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鞘氨醇杆菌属(Sphingobium)是一类具有很强的烷烃、杂环芳香烃降解能力的革兰氏阴性细菌。在NCBI公共数据库报道的95株已测序的鞘氨醇杆菌属基因组中,鲜有和纤维素降解相关。Sphingobium sp.LF-16是在以甘蔗渣为碳源的筛选培养基中筛选得到一株具有纤维素降解能力的菌株。通过对LF-16的基因组测序,得到了一条大小为4.57 Mb,GC含量为64.57%的环状染色体序列,经过基因预测发现该基因组序列共有4 340个编码基因,61个转运RNA。使用常用数据库对预测的基因集进行功能注释,获得了4 067个编码基因的功能描述信息。通过dbCAN数据库对其编码基因进行分析发现,LF-16共有242个基因的编码产物属于碳水化合物活性酶,其中属于糖苷水解酶家族的有143个,AA家族的辅助蛋白有20个。经分泌组预测,共有488个基因能够分泌到胞外,其中有87个是碳水化合物活性酶。通过与鞘氨醇杆菌属的其他8个菌株的基因组序列进行比较基因组学分析发现LF-16与Sphingobium yanoikuyae SHJ的亲缘关系最近,比除S.yanoikuyae SHJ之外的其他菌株的碳水化合物活性酶的编码基因数量要多20%～30%。
Abstract：S phingobiums are gram-negative bacteria with strong alkane and heterocyclic aromatic hydrocarbon degradation ability. Few of the 95 sequenced genomes of Sphingobiums reported in the NCBI public database are related to cellulose degradation. Sphingobium sp. LF-16 with cellulose degradation ability was screened from minimal medium with sugarcane bagasse as sole carbon source. After sequencing the genome of LF-16, a circular chromosome sequence with a size of 4.57 Mb and a GC content of 64.57% was obtained. Gene prediction showed that there were 4 340 encoding genes and 61 t RNA genes in the genome sequence. Using commonly database to annotate genes function, 4 067 genes were released. The encoding genes of LF-16 were analyzed in the dbCAN database, the results showed that 242 genes in LF-16 encoded carbohydrate active enzymes, of which 143 enzymes belonged to glycoside hydrolase(GH) family and 20 proteins belonged to the auxiliary activities(AAs) family. The secretome of LF-16 predicted that a total of 488 proteins could be secreted into the extracellular, of which 87 were carbohydrate active enzymes. By comparative genomics analysis with the genome sequences of the other 8 strains of Sphingobium, the relationship between LF-16 and Sphingobium yanoikuyae SHJ was found to be closest. FL-16 contained more 20%～30% coding genes of carbohydrate active enzymes than other strains except S. yanoikuyae SHJ.
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基本信息:
DOI：10.13417/j.gab.039.000599
中图分类号:Q933
引用信息:
[1]马晓丹,王凯,李明栋,等.一株鞘氨醇杆菌LF-16的基因组测序与分析[J].基因组学与应用生物学,2020,39(02):599-605.DOI:10.13417/j.gab.039.000599.
基金信息:
国家自然科学基金(31560019)资助
2020-02-25
2020-02-25