Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAi Silencing Components in the Cryptococcus Pathogenic Species Complex

RNAi is a ubiquitous pathway that serves central functions throughout eukaryotes, including maintenance of genome stability and repression of transposon expression and movement. However, a number of organisms have lost their RNAi pathways, including the model yeast Saccharomyces cerevisiae, the maize pathogen Ustilago maydis, the human pathogen Cryptococcus deuterogattii, and some human parasite pathogens, suggesting there may be adaptive benefits associated with both retention and loss of RNAi. By comparing the RNAi-deficient genome of the Pacific Northwest Outbreak C. deuterogattii strain R265 with the RNAi-proficient genomes of the Cryptococcus pathogenic species complex, we identified a set of conserved genes that were lost in R265 and all other C. deuterogattii isolates examined. Genetic and molecular analyses reveal several of these lost genes play roles in RNAi pathways. Four novel components were examined further. Znf3 (a zinc finger protein) and Qip1 (a homolog of N. crassa Qip) were found to be essential for RNAi, while Cpr2 (a constitutive pheromone receptor) and Fzc28 (a transcription factor) are involved in sex-induced but not mitosis-induced silencing. Our results demonstrate that the mitotic and sex-induced RNAi pathways rely on the same core components, but sex-induced silencing may be a more specific, highly induced variant that involves additional specialized or regulatory components. Our studies further illustrate how gene network polymorphisms involving known components of key cellular pathways can inform identification of novel elements and suggest that RNAi loss may have been a core event in the speciation of C. deuterogattii and possibly contributed to its pathogenic trajectory.

RNA干扰（RNA interference, RNAi）是广泛存在于真核生物中的保守通路，在各类真核生物中发挥核心功能，包括维持基因组稳定性、抑制转座子的表达与转座活动。然而，诸多物种已丢失其RNAi通路，例如模式生物酿酒酵母（Saccharomyces cerevisiae）、玉米病原菌玉米黑粉菌（Ustilago maydis）、人类致病菌德氏隐球菌（Cryptococcus deuterogattii）以及部分人体寄生致病菌，这提示RNAi的保留与丢失均可能带来适应性优势。本研究通过比对太平洋西北爆发株德氏隐球菌R265菌株的RNAi缺陷基因组，与隐球菌致病物种复合体中具备RNAi活性的基因组，鉴定出一套在R265菌株及所有已检测的德氏隐球菌分离株中均发生缺失的保守基因集合。遗传与分子分析显示，其中多个缺失基因参与RNAi通路的调控。研究对4个新型RNAi通路组分开展了深入研究：锌指蛋白Znf3与粗糙脉孢菌Qip的同源蛋白Qip1被证实为RNAi通路所必需；而组成型信息素受体Cpr2与转录因子Fzc28则仅参与性诱导基因沉默，不参与有丝分裂诱导基因沉默。本研究结果表明，有丝分裂与性诱导RNAi通路共享相同的核心组分，但性诱导沉默或许是一类特异性更强、诱导水平更高的RNAi变体，其功能依赖额外的特化或调控组分。本研究同时阐明，针对关键细胞通路已知组分的基因网络多态性分析，可为新型通路元件的鉴定提供重要指引；并提示RNAi的丢失或许是德氏隐球菌物种形成过程中的核心事件，亦可能对其致病轨迹产生了关键影响。