Intron retention-dependent gene regulation in Cryptococcus neoformans

Gonzalez-Hilarion, Sara; Paulet, Damien; Lee, Kyung Tae; Hon, Chung-Chau; Lechat, Pierre; Mogensen, Estelle; Moyrand, Frédérique; Proux, Caroline; Barboux, Rony; Bussotti, Giovanni; Hwang, Jungwook; Coppée, Jean Yves; Bahn, Yong-Sun; Janbon, Guilhem

doi:10.1038/srep32252

Cited by 51 publications

(74 citation statements)

References 68 publications

(85 reference statements)

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“…An mRNA molecule translated using an uAUG can be recognized as a premature stop codon bearing molecule and will be as such degraded by the nonsense-mediated mRNA decay (NMD) (41). To test this concept, we first sequenced RNA from C. deneoformans strains with the conserved NMD factor Upf1 deleted (33), finding 370 genes with increased mRNA abundance and 270 with decreased (Figure 4A, Table S2; 2-fold difference in levels at 1% FDR).…”

Section: Resultsmentioning

confidence: 99%

“…Briefly, early stationary phase was obtained after 18 h of growth (final OD 600 = 15) starting from at OD 600 =0.5. C. deneoformans strain NE579 ( upf1Δ ) (33) was grown in YPD at 30°C under agitation in exponential phase. Each Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 (82) cells grown in YPD at 30°C in stationary phase.…”

Section: Methodsmentioning

confidence: 99%

“…These introns influence gene expression and genome stability (29-31). The current genome annotation of pathogenic C. neoformans and deneoformans reference strains are based on both automatic and manual curations of gene structures using RNA-Seq data (32, 33). Although the high degree of interspecies conservation of intron numbers and positions within coding sequences suggest that these annotations are reliable (33), the regulatory regions (transcript leader and 3’ UTRs) at transcript extremities are less well identified.…”

Section: Introductionmentioning

confidence: 99%

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Start codon context controls translation initiation in the fungal kingdom

Wallace

Maufrais

Sales-Lee

et al. 2019

Preprint

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Eukaryotic protein synthesis initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but studies of S. cerevisiae suggest this context is of little importance in fungi. We tested this concept in two pathogenic Cryptococcus species by genome-wide mapping of translation and of mRNA 5’ and 3’ ends. We observed that upstream open reading frames (uORFs) are a major contributor to translation repression, that uORF use depends on the Kozak sequence context of its start codon, and that uORFs with strong contexts promote nonsense-mediated mRNA decay. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Further analysis shows that such dual-localization is also predicted to be common in Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that programs the expression and structures of proteins in fungi.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Start codon context controls translation initiation in the fungal kingdom

Wallace

Maufrais

Sales-Lee

et al. 2019

Preprint

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“…Subsequently, the cDNAs were subjected to PCR amplification in the presence of dCTP (␣33P) (PerkinElmer) with the primers for the following genes: ACT1, AFR1, and MDR1 for C. neoformans and ACT1, MDR1 (18), and PDR11 (20) for C. gattii. PCR products were resolved on a 7.5% polyacrylamide gel and quantified using a Typhoon 9200 imager and ImageQuant 5.2 software (Molecular Dynamics) (40).…”

Section: Methodsmentioning

confidence: 99%

Environmental Triazole Induces Cross-Resistance to Clinical Drugs and Affects Morphophysiology and Virulence of Cryptococcus gattii and C. neoformans

Bastos

Carneiro

Oliveira

et al. 2018

Antimicrob Agents Chemother

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and are environmental fungi that cause cryptococcosis, which is usually treated with amphotericin B and fluconazole. However, therapeutic failure is increasing because of the emergence of resistant strains. Because these species are constantly isolated from vegetal materials and the usage of agrochemicals is growing, we postulate that pesticides could be responsible for the altered susceptibility of these fungi to clinical drugs. Therefore, we evaluated the influence of the pesticide tebuconazole on the susceptibility to clinical drugs, morphophysiology, and virulence of and strains. The results showed that tebuconazole exposure caused cross-resistance (CR) between the agrochemical and clinical azoles (fluconazole, itraconazole, and ravuconazole) but not with amphotericin B. In some strains, CR was observed even after the exposure ceased. Further, tebuconazole exposure changed the morphology, including formation of pseudohyphae in H99, and the surface charge of the cells. Although the virulence of both species previously exposed to tebuconazole was decreased in mice, the tebuconazole-exposed colonies recovered from the lungs were more resistant to azole drugs than the nonexposed cells. This CR was confirmed when fluconazole was not able to reduce the fungal burden in the lungs of mice. The tolerance to azoles could be due to increased expression of the gene in both species and of efflux pump genes ( and ) in Our study data support the idea that agrochemical usage can significantly affect human pathogens present in the environment by affecting their resistance to clinical drugs.

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“…Our finding that intron retention correlates with high levels of spliceosome-bound precursor suggests another role for discard in the biogenesis of intron-retained RNA, a common form of alternative splicing. Intron retention has recently been shown to be regulated by environmental stresses in C. neoformans (Gonzalez-Hilarion et al, 2016) raising the possibility that there exist corresponding signal transduction mechanisms that impinge on fully assembled spliceosomes.…”

Section: Spliceosome Discard Of Native Transcriptsmentioning

confidence: 99%

Spliceosome profiling visualizes the operations of a dynamic RNPin vivoat nucleotide resolution

Burke

Longhurst

Merkurjev

et al. 2017

Preprint

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2 SummaryTools to understand how the spliceosome functions in vivo have lagged behind advances in its structural biology. We describe methods to globally profile spliceosome-bound precursor, intermediates and products at nucleotide resolution. We apply these tools to three divergent yeast species that span 600 million years of evolution. The sensitivity of the approach enables detection of novel cases of noncanonical catalysis including interrupted, recursive and nested splicing. Employing statistical modeling to understand the quantitative relationships between RNA features and the data, we uncover independent roles for intron size, position and number in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal ATP-dependent discard of numerous endogenous substrates at both the precursor and lariat-intermediate stages and connect discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology to investigate an RNP central to eukaryotic gene expression.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/224170 doi: bioRxiv preprint first posted online 3 Highlights•Measurement of spliceosome-bound precursor and intermediate in three species•Non-canonical splicing events revealed•Statistical modeling uncovers substrate features that predict catalytic efficiency•Discard of suboptimal substrates occurs in vivo and predicts intron-retained mRNAs peer-reviewed)

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Intron retention-dependent gene regulation in Cryptococcus neoformans

Cited by 51 publications

References 68 publications

Start codon context controls translation initiation in the fungal kingdom

Start codon context controls translation initiation in the fungal kingdom

Environmental Triazole Induces Cross-Resistance to Clinical Drugs and Affects Morphophysiology and Virulence of Cryptococcus gattii and C. neoformans

Spliceosome profiling visualizes the operations of a dynamic RNPin vivoat nucleotide resolution

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