Proteome and metabolome profiling of wild-type and YCA1 -knock-out yeast cells during acetic acid-induced programmed cell death

Abstract Background Programmed cell death (PCD) induced by acetic acid, the main by-product released during cellulosic hydrolysis, cast a cloud over lignocellulosic biofuel fermented by Saccharomyces cerevisiae and became a burning problem. Atg22p, an ignored integral membrane protein located in vacuole belongs to autophagy-related genes family; prior study recently reported that it is required for autophagic degradation and efflux of amino acids from vacuole to cytoplasm. It may alleviate the intracellular starvation of nutrition caused by Ac and increase cell tolerance. Therefore, we investigate the role of atg22 in cell death process induced by Ac in which attempt is made to discover new perspectives for better understanding of the mechanisms behind tolerance and more robust industrial strain construction. Results In this study, we compared cell growth, physiological changes in the absence and presence of Atg22p under Ac exposure conditions. It is observed that disruption and overexpression of Atg22p delays and enhances acetic acid-induced PCD, respectively. The deletion of Atg22p in S. cerevisiae maintains cell wall integrity, and protects cytomembrane integrity, fluidity and permeability upon Ac stress by changing cytomembrane phospholipids, sterols and fatty acids. More interestingly, atg22 deletion increases intracellular amino acids to aid yeast cells for tackling amino acid starvation and intracellular acidification. Further, atg22 deletion upregulates series of stress response genes expression such as heat shock protein family, cell wall integrity and autophagy. Conclusions The findings show that Atg22p possessed the new function related to cell resistance to Ac. This may help us have a deeper understanding of PCD induced by Ac and provide a new strategy to improve Ac resistance in designing industrial yeast strains for bioethanol production during lignocellulosic biofuel fermentation.

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Lack ofHXK2Induces Localization of Active Ras in Mitochondria and Triggers Apoptosis in the YeastSaccharomyces cerevisiae

Oxidative Medicine and Cellular Longevity ◽

10.1155/2013/678473 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 23

Author(s):

Loredana Amigoni ◽

Enzo Martegani ◽

Sonia Colombo

Keyword(s):

Cell Death ◽

Acetic Acid ◽

Plasma Membrane ◽

Programmed Cell Death ◽

Mitochondrial Dysfunction ◽

Type Strain ◽

Wild Type Strain ◽

Ros Production ◽

Ras Proteins ◽

Wild Type

We recently showed that activated Ras proteins are localized to the plasma membrane and in the nucleus in wild-type cells growing exponentially on glucose, while in thehxk2Δ strain they accumulated mainly in mitochondria. An aberrant accumulation of activated Ras in these organelles was previously reported and correlated to mitochondrial dysfunction, accumulation of ROS, and cell death. Here we show that addition of acetic acid to wild-type cells results in a rapid recruitment of Ras-GTP from the nucleus and the plasma membrane to the mitochondria, providing a further proof that Ras proteins might be involved in programmed cell death. Moreover, we show that Hxk2 protects against apoptosis inS. cerevisiae. In particular, cells lackingHXK2and showing a constitutive accumulation of activated Ras at the mitochondria are more sensitive to acetic-acid-induced programmed cell death compared to the wild type strain. Indeed, deletion ofHXK2causes an increase of apoptotic cells with several morphological and biochemical changes that are typical of apoptosis, including DNA fragmentation, externalization of phosphatidylserine, and ROS production. Finally, our results suggest that apoptosis induced by lack of Hxk2 may not require the activation of Yca1, the metacaspase homologue identified in yeast.

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Old Yellow Enzymes, Highly Homologous FMN Oxidoreductases with Modulating Roles in Oxidative Stress and Programmed Cell Death in Yeast

Journal of Biological Chemistry ◽

10.1074/jbc.m704058200 ◽

2007 ◽

Vol 282 (49) ◽

pp. 36010-36023 ◽

Cited By ~ 43

Author(s):

Osama Odat ◽

Samer Matta ◽

Hadi Khalil ◽

Sotirios C. Kampranis ◽

Raymond Pfau ◽

...

