The occurrence and function of alternative splicing in fungi

Fang, Shumei; Hou, Xue Xia; Qiu, Kaihua; He, Rui; Feng, Xiaoshuo; Liang, Xilong

doi:10.1016/j.fbr.2020.10.001

Cited by 20 publications

(24 citation statements)

References 100 publications

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“…Our results demonstrate clearly that more MoYpd1p isoforms exist than previously suggested, which may increase the signal diversity and provide the basis for further studies on signal transduction in fungal MSP systems. The discovery of the new isoform is consistent with recent studies which showed that AS events play a crucial role in the fungal kingdom [ 26 , 27 ]. The gene MoGRP1 , for example, encoding a glycine-rich RNA-binding protein, was identified as a splicing factor, which is essential for the removal of introns in M. oryzae .…”

Section: Discussionsupporting

confidence: 87%

Evidence of a New MoYpd1p Phosphotransferase Isoform in the Multistep Phosphorelay System of Magnaporthe oryzae

Bühring

Yemelin

Michna

et al. 2021

JoF

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Different external stimuli are perceived by multiple sensor histidine kinases and transmitted by phosphorylation via the phosphotransfer protein Ypd1p in the multistep phosphorelay system of the high osmolarity glycerol signaling pathway of filamentous fungi. How the signal propagation takes place is still not known in detail since multiple sensor histidine kinase genes in most filamentous fungi are coded in the genome, whereas only one gene for Ypd1p exists. That raises the hypothesis that various Ypd1p isoforms are produced from a single gene sequence, perhaps by alternative splicing, facilitating a higher variability in signal transduction. We found that the mRNA of MoYPD1 in the rice blast fungus Magnaporthe oryzae is subjected to an increased structural variation and amplified putative isoforms on a cDNA level. We then generated mutant strains overexpressing these isoforms, purified the products, and present here one previously unknown MoYpd1p isoform on a proteome level. Alternative splicing was found to be a valid molecular mechanism to increase the signal diversity in eukaryotic multistep phosphorelay systems.

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Section: Discussionsupporting

confidence: 87%

Evidence of a New MoYpd1p Phosphotransferase Isoform in the Multistep Phosphorelay System of Magnaporthe oryzae

Bühring

Yemelin

Michna

et al. 2021

JoF

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“…Although AS has been extensively studied, there has been no broad research regarding this mechanism in fungi. IR events, described as the retention of intron sequences that are supposed to be spliced in a pre-mRNA transcript, are likely the most prevalent AS events in fungi (Fang et al, 2020). In addition, AS mechanisms are also related to pathogenicity in fungal cells, as specific genes of human fungal pathogens can act independently on differentially expressed genes (Sieber et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Peptidase Regulation in Trichophyton rubrum Is Mediated by the Synergism Between Alternative Splicing and StuA-Dependent Transcriptional Mechanisms

Martins-Santana

Petrucelli²,

Sanches³

et al. 2022

Front. Microbiol.

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Trichophyton rubrum is the most common causative agent of dermatophytosis worldwide and uses keratinized substrates such as skin and nails as its main source of nutrition during infection. Its pathogenic character relies on colonization and viability maintenance at the target host sites. Since fungal physiology must adapt and respond to host conditions for the successful establishment of infection, biological mechanisms are constantly being triggered by T. rubrum to guarantee its survival in the host environment. The ability of this fungus to sense and modulate the secretion of specific proteases according to environmental pH signaling is considered as a pivotal virulence factor for effective invasion and persistence of infection in the host. Transcriptional regulation of genes encoding specific proteases, such as peptidases, is a key biological process that drives physiological modulation to meet fungal requirements. It accomplishes a robust balance among transcript isoforms that can be directed to perform distinct cellular functions. Thus, alternative splicing mechanisms are suitable for fungal cells to establish a balance toward reprogramming protein translation to impair or boost physiological conditions. In this study, we investigated the role of alternative splicing, especially intron retention events, in generating isoforms of virulence factors in T. rubrum mediated by transcriptional coordination of the protein StuA, a recently described transcription factor in this fungus. By analyzing the previous gene expression data provided by RNA-sequencing and after validation by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), we observed that two peptidase-coding genes (TERG_00734 and TERG_04614) could be direct targets of alternative splicing in the presence of keratin. Furthermore, protease isoforms generated by alternative splicing in T. rubrum were also detected in a co-culture with human keratinocytes, highlighting the role of these proteins in keratin deconstruction. Our results strongly suggest the influence of StuA on the regulation of virulence factors in T. rubrum and dermatophyte infections by triggering the transcription of the peptidase genes mentioned above in an alternative splicing-independent balance. The results elucidate how fungal cells drive alternate splicing to promote physiological adaptations and show that transcriptional regulation and virulence traits are robust elements required for dermatophyte infection.

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“…Genome-wide analyses of AS repertoires have been performed in a few fungal species [ 21–24 ]. Fungi cause plant and animal diseases and undergo transcriptional reprogramming to evade or compromise host immunity.…”

Section: Introductionmentioning

confidence: 99%

Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection

et al. 2022

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Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae , a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice- M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection.

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The occurrence and function of alternative splicing in fungi

Cited by 20 publications

References 100 publications

Evidence of a New MoYpd1p Phosphotransferase Isoform in the Multistep Phosphorelay System of Magnaporthe oryzae

Evidence of a New MoYpd1p Phosphotransferase Isoform in the Multistep Phosphorelay System of Magnaporthe oryzae

Peptidase Regulation in Trichophyton rubrum Is Mediated by the Synergism Between Alternative Splicing and StuA-Dependent Transcriptional Mechanisms

Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection

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