Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacteriumCatenovulumsp. CCB-QB4

Abstract

Background Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate.

Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles

“…Genome‐based taxonomy assigned MAG21 to the uncultured taxon GCA‐2401725, whereas the majority of CAZymes possess homologs in Catenovulum spp. (Supplementary Table 4), recently described for pectinolytic capacities (Furusawa et al ., 2021). Growth of the Catenovulum isolate CCB‐QB4 on unsaturated galacturonate has been linked to GH28 and GH105 enzymes, which are also encoded by MAG21 (Supplementary Table 4).…”

Saccharobesus litoralis gen. nov., sp. nov., a novel alginate-degrading bacterium isolated from the surface of intertidal algal turf

“…The study revealed that strain CCB-QB4 T , possessed 183 glycoside hydrolases and 43 polysaccharide lyases including many alginate lyases in the genome [8]. Furthermore, in 2021, we found that CCB-QB4 T degraded and used uronic acid-containing polysaccharides, namely alginate, pectin, ulvan and gellan gum, as a carbon source [9]. Based on the polyphasic evidence in the current study, we propose that strain CCB-QB4 T represents a novel genus of the family Alteromonadaceae.…”

“…As for growth conditions, strain CCB-QB4 T was incapable of growing at 10 °C as compared to the other four strains [1–3, 7]. Our previous report demonstrated that strain CCB-QB4 T obligately required carbon sources, such as glucose and uronic acid-containig polysaccharides, in culture broth [9]. Similarly, MB supplemented with glucose was used to culture cells belonging to the genus Catenovulum [1–3].…”