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

Jeon, Jongbum; Kim, Ki-Tae; Choi, Jaeyoung; Cheong, Kwang Ho; Ko, Jae–Ho; Choi, Gobong; Lee, Hyunjun; Lee, Gir-Won; Park, Sook-Young; Kim, Seongbeom; Kim, Sun Tae; Min, Cheol Woo; Kang, Seogchan; Lee, Yong‐Hwan

doi:10.1080/15476286.2022.2043040

Cited by 17 publications

(15 citation statements)

References 95 publications

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“…However, diseases and pests are important factors determining the yield and quality of rice [2,3]. Rice blasts caused by Magnaporthe oryzae (M. oryzae) can occur in all growth stages of rice and reduce rice yield by up to 50% in severe cases [4]. Currently, chemical control is the most common solution to this problem, and commonly used chemical fungicides include isoprothiolane, tricyclazole, pyraclostrobin, etc.…”

Section: Introductionmentioning

confidence: 99%

Natural Product Citronellal can Significantly Disturb Chitin Synthesis and Cell Wall Integrity in Magnaporthe oryzae

Zhou

et al. 2022

JoF

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Background: Natural products are often favored in the study of crop pests and diseases. Previous studies have shown that citronellal has a strong inhibition effect on Magnaporthe oryzae. The objective of this study was to clarify its mechanism of action against M. oryzae. Results: Firstly, the biological activity of citronellal against M. oryzae was determined by direct and indirect methods, and the results show that citronellal had a strong inhibition effect on M. oryzae with EC50 values of 134.00 mg/L and 70.48 μL/L air, respectively. Additionally, a preliminary study on its mechanism of action was studied. After citronellal treatment, electron microscopy revealed that the mycelium became thin and broken; scanning electron microscopy revealed that the mycelium was wrinkled and distorted; and transmission electron microscopy revealed that the mycelium cell wall was invaginated, the mass wall of mycelium was separated, and the organelles were blurred. The mycelium was further stained with CFW, and the nodes were blurred, while the mycelium was almost non-fluorescent after PI staining, and there was no significant difference in the relative conductivity of mycelium. In addition, chitinase was significantly enhanced, and the expression of chitin synthesis-related genes was 17.47-fold upregulated. Finally, we found that the efficacy of citronellal against the rice blast was as high as 82.14% according to indoor efficacy tests. Conclusion: These results indicate that citronellal can affect the synthesis of chitin in M. oryzae and damage its cell wall, thereby inhibiting the growth of mycelium and effectively protecting rice from rice blasts.

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Section: Introductionmentioning

confidence: 99%

Natural Product Citronellal can Significantly Disturb Chitin Synthesis and Cell Wall Integrity in Magnaporthe oryzae

Zhou

et al. 2022

JoF

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“…As observed for gene annotation (see before), the best strategy is to filter Iso-Seq sequences with RNA-Seq data to withdraw transcript isoforms with weak quantitative support, with the caveat that some transcripts might be excluded. As observed in other fungal genomes ( [77], [82], and references quoted within), most alternative splicing events were intron retention (IR). Indeed, we identified 58% of alternative transcripts with IR after NMD filtering (Table 1).…”

Section: Iso-seq Long Reads Reveals the Complexity Of Transcripts In ...mentioning

confidence: 73%

Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence

Lapalu

Lamothe

Petit

et al. 2023

Preprint

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Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5' and 3'UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

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“…Alternative splicing could produce multiple transcripts of mRNA to regulate the gene expression [ 19 ]. Then, we investigated the mechanism of how metformin regulated the expression of LGR4 in HCC.…”

Section: Discussionmentioning

confidence: 99%

Metformin Suppresses Hepatocellular Carcinoma through Regulating Alternative Splicing of LGR4

Han

Miao

Jin

et al. 2022

Journal of Oncology

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Background and aims. Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related deaths worldwide. The role of leucine-rich repeats containing G protein-coupled receptor 4 (LGR4) in HCC remains unclear. Metformin can prevent and control the development of a variety of cancers, especially in HCC. Alternative splicing (AS) can produce many cancer-driving genes. We aim to uncover that metformin regulates HCC development through alternative splicing of LGR4. Methods. First, the expression of LGR4 in HCC tumor tissues and cell lines was detected by western blotting and immunofluorescence. The ability of cell proliferation, migration, and invasion was detected with CCK8, wound-healing, and transwell assays when overexpressing LGR4 or treating with metformin. The β-catenin expression was detected by immunofluorescence. In order to investigate novel AS-associated LGR4, we discarded LGR4 isoforms from GSO databases. We used siRNA to knock down the specific isoform to check the cell proliferation, migration, and invasion when treated with metformin. Results. The level of LGR4 expression was higher in HCC cell lines and tumor tissues. The HCC cell proliferation, migration, and invasion were increased when overexpressing LGR4, which could be reduced by metformin treatment. The GEO database (GSE190076) showed that LGR4 had switching properties in HCC cell lines treated with metformin. We used siRNA to knock down the specific isoform, and the result showed that the specific isoform siRNA could promote the inhibition of cell invasion caused by metformin treatment. Conclusions. LGR4 could promote the ability of cell proliferation, migration, and invasion in HCC, which could be reduced by metformin through alternative splicing.

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

Cited by 17 publications

References 95 publications

Natural Product Citronellal can Significantly Disturb Chitin Synthesis and Cell Wall Integrity in Magnaporthe oryzae

Natural Product Citronellal can Significantly Disturb Chitin Synthesis and Cell Wall Integrity in Magnaporthe oryzae

Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence

Metformin Suppresses Hepatocellular Carcinoma through Regulating Alternative Splicing of LGR4

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