Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast

Novačić, Ana; Šupljika, Nada; Bekavac, Nikša; Žunar, Bojan; Stuparević, Igor

doi:10.1128/spectrum.00295-21

Cited by 4 publications

(7 citation statements)

References 45 publications

(69 reference statements)

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“…Comparison of Ssd1-associated mRNAs identified by CRAC analysis [46] with previous RIP and transcriptome data [47][48][49] showed that 11 mRNAs were systematically bound by Ssd1 (Table 1). Among these 11 mRNAs, 8 were also highly enriched by eIF2A, including CTS1, SUN4 and SRL1 (Fig 1 , Table 1, S5 Table and S1 Dataset).…”

Section: Eif2a Requires the Presence Of Ssd1 To Associate With Severa...mentioning

confidence: 69%

“…Interestingly, we observed a robust enrichment of Ssd1 (Fig 5B). Ssd1 is a RNA-binding protein (RBP) and previous studies have reported that Ssd1 binds to about a hundred mRNA coding for proteins involved in cell wall biogenesis [46][47][48][49]. Ssd1 directly recognizes a consensus motif usually located in the 5' UTR of these mRNA targets [46].…”

Section: The Rna Binding Protein Ssd1 Is Highly Enriched By Eif2a Ind...mentioning

confidence: 99%

“…eIF2A shares common targets with Ssd1. Ssd1 mRNA targets systematically identified by RIP [47][48][49] and CRAC [46] experiments. The functions were extracted from SGD https://www.yeastgenome.org/.…”

Section: Plos Onementioning

confidence: 99%

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eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae

Meyer,

Courtin,

Gomard

et al. 2023

PLoS ONE

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Translation initiation is a complex and highly regulated process that represents an important mechanism, controlling gene expression. eIF2A was proposed as an alternative initiation factor, however, its role and biological targets remain to be discovered. To further gain insight into the function of eIF2A in Saccharomyces cerevisiae, we identified mRNAs associated with the eIF2A complex and showed that 24% of the most enriched mRNAs encode proteins related to cell wall biogenesis and maintenance. In agreement with this result, we showed that an eIF2A deletion sensitized cells to cell wall damage induced by calcofluor white. eIF2A overexpression led to a growth defect, correlated with decreased synthesis of several cell wall proteins. In contrast, no changes were observed in the transcriptome, suggesting that eIF2A controls the expression of cell wall-related proteins at a translational level. The biochemical characterization of the eIF2A complex revealed that it strongly interacts with the RNA binding protein, Ssd1, which is a negative translational regulator, controlling the expression of cell wall-related genes. Interestingly, eIF2A and Ssd1 bind several common mRNA targets and we found that the binding of eIF2A to some targets was mediated by Ssd1. Surprisingly, we further showed that eIF2A is physically and functionally associated with the exonuclease Xrn1 and other mRNA degradation factors, suggesting an additional level of regulation. Altogether, our results highlight new aspects of this complex and redundant fine-tuned regulation of proteins expression related to the cell wall, a structure required to maintain cell shape and rigidity, providing protection against harmful environmental stress.

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Section: Eif2a Requires the Presence Of Ssd1 To Associate With Severa...mentioning

confidence: 69%

Section: The Rna Binding Protein Ssd1 Is Highly Enriched By Eif2a Ind...mentioning

confidence: 99%

See 1 more Smart Citation

eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae

Meyer,

Courtin,

Gomard

et al. 2023

PLoS ONE

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“…The results showed that under the heat shock condition, the macro morphology and micro morphology of the strain were changed to some extent. Yeast cell wall is the basic structure that determines cell shape and protects cells from environmental in uences, and heat stress can adversely affect the integrity of cell wall and cell membrane [33,34]-[. The cell membrane has selective transmitability, which can control the entry and exit of substances into and out of cells, and the components of cells such as nucleic acids will not be lost to the outside of cells.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome research on differentially expressed genes in a thermotolerant yeast strain from Daqu of Luzhou-flavor liquors

Yan-bo¹,

Gu²,

Li³

et al. 2023

Preprint

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Yeast is one of the microorganisms widely used in fermentation industry, and its high temperature resistance plays an important role in fermentation. However, the complex regulatory process of cell tolerance to heat stress has not been fully understood. Therefore, this study carried out basic research on high temperature resistant yeast at 28℃, 37℃ and 43℃, including morphological observation, determination of trehalose content and cell membrane permeability, and combined with RNA-seq technology to screen differentially expressed genes in yeast responding to high temperature stress at the transcriptome level. The results showed that under heat treatment conditions, the macroscopic and microscopic morphology of yeast cells were changed, the selective permeability of cell membrane was changed, and the intracellular trehalose was accumulated. Different nitrogen sources and inorganic salt ions can improve the high temperature tolerance of yeast ZG-3. In addition, a total of 517 differentially expressed genes were screened by comparing the temperature resistant yeast at 28℃ with that at 37℃, among which 435 genes were up-regulated and 82 genes were down-regulated. A total of 632 differentially expressed genes were screened at 37℃ compared with that at 43℃, among which 393 genes were up-regulated and 239 genes were down-regulated. Among them, SSA3, SSA4, HSP82, SSE1, KAR2, FES1, HSP26, HSP42 genes of the heat shock protein family were significantly up-regulated, which improved the basic and acquired heat tolerance of yeast. This study combined physical and chemical properties analysis and transcriptome analysis to preliminarily explore the differentially expressed genes in yeast in response to high temperature stress, which provides a theoretical basis for further study of yeast high temperature tolerance.

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“…Moreover, some of its strains show a well-established probiotic effect [21]. Being well-studied and easy to genetically modify [22][23][24], S. cerevisiae is also readily chosen as a workhorse in modern bioprocesses aimed at the biosynthesis of biofuels, recombinant proteins, and biologically active small molecules [25], such as caffeine, resveratrol, morphine, and artemisinin [26]. Finally, it serves as a chassis for many eukaryotic whole-cell biosensors [27].…”

Section: Introductionmentioning

confidence: 99%

Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae

et al. 2022

Self Cite

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Background Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive. Methods We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging. Results When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients. Conclusions F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability. Graphical Abstract

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Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast

Abstract: Stressful conditions such as high temperatures can compromise cellular integrity and cause bursting. In microorganisms surrounded by a cell wall, such as yeast, the cell wall is the primary shield that protects cells from environmental stress.

Cited by 4 publications

References 45 publications

eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae

eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae

Transcriptome research on differentially expressed genes in a thermotolerant yeast strain from Daqu of Luzhou-flavor liquors

Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae

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