Zaccaron Alex Z, Chen Li-Hung, Stergiopoulos Ioannis
Department of Plant Pathology, University of California Davis (UC Davis), Davis, California United States of America.
Integrative Genetics and Genomics Graduate Group, University of California Davis (UC Davis), California, United States of America.
PLoS Pathog. 2024 Dec 18;20(12):e1012791. doi: 10.1371/journal.ppat.1012791. eCollection 2024 Dec.
Alternative splicing (AS) is a key element of eukaryotic gene expression that increases transcript and proteome diversity in cells, thereby altering their responses to external stimuli and stresses. While AS has been intensively researched in plants and animals, its frequency, conservation, and putative impact on virulence, are relatively still understudied in plant pathogenic fungi. Here, we profiled the AS events occurring in genes of Cladosporium fulvum isolates Race 5 and Race 4, during nearly a complete compatible infection cycle on their tomato host. Our studies revealed extensive heterogeneity in the transcript isoforms assembled from different isolates, infections, and infection timepoints, as over 80% of the transcript isoforms were singletons that were detected in only a single sample. Despite that, nearly 40% of the protein-coding genes in each isolate were predicted to be recurrently AS across the disparate infection timepoints, infections, and the two isolates. Of these, 37.5% were common to both isolates and 59% resulted in multiple protein isoforms, thereby putatively increasing proteome diversity in the pathogen by 31% during infections. An enrichment analysis showed that AS mostly affected genes likely to be involved in the transport of nutrients, regulation of gene expression, and monooxygenase activity, suggesting a role for AS in finetuning adaptation of C. fulvum on its tomato host during infections. Tracing the location of the AS genes on the fungal chromosomes showed that they were mostly located in repeat-rich regions of the core chromosomes, indicating a causal connection between gene location on the genome and propensity to AS. Finally, multiple cases of differential isoform usage in AS genes of C. fulvum were identified, suggesting that modulation of AS at different infection stages may be another way by which pathogens refine infections on their hosts.
可变剪接（Alternative splicing，AS）是真核基因表达的关键要素，它增加了细胞中转录本和蛋白质组的多样性，从而改变细胞对外界刺激和压力的反应。虽然可变剪接在植物和动物中已得到深入研究，但在植物病原真菌中，其频率、保守性以及对毒力的潜在影响仍相对研究较少。在此，我们分析了番茄叶霉病菌（Cladosporium fulvum）5号和4号生理小种分离株在其番茄寄主上几乎完整的亲和性侵染周期中基因发生的可变剪接事件。我们的研究揭示了从不同分离株、侵染以及侵染时间点组装的转录本异构体存在广泛的异质性，超过80%的转录本异构体是仅在单个样本中检测到的单例。尽管如此，预计每个分离株中近40%的蛋白质编码基因在不同的侵染时间点、侵染以及两个分离株之间会反复发生可变剪接。其中，37.5%在两个分离株中是共有的，59%产生多种蛋白质异构体，从而在侵染期间可能使病原菌的蛋白质组多样性增加31%。富集分析表明，可变剪接主要影响可能参与营养物质运输、基因表达调控和单加氧酶活性的基因，这表明可变剪接在番茄叶霉病菌侵染其番茄寄主过程中微调适应性方面发挥作用。追踪可变剪接基因在真菌染色体上的位置表明，它们大多位于核心染色体富含重复序列的区域，这表明基因组上的基因位置与可变剪接倾向之间存在因果联系。最后，鉴定出番茄叶霉病菌可变剪接基因中多个不同异构体使用的案例，这表明在不同侵染阶段对可变剪接的调控可能是病原菌优化对寄主侵染的另一种方式。
