae-associated flavobacterium, which can use most algal polysaccharides as sole carbon sources has been also published (Barbeyron et al, 2016, Environmental Microbiology, cover of the december issue) . In comparison with the genome of 125 Marine Heterotrophic Bacteria (MHB), Z. galactanivorans displays the highest potential for polysaccharide degradation, with 141 glycoside hydrolases (GH), 15 polysaccharide lyases (PL) and 71 sulfatases. Most of these genes are co-localized in 50 Polysaccharides Utilization Loci (PULs), including 22 PULs that contain sulfatase genes. Finally, using statistical and clustering analyses of the 126 MHB genomes we show that their carbohydrate catabolism correlates both with taxonomy and habitat.

Outlook

The next steps will be to finalize the transcriptomic and catabolic analyses of the representative strains of the different flavobacterial genera. These data will be correlated to the results from the comparative genomic analyses and the metabolic network predictions in order to select new enzyme candidates. The biochemical and crystallographic studies of the round 1 enzymes will be pursued in parallel.

Scientific outputs and patents

1. Martin et al (2015) The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria. Frontiers in Microbiology, 6:1487
2. Martin et al (2016) Discovering novel enzymes by functional screening of plurigenomic libraries from alga-associated Flavobacteriia and Gammaproteobacteria. Microbiological Research, 186, 52-61.
3. Barbeyron et al (2016) Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans. Environmental Microbiology, 18, 4610-4627. (selected as journal cover)

Partners

CEA/DSV/IG//Genoscope/LABGeM Commissariat à l'Energie Atomique/Direction des sciences du vivants/Institut Génomique/Génoscope/LABGeM

CNRS "Laboratoire de Biologie Intégrative des Modèles Marins", UMR 8227, Station Biologique de Roscoff

INRA “Virologie et Immunologie Moléculaires”, INRA Jouy en Josas, UR 892

ANR grant: 495 290 euros
Beginning and duration: octobre 2014 - 48 mois

Submission abstract

Brown, green and red macroalgae (commonly referred to as seaweeds) dominate the primary production in coastal ecosystems and represent a huge biomass which is mainly constituted of polysaccharides. These diverse and complex polymers essentially differ from land plant polysaccharides. Notably, seaweeds are characterized by their abundance in uronic and sulfated polysaccharides: alginates and fucoidans in brown algae; ulvans in green algae; agars, porphyrans and carrageenans in red algae. Such sulfated polysaccharides are absent in land plants and are reminiscent of the sulfated glycosaminoglycans from the extracellular matrix of animals. Some algal polysaccharides are already used in industries as thickeners and gelling agents (e.g. alginates, agars, carrageenans). These biomolecules display also interesting biological activities (e.g. immune-stimulant, anti-viral, anti-coagulant). Despite these promising properties, algal biomass is underexploited and high value products based on algal polysaccharides and oligosaccharides remain rare. The main bottleneck for the development of a seaweed-based bioeconomy is the lack of enzymes which can specifically cleave algal polysaccharides or modify their structure, and thus allow the tailoring of their biological properties. Indeed, commercial enzymes essentially originate from terrestrial organisms which degrade plant biomass and thus are inefficient or inactive on algal biomass. Although few specific enzymes were discovered the last years (mainly due to the efforts of our group), the pathways for the biodegradation of algal polysaccharides remain largely uncharacterized. The most relevant sources of specific enzymes are marine bacteria which feed on seaweeds and thus naturally “crack” algal biomass. Among these microorganisms, marine flavobacteria are recognized as the key players in the recycling of seaweeds. In the context of the emergence of blue biotechnologies in France, the BLUE ENZYMES project aims at discovering novel enzymes from marine flavobacteria involved in the bioconversion of algal polysaccharides, using a multidisciplinary strategy combining catabolic and transcriptomic profiling, comparative genomics and reconstruction of metabolic networks. The most promising candidate enzymes will be overexpressed in Escherichia coli using a medium throughput approach. After an activity screening step using algal polysaccharides and oligosacccharides, the novel active enzymes will be studied in depth at both the biochemical and structural level. Our consortium will focus on three key genera of marine flavobacteria, Zobellia, Mariniflexile and Tenacibaculum. As preliminary results, we have already sequenced the genome of 28 species (5 Zobellia, 5 Mariniflexile and 18 Tenacibaculum) which will be exploited in BLUE ENZYMES.

 

ANR Programme: Biotechnologies : biotransformation des ressources biologiques (DS0503) 2014

Project ID: ANR-14-CE19-0020

Project coordinator:
Monsieur Gurvan MICHEL ("Laboratoire de Biologie Intégrative des Modèles Marins", UMR 8227, Station Biologique de Roscoff)

 

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The project coordinator is the author of this abstract and is therefore responsible for the content of the summary. The ANR disclaims all responsibility in connection with its content.