Functional characterization of a novel “ulvan utilization loci” found in Alteromonas sp. LOR genome

Green algae belonging to the genus Ulvales are known to produce ulvan which is one of the main polysaccharide components of their cell wall. Ulvan is composed of 3O-sulfate-rhamnose (Rha3S), glucuronic acid (GlcA), iduronic acid (IduA) and xylose (Xyl) distributed in three disaccharide repetition moieties: [→ 4)-β-D-GlcA-(1 → 4)-α-L-Rha3S-(1 →], [→ 4)-α-L-IdoA-(1 → 4)-α-L-Rha3S(1 →] and [→ 4)-β-D-Xyl-(1 → 4)-α-L-Rha3S(1 →]. The ability of bacteria to degrade complex algal polysaccharides such as ulvan is usually encoded in clusters of genes referred to as polysaccharide utilization loci (PUL). Full saccharification of ulvan is expected to require an ulvan lyase, which cleaves the β-(1 → 4)-glycosidic bond between Rha3S and GluA or IduA through a β-elimination mechanism. In addition, enzymes with β-glucuronyl hydrolase, rhamnosidase, xylosidase and sulfatase activity are also expected. Recently, the genomes of several ulvan degrading bacteria were sequenced, which led to the identification of a new family of polysaccharide lyases family 24 (PL24). In this work, we have continued to mine the genomic data of one of the sequenced strains, Alteromonas sp. LOR. Here we report the identification of an ulvan associated PUL residing between open reading frames (lor_19 – lor_34). This PUL contains a TonB dependent receptor, along with an experimentally verified rhamnosidase, a β-glucuronyl hydrolase and predicted sulfatases. Interestingly, we also identified in the PUL a new ulvan lyase (LOR_29) which showed no homology to previously reported ulvan lyases making it a founding member of yet another new family of polysaccharide lyases (PL25). Finally, this enzyme prompted us to mine other genomes where we identified additional potential ulvan PULs harboring this gene in other bacterial species. Taken together our report provides further insight into ulvan degradation mechanisms in bacteria and reveals a new family of polysaccharide lyases.