da Silva Daniela M G, Pedrosa Filipa R, Ângela Taipa M, Costa Rodrigo, Keller-Costa Tina
Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
ISME Commun. 2023 Oct 14;3(1):109. doi: 10.1038/s43705-023-00316-7.
Chitin is the most abundant natural polymer in the oceans, where it is primarily recycled by chitin-degrading microorganisms. Endozoicomonadaceae (Oceanospirillales) bacteria are prominent symbionts of sessile marine animals, particularly corals, and presumably contribute to nutrient cycling in their hosts. To reveal the chitinolytic potential of this iconic, animal-dwelling bacterial family, we examined 42 publicly available genomes of cultured and uncultured Endozoicomonadaceae strains for the presence of chitinase-encoding genes. Thirty-two of 42 Endozoicomonadaceae genomes harbored endo-chitinase- (EC 3.2.1.14), 25 had exo-chitinase- (EC 3.2.1.52) and 23 polysaccharide deacetylase-encoding genes. Chitinases were present in cultured and uncultured Endozoicomonadaceae lineages associated with diverse marine animals, including the three formally described genera Endozoicomonas, Paraendozoicomonas and Kistimonas, the new genus Candidatus Gorgonimonas, and other, yet unclassified, groups of the family. Most endo-chitinases belonged to the glycoside hydrolase family GH18 but five GH19 endo-chitinases were also present. Many endo-chitinases harbored an active site and a signal peptide domain, indicating the enzymes are likely functional and exported to the extracellular environment where endo-chitinases usually act. Phylogenetic analysis revealed clade-specific diversification of endo-chitinases across the family. The presence of multiple, distinct endo-chitinases on the genomes of several Endozoicomonadaceae species hints at functional variation to secure effective chitin processing in diverse micro-niches and changing environmental conditions. We demonstrate that endo-chitinases and other genes involved in chitin degradation are widespread in the Endozoicomonadaceae family and posit that these symbionts play important roles in chitin turnover in filter- and suspension-feeding animals and in benthic, marine ecosystems at large.
几丁质是海洋中最丰富的天然聚合物，主要由降解几丁质的微生物进行循环利用。内共生单胞菌科（海洋螺菌目）细菌是固着海洋动物（尤其是珊瑚）的重要共生菌，可能在其宿主的营养循环中发挥作用。为了揭示这个标志性的、栖息于动物体内的细菌家族的几丁质分解潜力，我们检查了42个已公开的培养和未培养的内共生单胞菌科菌株的基因组中几丁质酶编码基因的存在情况。42个内共生单胞菌科基因组中的32个含有内切几丁质酶（EC 3.2.1.14），25个含有外切几丁质酶（EC 3.2.1.52）和23个多糖脱乙酰酶编码基因。几丁质酶存在于与各种海洋动物相关的培养和未培养的内共生单胞菌科谱系中，包括三个正式描述的属：内共生单胞菌属、副内共生单胞菌属和基斯提单胞菌属，新属“候选戈尔戈尼单胞菌属”，以及该科其他尚未分类的类群。大多数内切几丁质酶属于糖苷水解酶家族GH18，但也存在5个GH19内切几丁质酶。许多内切几丁质酶含有活性位点和信号肽结构域，表明这些酶可能具有功能并被分泌到细胞外环境中，而内切几丁质酶通常在细胞外环境中发挥作用。系统发育分析揭示了整个家族内切几丁质酶的分支特异性多样化。几个内共生单胞菌科物种的基因组中存在多个不同的内切几丁质酶，这暗示了功能上的差异，以确保在不同的微生境和不断变化的环境条件下有效地处理几丁质。我们证明，内切几丁质酶和其他参与几丁质降解的基因在内共生单胞菌科中广泛存在，并认为这些共生菌在滤食性和悬浮性摄食动物以及整个底栖海洋生态系统的几丁质周转中发挥着重要作用。
