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Yeast Cell Signalling Pathways

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 26953

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Dr. Vitor Teixeira

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Yeast Signalling Networks Group, i3s—Instituto de Investigação e Inovação em Saúde, Universidade do Port, Porto, Portugal
Interests: lipid and energy metabolism; lipid metabolic pathways; interorganelle membrane contact sites; organelle dysfunction in disease; aging; lipid-related diseases; molecular disease mechanisms in lipid disorders
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Special Issue Information

Dear Colleagues,

In order to respond to metabolic and environmental cues, cells are equipped with a sophisticated array of receptors and proteins that are able to receive and transduce signals by triggering a chain of events that not only carries the input but also amplifies it though coordinated activation of multiple protein complexes and signaling effectors. The ability to integrate multiple signals into a unified action plan is, by far, one of the most open questions in the field. And, yet, cells aren’t simply targets but also convey messages to other cells both near and far.

A new view of signaling networks as integrative systems is now emerging with the fast-evolving era of ´omics´, that has served as a novel paradigm that has long surpassed the classical single-gene or protein-centric approach common in biological research, providing us with a conceptual view of dynamically exchanging networks of chemical and protein interactions, where concepts of concentration, compartmentalization, and phase transition and diffusion are at the foundation of interconnectivity and high-throughput signaling responses, with compelling beauty and intricacy.

In this Special Issue, we would like to highlight the dynamic nature of yeast signaling transduction with emphasis on (i) challenges on the extent of complexity that underlies biological responses and events, (ii) the specific and non-specific interactions of proteins with lipids and other proteins, (iii) expansive diversity of proteins and interaction/binding motifs and interfaces responsible for transducing signals, (iv) various therapeutic strategies arising from basic and applied research in signal transduction using this model system, and (v) emerging and novel areas in molecular medicine and rational drug design.

Dr. Vitor Teixeira
Guest Editor

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Keywords

yeast
signal transduction
intracellular and intercellular communication
cell surface receptors
protein kinases and phosphatases
transcription factors
signal networks
posttranslational modification
biomedical research

Published Papers (10 papers)

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Editorial

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6 pages, 226 KiB

Open AccessEditorial

Special Issue: Yeast Cell Signaling Pathways (Volume 1)

by Vitor Teixeira

Int. J. Mol. Sci. 2023, 24(5), 4929; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054929 - 03 Mar 2023

Viewed by 990

Abstract

This Special Issue was devoted to unravelling novel aspects of yeast biology and signal transduction in numerous yet intricate basic processes [...] Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

Research

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21 pages, 4912 KiB

Open AccessArticle

Neomycin Interferes with Phosphatidylinositol-4,5-Bisphosphate at the Yeast Plasma Membrane and Activates the Cell Wall Integrity Pathway

by Elena Jiménez-Gutiérrez, Teresa Fernández-Acero, Esmeralda Alonso-Rodríguez, María Molina and Humberto Martín

Int. J. Mol. Sci. 2022, 23(19), 11034; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911034 - 20 Sep 2022

Cited by 1 | Viewed by 1696

Abstract

The cell wall integrity pathway (CWI) is a MAPK-mediated signaling route essential for yeast cell response to cell wall damage, regulating distinct aspects of fungal physiology. We have recently proven that the incorporation of a genetic circuit that operates as a signal amplifier into this pathway allows for the identification of novel elements involved in CWI signaling. Here, we show that the strong growth inhibition triggered by pathway hyperactivation in cells carrying the “Integrity Pathway Activation Circuit” (IPAC) also allows the easy identification of new stimuli. By using the IPAC, we have found various chemical agents that activate the CWI pathway, including the aminoglycoside neomycin. Cells lacking key components of this pathway are sensitive to this antibiotic, due to the disruption of signaling upon neomycin stimulation. Neomycin reduces both phosphatidylinositol-4,5-bisphosphate (PIP₂) availability at the plasma membrane and myriocin-induced TORC2-dependent Ypk1 phosphorylation, suggesting a strong interference with plasma membrane homeostasis, specifically with PIP₂. The neomycin-induced transcriptional profile involves not only genes related to stress and cell wall biogenesis, but also to amino acid metabolism, reflecting the action of this antibiotic on the yeast ribosome. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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23 pages, 7437 KiB

Open AccessArticle

Vps21 Directs the PI3K-PI(3)P-Atg21-Atg16 Module to Phagophores via Vps8 for Autophagy

by Lei Zhao, Weiming You, Dan Sun, Hui Xu, Xia You, Haiqian Xu, Zulin Wu, Zhiping Xie and Yongheng Liang

Int. J. Mol. Sci. 2022, 23(17), 9550; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23179550 - 23 Aug 2022

