Data_Sheet_1_Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches.PDF

About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9T (ATCC 43555T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.

海洋藻类生物量中约有一半由多糖组成。这些复杂的聚合物大多具有显著的聚阴离子特性。例如，红藻细胞壁主要由硫酸化的半乳聚糖、琼脂和角叉菜胶构成，而褐藻细胞壁则含有海藻酸和含岩藻糖的硫酸化多糖（FCSP）。某些海洋异养细菌已发展出在如此大型藻类多糖上生长的能力。伪枝孢藻（Pseudoalteromonas carrageenovora 9T, ATCC 43555T）便是其中之一，该菌种于1955年从海洋中分离出来，曾是研究角叉菜胶分解的早期模式生物。在此，我们展示了P. carrageenovora的基因组分析。其基因组由两个染色体和一个包含109个编码蛋白基因的大型质粒组成。P. carrageenovora拥有丰富的碳水化合物活性酶（CAZymes）库，特别是针对大型藻类多糖（如层粘菌素、海藻酸、FCSP、角叉菜胶）的降解。我们通过筛选P. carrageenovora对大量碳水化合物的生长反应，证实了这些预测的能力。大多数CAZyme基因构成簇，位于大型染色体或小型染色体上。令人惊讶的是，所有与角叉菜胶分解相关的基因都位于质粒上，这表明P. carrageenovora通过水平基因转移（HGT）获得了其标志性的角叉菜胶降解能力。尽管P. carrageenovora能够以λ-角叉菜胶为唯一碳源，但基因组学和生理学分析表明，其分解κ-和ι-角叉菜胶的途径尚不完整。这是由于缺乏最近发现的3,6-去氧-D-半乳糖苷酶基因（GH127和GH129家族）。与52种伪枝孢藻菌株的基因组比较证实，角叉菜胶分解仅在少数物种中近期获得。尽管纤维素生物合成位点和海藻酸利用位点位于染色体上，它们也经历了水平基因转移。然而，这些HGT事件发生在伪枝孢藻属的进化早期，纤维素和海藻酸相关位点主要存在于一个大型、晚分化的类群（LDC）中。总之，降解大型藻类细胞壁多糖的能力并非伪枝孢藻属的原始特征。P. carrageenovora中的这种分解能力源于一系列的HGT，可能允许其适应在大型藻类表面的生活。