The cruciform DNA‐binding protein Crp1 stimulates the endonuclease activity of Mus81–Mms4 in <i>Saccharomyces cerevisiae</i>

Phung, Huong Thi Thu; Tran, Diem Hong; Nguyen, Ta Xuan

doi:10.1002/1873-3468.13931

Cited by 5 publications

(4 citation statements)

References 61 publications

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“…In addition to the MDR transporters, the CP -1 group contains 14 novel mother-specific proteins, including several other transporter proteins (Atr1, Ftr1, Hxt6, Mep1, Mep3, Qdr2, and Qdr3), proteins with roles in signaling (Gpa2, Mid2, Psr1), and three relatively uncharacterized proteins, including Ybr016w, which is a tail-anchored plasma membrane protein that is orthologous to human CYSTM1 (cysteine rich transmembrane module containing 1), Ina1, an uncharacterized protein whose paralog protein, Fat3, is required for fatty acid uptake 39 , and Crp1, an uncharacterized protein whose paralog protein, Mdg1, appears to modulate pheromone-mediated signaling and cell polarization 40 ( Table S2b ).…”

Section: Resultsmentioning

confidence: 99%

PIFiA: Self-supervised Approach for Protein Functional Annotation from Single-Cell Imaging Data

Anastasia

Brechalov

Friesen

et al. 2023

Preprint

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Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail to learn robust and noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA, (Protein Image-based Functional Annotation), a self-supervised approach for protein functional annotation from single-cell imaging data. We imaged the global yeast ORF-GFP collection and applied PIFiA to generate protein feature profiles from single-cell images of fluorescently tagged proteins. We show that PIFiA outperforms existing approaches for molecular representation learning and describe a range of downstream analysis tasks to explore the information content of the feature profiles. Specifically, we cluster extracted features into a hierarchy of functional organization, study cell population heterogeneity, and develop techniques to distinguish multi-localizing proteins and identify functional modules. Finally, we confirm new PIFiA predictions using a colocalization assay, suggesting previously unappreciated biological roles for several proteins. Paired with a fully interactive website (https://thecellvision.org/pifia/), PIFiA is a resource for the quantitative analysis of protein organization within the cell.

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Section: Resultsmentioning

confidence: 99%

PIFiA: Self-supervised Approach for Protein Functional Annotation from Single-Cell Imaging Data

Anastasia

Brechalov

Friesen

et al. 2023

Preprint

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“…We find that the diploid line with the lowest CN (33) has a homozygous missense mutation, K37T, in a gene implicated in rDNA stability, MUS81 ( fig. 7 A ; Ii et al 2007 ; Thu et al 2015 ; Phung et al 2020 ). Unlike this point mutation, mus81 Δ results in increased CN ( Ii et al 2007 ).…”

Section: Resultsmentioning

confidence: 99%

Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast

Sharp,

Smith,

Driscoll

et al. 2023

Genome Biology and Evolution

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The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.

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“…We find that the diploid line with the lowest CN (33) has a homozygous missense mutation, K37T, in a gene implicated in rDNA stability, MUS81 (Fig. 7A; Ii et al 2007;Thu et al 2015;Phung et al 2020). Unlike this point mutation, mus81𝛥 results in increased CN (Ii et al 2007).…”

Section: Molecular Patterns Of Rdna Variationmentioning

confidence: 86%

Contribution of spontaneous mutations to quantitative and molecular variation at the highly repetitive rDNA locus in yeast

Sharp

Smith

Driscoll

et al. 2022

Preprint

View full text Add to dashboard Cite

The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that un-selected mutations throughout the genome can disrupt copy number maintenance. In consequence, copy number generally declines, consistent with a model of regulation where copy number is normally increased when low. This pattern holds across ploidy levels and strains in the standard lab environment, but differs under some stressful conditions. We identify several alleles, gene categories and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself is distinct from the rest of the genome, and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.

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The cruciform DNA‐binding protein Crp1 stimulates the endonuclease activity of Mus81–Mms4 in Saccharomyces cerevisiae

Cited by 5 publications

References 61 publications

PIFiA: Self-supervised Approach for Protein Functional Annotation from Single-Cell Imaging Data

PIFiA: Self-supervised Approach for Protein Functional Annotation from Single-Cell Imaging Data

Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast

Contribution of spontaneous mutations to quantitative and molecular variation at the highly repetitive rDNA locus in yeast

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