Cited by 4 | Viewed by 2843

Abstract

Phosphatidylinositol 3-phosphate (PI(3)P) serves important functions in endocytosis, phagocytosis, and autophagy. PI(3)P is generated by Vps34 of the class III phosphatidylinositol 3-kinase (PI3K) complex. The Vps34-PI3K complex can be divided into Vps34-PI3K class II (containing Vps38, endosomal) and Vps34-PI3K class I (containing Atg14, autophagosomal). Most PI(3)Ps are associated with endosomal membranes. In yeast, the endosomal localization of Vps34 and PI(3)P is tightly regulated by Vps21-module proteins. At yeast phagophore assembly site (PAS) or mammalian omegasomes, PI(3)P binds to WD-repeat protein interacting with phosphoinositide (WIPI) proteins to further recruit two conjugation systems, Atg5-Atg12·Atg16 and Atg8-PE (LC3-II), to initiate autophagy. However, the spatiotemporal regulation of PI(3)P during autophagy remains obscure. Therefore, in this study, we determined the effect of Vps21 on localization and interactions of Vps8, Vps34, Atg21, Atg8, and Atg16 upon autophagy induction. The results showed that Vps21 was required for successive colocalizations and interactions of Vps8-Vps34 and Vps34-Atg21 on endosomes, and Atg21-Atg8/Atg16 on the PAS. In addition to disrupted localization of the PI3K complex II subunits Vps34 and Vps38 on endosomes, the localization of the PI3K complex I subunits Vps34 and Atg14, as well as Atg21, was partly disrupted from the PAS in vps21∆ cells. The impaired PI3K-PI(3)P-Atg21-Atg16 axis in vps21∆ cells might delay autophagy, which is consistent with the delay of early autophagy when Atg21 was absent. This study provides the first insight into the upstream sequential regulation of the PI3K-PI(3)P-Atg21-Atg16 module by Vps21 in autophagy. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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14 pages, 4147 KiB

Open AccessArticle

The Ceramide Synthase Subunit Lac1 Regulates Cell Growth and Size in Fission Yeast

by Ignacio Flor-Parra, Susana Sabido-Bozo, Atsuko Ikeda, Kazuki Hanaoka, Auxiliadora Aguilera-Romero, Kouichi Funato, Manuel Muñiz and Rafael Lucena

Int. J. Mol. Sci. 2022, 23(1), 303; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010303 - 28 Dec 2021

Cited by 7 | Viewed by 2483

Abstract

Cell division produces two viable cells of a defined size. Thus, all cells require mechanisms to measure growth and trigger cell division when sufficient growth has occurred. Previous data suggest a model in which growth rate and cell size are mechanistically linked by ceramide-dependent signals in budding yeast. However, the conservation of mechanisms that govern growth control is poorly understood. In fission yeast, ceramide synthase is encoded by two genes, Lac1 and Lag1. Here, we characterize them by using a combination of genetics, microscopy, and lipid analysis. We showed that Lac1 and Lag1 co-immunoprecipitate and co-localize at the endoplasmic reticulum. However, each protein generates different species of ceramides and complex sphingolipids. We further discovered that Lac1, but not Lag1, is specifically required for proper control of cell growth and size in Schizosaccharomyces pombe. We propose that specific ceramide and sphingolipid species produced by Lac1 are required for normal control of cell growth and size in fission yeast. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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21 pages, 6279 KiB

Open AccessArticle

The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast

by Konstantina Amoiradaki, Kate R. Bunting, Katherine M. Paine, Josephine E. Ayre, Karen Hogg, Kamilla M. E. Laidlaw and Chris MacDonald

Int. J. Mol. Sci. 2021, 22(22), 12477; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212477 - 19 Nov 2021

Cited by 4 | Viewed by 2966

Abstract

Intracellular trafficking pathways control residency and bioactivity of integral membrane proteins at the cell surface. Upon internalisation, surface cargo proteins can be delivered back to the plasma membrane via endosomal recycling pathways. Recycling is thought to be controlled at the metabolic and transcriptional level, but such mechanisms are not fully understood. In yeast, recycling of surface proteins can be triggered by cargo deubiquitination and a series of molecular factors have been implicated in this trafficking. In this study, we follow up on the observation that many subunits of the Rpd3 lysine deacetylase complex are required for recycling. We validate ten Rpd3-complex subunits in recycling using two distinct assays and developed tools to quantify both. Fluorescently labelled Rpd3 localises to the nucleus and complements recycling defects, which we hypothesised were mediated by modulated expression of Rpd3 target gene(s). Bioinformatics implicated 32 candidates that function downstream of Rpd3, which were over-expressed and assessed for capacity to suppress recycling defects of rpd3∆ cells. This effort yielded three hits: Sit4, Dit1 and Ldb7, which were validated with a lipid dye recycling assay. Additionally, the essential phosphatidylinositol-4-kinase Pik1 was shown to have a role in recycling. We propose recycling is governed by Rpd3 at the transcriptional level via multiple downstream target genes. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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18 pages, 2796 KiB