Keyword(s):

Oxidative Stress ◽

Cell Death ◽

Programmed Cell Death ◽

Antioxidant Activities ◽

Ros Generation ◽

Oxidized Glutathione ◽

Wild Type ◽

Antioxidant Genes ◽

Knock Out ◽

Chronological Aging

In a genetic screen to identify modifiers of Bax-dependent lethality in yeast, the C terminus of OYE2 was isolated based on its capacity to restore sensitivity to a Bax-resistant yeast mutant strain. Overexpression of full-length OYE2 suppresses Bax lethality in yeast, lowers endogenous reactive oxygen species (ROS), increases resistance to H2O2-induced programmed cell death (PCD), and significantly lowers ROS levels generated by organic prooxidants. Reciprocally, Δoye2 yeast strains are sensitive to prooxidant-induced PCD. Overexpression and knock-out analysis indicate these OYE2 antioxidant activities are opposed by OYE3, a highly homologous heterodimerizing protein, which functions as a prooxidant promoting H2O2-induced PCD in wild type yeast. To exert its effect OYE3 requires the presence of OYE2. Deletion of the 12 C-terminal amino acids and catalytic inactivation of OYE2 by a Y197F mutation enhance significantly survival upon H2O2-induced PCD in wild type cells, but accelerate PCD in Δoye3 cells, implicating the oye2p-oye3p heterodimer for promoting cell death upon oxidative stress. Unexpectedly, a strain with a double knock-out of these genes (Δoye2 oye3) is highly resistant to H2O2-induced PCD, exhibits increased respiratory capacity, and undergoes less cell death during the adaptive response in chronological aging. Simultaneous deletion of OYE2 and other antioxidant genes hyperinduces endogenous levels of ROS, promoting H2O2-induced cell death: in Δoye2 glr1 yeast high levels of oxidized glutathione elicited gross morphological aberrations involving the actin cytoskeleton and defects in organelle partitioning. Altering the ratio of reduced to oxidized glutathione by exogenous addition of GSH fully reversed these alterations. Based on this work, OYE proteins are firmly placed in the signaling network connecting ROS generation, PCD modulation, and cytoskeletal dynamics in yeast.

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Silencing of BRCA2 decreases anoikis and its heterologous expression sensitizes yeast cells to acetic acid-induced programmed cell death

APOPTOSIS ◽

10.1007/s10495-014-1006-z ◽

2014 ◽

Vol 19 (9) ◽

pp. 1330-1341 ◽

Cited By ~ 3

Author(s):

Nicoletta Guaragnella ◽

Ersilia Marra ◽

Alvaro Galli ◽

Loredana Moro ◽

Sergio Giannattasio

Keyword(s):

Cell Death ◽

Acetic Acid ◽

Programmed Cell Death ◽

Heterologous Expression ◽

Yeast Cells

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Achievements and perspectives in yeast acetic acid-induced programmed cell death pathways

Biochemical Society Transactions ◽

10.1042/bst0391538 ◽

2011 ◽

Vol 39 (5) ◽

pp. 1538-1543 ◽

Cited By ~ 28

Author(s):

Nicoletta Guaragnella ◽

Lucia Antonacci ◽

Salvatore Passarella ◽

Ersilia Marra ◽

Sergio Giannattasio

Keyword(s):

Cell Death ◽

Acetic Acid ◽

Programmed Cell Death ◽

Time Course ◽

Reactive Oxygen Species Generation ◽

Yeast Cells ◽

Model Organisms ◽

Dependent Manner ◽

Cell Death Pathways ◽

Cyt C

The use of non-mammalian model organisms, including yeast Saccharomyces cerevisiae, can provide new insights into eukaryotic PCD (programmed cell death) pathways. In the present paper, we report recent achievements in the elucidation of the events leading to PCD that occur as a response to yeast treatment with AA (acetic acid). In particular, ROS (reactive oxygen species) generation, cyt c (cytochrome c) release and mitochondrial function and proteolytic activity will be dealt with as they vary along the AA-PCD time course by using both wild-type and mutant yeast cells. Two AA-PCD pathways are described sharing common features, but distinct from one another with respect to the role of ROS and mitochondria, the former in which YCA1 acts upstream of cyt c release and caspase-like activation in a ROS-dependent manner and the latter in which cyt c release does not occur, but caspase-like activity increases, in a ROS-independent manner.

