Transcriptomic comparison of aerial and root cells of a wild yeast biofilm colony

Wild yeast and many clinical strains form complex, biofilm colonies, providing protection from desiccation, drugs and other stresses. Few transcriptomic studies have focused on sub-surface invasive “roots” due to the challenges of cell isolation from agar and subpopulation cross-contamination. Here we present, a first transcriptomic analysis via RNA sequencing of root and aerial cells, separated by a novel method. We identified 719 coding genes with upregulated root expression, mainly involved in ribosome structure/biogenesis, biosynthesis and translation and 529 loci/genes with upregulated aerial expression, mainly involved in meiosis/sporulation, stress defense and protein degradation; all indicating that aerial cells are resting and root cells are metabolically active cells. On the basis of 172 root-upregulated and 233 aerial-upregulated non-coding loci detected, anti-regulated gene/lncRNA pairs have been identified that may contribute to negative regulation of gene expression. Importantly, cells showing typical markers of “roots” correspond with cells embedded in extracellular matrix and cells showing typical markers of “aerial” parts with ECM-free cells.野生酵母与诸多临床菌株可形成复杂的生物膜（biofilm）菌落，能够抵御干燥、药物及其他胁迫压力。由于难以从琼脂培养基中分离细胞且易出现亚种群交叉污染，目前针对这类亚表层侵入性“根状”结构的转录组学研究寥寥无几。本研究首次通过RNA测序技术，对经新型方法分离得到的根状细胞与气生细胞开展转录组学分析。本研究共鉴定出719个在根状细胞中表达上调的编码基因，其功能主要富集于核糖体结构/生物发生、生物合成及翻译过程；同时鉴定出529个在气生细胞中表达上调的基因座/编码基因，功能主要涉及减数分裂/孢子形成、胁迫防御与蛋白质降解。上述结果表明，气生细胞为静息状态细胞，而根状细胞则为代谢活跃细胞。基于本次检测到的172个根状细胞上调非编码基因座与233个气生细胞上调非编码基因座，本研究鉴定出多组反向调控基因/长链非编码RNA（lncRNA）对，其可能参与基因表达的负调控过程。值得注意的是，携带“根状”结构典型标志物的细胞与包埋于细胞外基质（ECM）中的细胞高度吻合，而携带“气生”部分典型标志物的细胞则对应无ECM包被的细胞。