一株糖降解噬糖菌FZY0027的多糖水解活性及基因组分析

Polysaccharide hydrolysis activity and genomic information of Saccharophagus degradans FZY0027

摘要:

【目的】潮间带海水中分离获得一株具有水解多糖能力的菌株FZY0027，分析其对不同多糖的水解能力和基因组特征。【方法】通过形态观察、16S rRNA基因测序和基于Illumina NovaSeq和OxfordNanopore PromethION测序技术全基因组测序对菌株FZY0027进行鉴定。使用dbCAN、EasyCGTree、BRIG和Easyfig等生物信息学软件将菌株FZY0027和降解糖噬糖菌(Saccharophagus degradans) 2-40^T进行比较。使用3,5-二硝基水杨酸(3,5-dinitrosalicylic acid, DNS)法测定多糖水解活性。【结果】菌株FZY0027与S. degradans 2-40^T的16S rRNA基因序列相似度达到99.9%，初步鉴定为降解糖噬糖菌(S. degradans) FZY0027。该菌株在水解淀粉、木聚糖和甘露聚糖时产生的还原糖浓度最高，分别为2.28、1.75和1.10 mg/mL。菌株FZY0027基因组全长5 178 381 bp，共编码4 156个基因，G+C含量为45.8%。菌株FZY0027与S. degradans 2-40^T的平均核苷酸一致性(average nucleotide identity, ANI)、平均氨基酸一致性(average amino acid identity, AAI)和DNA-DNA分子杂交(digital DNA-DNA hybridization, dDDH)值分别为96.5%、96.7%和70.0%。经碳水化合物活性酶数据库注释获得303个基因，其中，菌株FZY0027和S. degradans 2-40^T分别有糖苷水解酶(glycoside hydrolases, GHs)结构域的基因137个和130个。菌株FZY0027具有多个参与淀粉、木聚糖等多糖水解的基因，这与菌株FZY0027对淀粉和木聚糖的水解能力强的结果一致。然而，与S. degradans 2-40^T相比，菌株FZY0027在实验条件下只能水解少数多糖，这可能需要特定的诱导条件才能充分发挥其多糖水解能力。【结论】菌株FZY0027是一株多能型多糖水解菌，具有潜在开发价值。

关键词:降解糖噬糖菌;多糖水解活性;基因组;生物信息学分析

Abstract:

[Objective] To analyze the polysaccharide hydrolysis activity and genomic characteristics of a Gram-negative bacterial strain FZY0027 isolated from intertidal seawater. [Methods] The strain FZY0027 was identified based on the morphological characteristics, 16S rRNA gene sequence, and the whole genome sequence determined by Illumina NovaSeq and Oxford Nanopore PromethION. Bioinformatics tools such as dbCAN, EasyCGTree, BRIG, and Easyfig were used to compare the strain FZY0027 with Saccharophagus degradans 2-40^T. The 3,5-dinitrosalicylic acid (DNS) method was employed to measure the polysaccharide hydrolysis activity of strain FZY0027. [Results] The 16S rRNA gene sequence showed the similarity of 99.9% between strain FZY0027 and S. degradans 2-40^T, and thus strain FZY0027 was preliminarily identified as S. degradans FZY0027. The highest levels of reducing sugars (2.28, 1.75, and 1.10 mg/mL, respectively) were produced by FZY0027 through the hydrolysis of starch, xylan, and mannose. The genome of strain FZY0027 was 5 178 381 bp, encoding a total of 4 156 genes, with the G+C content of 45.8%. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain FZY0027 and S. degradans 2-40^T were 96.5%, 96.7%, and 70.0%, respectively. A total of 303 genes were annotated in the Carbohydrate-Active Enzyme database, and there was a significant difference in the number (137 and 130, respectively) of genes encoding glycoside hydrolases (GHs) between strain FZY0027 and S. degradans 2-40^T. Strain FZY0027 carried multiple genes involved in the hydrolysis of starch and xylan, which was corresponding to its strong ability to hydrolyse starch and xylan. However, compared with S. degradans 2-40^T, strain FZY0027 could only hydrolyse a few polysaccharides under the experimental conditions in this study, which suggested that this strain may require specific culture conditions to fully exert its polysaccharide hydrolysis ability. [Conclusion] Strain FZY0027 is a versatile polysaccharide-hydrolyzing bacterium with the potential for bioresource utilization.

Key words:Saccharophagus degradans;polysaccharide hydrolysis activity;genome;bioinformatics analysis