A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan

Abstract

Algal cell wall polysaccharides constitute a large fraction in the biomass of marine primary producers and are thus important in nutrient transfer between trophic levels in the marine ecosystem. In order for this transfer to take place, polysaccharides must be degraded into smaller mono-and disaccharide units, which are subsequently metabolized, and key components in this degradation are bacterial enzymes. The marine bacterium Colwellia echini A3 T is a potent enzyme producer since it completely hydrolyzes agar and -carrageenan. Here, we report that the genome of C. echini A3 T harbors two large gene clusters for the degradation of carrageenan and agar, respectively. Phylogenetical and functional studies combined with transcriptomics and in silico structural modeling revealed that the carrageenolytic cluster encodes furcellaranases, a new class of glycoside hydrolase family 16 (GH16) enzymes that are key enzymes for hydrolysis of furcellaran, a hybrid carrageenan containing both ␤and -carrageenan motifs. We show that furcellaranases degrade furcellaran into neocarratetraose-43-O-monosulfate [DA-(␣1,3)-G4S-(␤1,4)-DA-(␣1,3)-G], and we propose a molecular model of furcellaranases and compare the active site architectures of furcellaranases, -carrageenases, ␤-agarases, and ␤-porphyranases. Furthermore, C. echini A3 T was shown to encode -carrageenases, -carrageenases, and members of a new class of enzymes, active only on hybrid ␤/-carrageenan tetrasaccharides. On the basis of our genomic, transcriptomic, and functional analyses of the carrageenolytic enzyme repertoire, we propose a new model for how C. echini A3 T degrades complex sulfated marine polysaccharides such as furcellaran, -carrageenan, and -carrageenan. IMPORTANCE Here, we report that a recently described bacterium, Colwellia echini, harbors a large number of enzymes enabling the bacterium to grow on -carrageenan and agar. The genes are organized in two clusters that encode enzymes for the total degradation of -carrageenan and agar, respectively. As the first, we report on the structure/ function relationship of a new class of enzymes that hydrolyze furcellaran, a partially sulfated ␤/-carrageenan. Using an in silico model, we hypothesize a molecular structure of furcellaranases and compare structural features and active site architectures of furcellaranases with those of other GH16 polysaccharide hydrolases, such as -carrageenases, ␤-agarases, and ␤-porphyranases. Furthermore, we describe a new class of enzymes distantly related to GH42 and GH160 ␤-galactosidases and show that this new class of enzymes is active only on hybrid ␤/-carrageenan oligosaccharides. Finally, we propose a new model for how the carrageenolytic enzyme repertoire enables C. echini to metabolize ␤/-, -, and -carrageenan.

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

“…Based on a KEGG analysis, we also deduced that strain PS06 has alternative pathways for carbon, despite some missing genes involved in the glyoxylate cycle, anabolic pathway for C 2 compounds, malonate semialdehyde pathway (aldehyde oxidation) [ 54 ], and d -galactonate degradation (i.e., DeLey–Doudoroff pathway) [ 55 ]. Genes in the DeLey–Doudoroff pathway have been identified in algal polysaccharide-degrading marine microorganisms [ 56 , 57 ]. Although strain PS06 did not use d -galactose as a growth substrate, it might be able to use it for ascorbate biosynthesis [ 58 , 59 ].…”

Sweet and magnetic: Succession and CAZyme expression of marine bacterial communities encountering a mix of alginate and pectin particles

“…6A). In contrast, CAZyme genes in gammaproteobacterial MAGs were largely scattered throughout the genomes, although PUL-like operons occur in related taxa [60,93,94].…”

“…Hence, particle colonization largely related to few dominant taxa, comparable to other marine polysaccharide particles [13,15]. Enrichment of these taxa compared to the FL fraction (Kruskal-Wallis test, p < 0.001) mirrors their occurrence on marine algae, with considerable CAZyme repertoires in some representatives [59][60][61][62]. The Colwellia population comprised an assemblage of diverse ASVs, appearing from nearly undetectable levels in the ambient community ( Supplementary Fig.…”

“…Divergent CAZyme repertoires in related Colwellia spp. presumably reflect their different niches, as C. echini has been isolated from a sea urchin [60].…”

Characterisation of an exo-(α-1,3)-3,6-anhydro-d-galactosidase produced by the marine bacterium Zobellia galactanivorans DsijT: Insight into enzyme preference for natural carrageenan oligosaccharides and kinetic characterisation on a novel chromogenic substrate

“…PULs are a rich enzymatic resource, unlocking an unknown PUL specificity for a defined polysaccharide can result in the discovery of novel CAZyme families and/or novel activities within already created CAZyme families (http://www.cazy.org/) [14]. Recently several marine bacterial PULs have been described [15][16][17], including PULs specific for the complex red algal extracellular matrix polysaccharide carrageenan [6,8,18,19].…”