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Knock-out of metacaspase and/or cytochromecresults in the activation of a ROS-independent acetic acid-induced programmed cell death pathway in yeast

FEBS Letters ◽

10.1016/j.febslet.2010.07.044 ◽

2010 ◽

Vol 584 (16) ◽

pp. 3655-3660 ◽

Cited By ~ 17

Author(s):

Nicoletta Guaragnella ◽

Salvatore Passarella ◽

Ersilia Marra ◽

Sergio Giannattasio

Keyword(s):

Cell Death ◽

Acetic Acid ◽

Programmed Cell Death ◽

Knock Out ◽

Cell Death Pathway

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Cytochrome c Release and Mitochondria Involvement in Programmed Cell Death Induced by Acetic Acid in Saccharomyces cerevisiae

Molecular Biology of the Cell ◽

10.1091/mbc.e01-12-0161 ◽

2002 ◽

Vol 13 (8) ◽

pp. 2598-2606 ◽

Cited By ~ 261

Author(s):

Paula Ludovico ◽

Fernando Rodrigues ◽

Agostinho Almeida ◽

Manuel T. Silva ◽

Antoni Barrientos ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Death ◽

Acetic Acid ◽

Cytochrome C ◽

Programmed Cell Death ◽

Yeast Cells ◽

Cytochrome C Release ◽

Apoptotic Pathway ◽

Enzymatic Assays ◽

Species Production

Evidence is presented that mitochondria are implicated in the previously described programmed cell death (PCD) process induced by acetic acid in Saccharomyces cerevisiae. In yeast cells undergoing a PCD process induced by acetic acid, translocation of cytochrome c (CytC) to the cytosol and reactive oxygen species production, two events known to be proapoptotic in mammals, were observed. Associated with these events, reduction in oxygen consumption and in mitochondrial membrane potential was found. Enzymatic assays showed that the activity of complexbc 1 was normal, whereas that of cytochrome c oxidase (COX) was strongly decreased. This decrease is in accordance with the observed reduction in the amounts of COX II subunit and of cytochromesa+a 3 . The acetic acid-induced PCD process was found to be independent of oxidative phosphorylation because it was not inhibited by oligomycin treatment. The inability ofS. cerevisiae mutant strains (lacking mitochondrial DNA, heme lyase, or ATPase) to undergo acetic acid-induced PCD and in the ATPase mutant (knockout in ATP10) the absence of CytC release provides further evidence that the process is mediated by a mitochondria-dependent apoptotic pathway. The understanding of the involvement of a mitochondria-dependent apoptotic pathway inS. cerevisiae PCD process will be most useful in the further elucidation of an ancestral pathway common to PCD in metazoans.

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Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae

Cell Death Discovery ◽

10.1038/s41420-020-00392-x ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Francesco Monticolo ◽

Emanuela Palomba ◽

Maria Luisa Chiusano

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Death ◽

Acetic Acid ◽

Programmed Cell Death ◽

Differential Expression ◽

Ribosomal Proteins ◽

Relative Proportion ◽

Duplication Event ◽

Genome Duplication Event ◽

Cell Death Pathway

AbstractProgrammed cell death involves complex molecular pathways in both eukaryotes and prokaryotes. In Escherichia coli, the toxin–antitoxin system (TA-system) has been described as a programmed cell death pathway in which mRNA and ribosome organizations are modified, favoring the production of specific death-related proteins, but also of a minor portion of survival proteins, determining the destiny of the cell population. In the eukaryote Saccharomyces cerevisiae, the ribosome was shown to change its stoichiometry in terms of ribosomal protein content during stress response, affecting the relative proportion between ohnologs, i.e., the couple of paralogs derived by a whole genome duplication event. Here, we confirm the differential expression of ribosomal proteins in yeast also during programmed cell death induced by acetic acid, and we highlight that also in this case pairs of ohnologs are involved. We also show that there are different trends in cytosolic and mitochondrial ribosomal proteins gene expression during the process. Moreover, we show that the exposure to acetic acid induces the differential expression of further genes coding for products related to translation processes and to rRNA post-transcriptional maturation, involving mRNA decapping, affecting translation accuracy, and snoRNA synthesis. Our results suggest that the reprogramming of the overall translation apparatus, including the cytosolic ribosome reorganization, are relevant events in yeast programmed cell death induced by acetic acid.

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