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Marine Glycobiology Group

The marine environment is actually considered to be one of the most vast, largely untapped resources for interesting and novel biomolecules. But, at the same time, this environment is also the less uncovered with respect to the assignment of precise biological functions to genes, proteins and enzymes. This contradictory situation makes the marine environment very attractive for bioprospecting to discover new functions and molecules, but the lack of niche specific information renders our advanced screening technologies rather inefficient for the exploration of the vast pool of proteins and enzymes. Thus, the marine enzyme discovery has basically been performed by the isolation and purification of defined activities and, as a consequence, is tightly following the need dictated by the abundance and use of the corresponding substrates.

The majority of the organic matter produced by marine red, brown and green macroalgae and seagrasses are polysaccharides that represent at least 50% of algal dry weight, a huge resource for renewable biomass in the ocean. Due to their interesting gelling properties, many of the major marine polysaccharides are already exploited for industrial applications. But, significantly, algal biomass also displays huge chemical diversity by its abundance in a variety of uronic and sulfated polysaccharides that are largely unexploited, offering many novel industrial opportunities. Enzymes, specifically degrading these original polysaccharides, are potentially the key to new applications in producing defined sub-structures of these bioactive molecules.

In the marine environment, the naturally occurring algal biomass is largely recycled by marine heterotrophic bacteria and particularly marine Bacteroidetes. They thus possess all the enzymatic ‘tools’ to break down the complex natural carbon source into smallest building-blocks that can be assimilated by the bacterium. The recent availability of genomic data on heterotrophic marine bacteria emphasises the crucial role that microbes play in the global carbon cycle. However, the massive presence of proteins of unknown function hampers our understanding of the detailed mechanisms by which this carbon cycle is fine-tuned. Moreover, genome data from marine organisms are essentially annotated in light of the knowledge accumulated on bacteria and fungi that decompose terrestrial plants. But marine algal polysaccharides clearly differ from their terrestrial counterparts, and their associated enzymes usually constitute novel protein families.

In our lab, we are trying to uncover the essentials of the enzymatic systems that heterotrophic marine bacteria have developed to catabolise the abundant carbon source. Within a large effort on ‘marine genomics’ that was undertaken in the European network of excellence, we have sequenced and annotated the complete genome of a marine flavobacterium, Zobellia galactanivorans, that was isolated in Roscoff, France, from the red algae Delesseria sanguinea. This bacterium from the Bacteroidetes phylum has turned out to be an excellent model for macro-algal polysaccharide degradation. To understand the complete catabolic pathways, we are currently applying knowledge-based strategies using bioinformatics genome screening, comparative genomics and transcriptomics to select potential new genes with catabolic functions. We then undertake the full pipeline from medium throughput, parallel cloning, heterologous expression and affinity-based purification of the selected potential enzymes for the structural and biochemical characterisation of candidate ‘hypothetical conserved proteins’, or members of phylogenetic sub-families, to identify new enzyme functions that are missing in the metabolic pathways by which marine polysaccharides are degraded in the marine environment.

The recent success of this strategy has allowed us to discover new activities, such as novel polysaccharidases specific to the sulfated polysaccharide present in the red algal Porphyra species (reference 1), and to identify the first exo-acting 1,3-α-3,6-anhydro-L-galactosidase that we characterised at biochemical and 3D structural level (reference 2). With these new activities, we are on our way to building an entire picture of the complete pathway for the catabolisation of the complex, natural, red algal cell wall polysaccharide called agar.

References:

1. Hehemann J.H., Correc G., Barbeyron T., Helbert W., Czjzek M, Michel G. (2010) Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 464, 908-912.

2. Rebuffet E, Groisillier A, Thompson A, Jeudy A, Barbeyron T, Czjzek M, Michel G. (2011) Discovery and structural characterization of a novel glycosidase family of marine origin. Environ Microbiol. 13(5):1253-70.

Mirjam Czjzek and Gurvan Michel
Directors of Research of the French National Research Center
Marine Institute ‘Station Biologique de Roscoff’
CNRS