Transcriptomics analysis of Candida albicans with capsule
唐晓媛 1陈亚运 2陈玲霞 2刘志平 2刘志春2
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作者信息
1. 赣南医科大学第一附属医院呼吸与危重症医学科
2. 赣南医科大学基础医学院,江西 赣州 341000
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摘要
目的:探讨具有荚膜的白色念珠菌转录组学特征.方法:⑴采用feature Counts(1.5.0-p3)获得基因或转录本的表达量,通过DESeq2软件(1.20.0)筛选出具有荚膜的白色念珠菌的差异表达基因(Different Express Gene,DEG),使用"clusterProfiler"R包对差异表达基因进行基因本体(Gene Ontology,GO)富集分析和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)富集分析,并筛选关键基因.⑵RT-PCR验证白色念珠菌无荚膜菌株与荚膜菌株部分差异表达基因mRNA表达.结果:C1-1与SC5314相比,差异表达基因达到2 586个,其中显著上调的有1 184个,显著下调的有1 402个.对差异表达基因进行GO富集分析发现,DEGs主要富集在蛋白质代谢过程、膜的构成和膜的固有成分及结构分子活性和核糖体结构性成分.对差异表达基因进行KEGG富集分析发现,DEGs富集在核糖体、丙酮酸盐代谢、过氧化物酶体、细胞周期、氨基糖和核苷酸糖代谢等通路.对新转录本进行GO、KEGG、Pfam等数据库注释,共预测关键基因113个,其中GO数据库注释关键基因1个,具有氧化还原酶活性,可能参与荚膜的生物代谢过程;KEGG数据库注释关键基因3个,参与白色念珠菌的氧代羧酸、柠檬酸盐循环、氨基酸等代谢活动.与白色念珠菌无荚膜菌株相比,荚膜菌株Efg1、Thr1 mRNA表达均降低.结论:白色念珠菌荚膜菌株与无荚膜菌株在基因表达总体水平和相关代谢通路基因表达水平上存在明显的差异.
Abstract
Objective:To study the transcriptomic characteristics of Candida albicans with capsules.Methods:⑴feature Counts(1.5.0-p3)were used to obtain the expression levels of genes or transcripts,and DESeq2 software(1.20.0)was used to screen out different express genes(DEG)of Candida albicans with capsules.The gene ontology(GO)enrichment analysis and the kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis were conducted using the"clusterProfiler"R package.And screen for key genes.⑵ RT-PCR verified the mRNA expression of some differentially expressed genes between uncapsulated strains and capsulated strains of Candida albicans.Results:Compared with SC5314,C1-1 had 2 586 differentially expressed genes,of which 1 184 were significantly up-regulated and 1 402 were significantly down-regulated.GO enrichment analysis of differentially expressed genes showed that DEGs was mainly enriched in protein metabolism,membrane composition,membrane intrinsic components and structural molecular activity,and ribosome structural components.KEGG analysis of differentially expressed genes showed that DEGs was enriched in ribosome,pyruvate metabolism,peroxisome,cell cycle,amino sugar and nucleotide sugar metabolism.The new transcript was annotated by GO,KEGG,Pfam and other databases,and a total of 113 key genes were predicted,among which 1 key gene was annotated by GO database,which had oxidoreductase activity and might participate in the biological metabolic process of the capsule.KEGG database annotated 3 key genes involved in the metabolic activities of oxycarboxylic acid,citrate cycle and amino acid of Candida albicans.Compared with uncapsulated strains of Candida albicans,Efg1 and Thr1 mRNA expressions of capsulated strains decreased.Conclusion:There are significant differences in gene expression levels and related metabolic pathways between capsulated and uncapsulated strains of Candida albicans.
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