Open AccessArticle

Candida albicans Sfp1 Is Involved in the Cell Wall and Endoplasmic Reticulum Stress Responses Induced by Human Antimicrobial Peptide LL-37

by Chun-Min Hsu, Yi-Ling Liao, Che-Kang Chang and Chung-Yu Lan

Int. J. Mol. Sci. 2021, 22(19), 10633; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910633 - 30 Sep 2021

Cited by 18 | Viewed by 2475

Abstract

Candida albicans is a commensal fungus of humans but can cause infections, particularly in immunocompromised individuals, ranging from superficial to life-threatening systemic infections. The cell wall is the outermost layer of C. albicans that interacts with the host environment. Moreover, antimicrobial peptides (AMPs) are important components in innate immunity and play crucial roles in host defense. Our previous studies showed that the human AMP LL-37 binds to the cell wall of C. albicans, alters the cell wall integrity (CWI) and affects cell adhesion of this pathogen. In this study, we aimed to further investigate the molecular mechanisms underlying the C. albicans response to LL-37. We found that LL-37 causes cell wall stress, activates unfolded protein response (UPR) signaling related to the endoplasmic reticulum (ER), induces ER-derived reactive oxygen species and affects protein secretion. Interestingly, the deletion of the SFP1 gene encoding a transcription factor reduced C. albicans susceptibility to LL-37, which is cell wall-associated. Moreover, in the presence of LL-37, deletion of SFP1 attenuated the UPR pathway, upregulated oxidative stress responsive (OSR) genes and affected bovine serum albumin (BSA) degradation by secreted proteases. Therefore, these findings suggested that Sfp1 positively regulates cell wall integrity and ER homeostasis upon treatment with LL-37 and shed light on pathogen-host interactions. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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25 pages, 4362 KiB

Open AccessArticle

Target of Rapamycin Complex 1 (TORC1), Protein Kinase A (PKA) and Cytosolic pH Regulate a Transcriptional Circuit for Lipid Droplet Formation

by Vitor Teixeira, Telma S. Martins, William A. Prinz and Vítor Costa

Int. J. Mol. Sci. 2021, 22(16), 9017; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22169017 - 20 Aug 2021

Cited by 8 | Viewed by 3618

Abstract

Lipid droplets (LDs) are ubiquitous organelles that fulfill essential roles in response to metabolic cues. The identification of several neutral lipid synthesizing and regulatory protein complexes have propelled significant advance on the mechanisms of LD biogenesis in the endoplasmic reticulum (ER). However, our understanding of signaling networks, especially transcriptional mechanisms, regulating membrane biogenesis is very limited. Here, we show that the nutrient-sensing Target of Rapamycin Complex 1 (TORC1) regulates LD formation at a transcriptional level, by targeting DGA1 expression, in a Sit4-, Mks1-, and Sfp1-dependent manner. We show that cytosolic pH (pHc), co-regulated by the plasma membrane H+-ATPase Pma1 and the vacuolar ATPase (V-ATPase), acts as a second messenger, upstream of protein kinase A (PKA), to adjust the localization and activity of the major transcription factor repressor Opi1, which in turn controls the metabolic switch between phospholipid metabolism and lipid storage. Together, this work delineates hitherto unknown molecular mechanisms that couple nutrient availability and pHc to LD formation through a transcriptional circuit regulated by major signaling transduction pathways. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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Review

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13 pages, 1631 KiB

Open AccessReview

Cell–Cell Mating Interactions: Overview and Potential of Single-Cell Force Spectroscopy

by Peter N. Lipke, Jason M. Rauceo and Albertus Viljoen

Int. J. Mol. Sci. 2022, 23(3), 1110; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031110 - 20 Jan 2022

Cited by 5 | Viewed by 2262

Abstract

It is an understatement that mating and DNA transfer are key events for living organisms. Among the traits needed to facilitate mating, cell adhesion between gametes is a universal requirement. Thus, there should be specific properties for the adhesion proteins involved in mating. Biochemical and biophysical studies have revealed structural information about mating adhesins, as well as their specificities and affinities, leading to some ideas about these specialized adhesion proteins. Recently, single-cell force spectroscopy (SCFS) has added important findings. In SCFS, mating cells are brought into contact in an atomic force microscope (AFM), and the adhesive forces are monitored through the course of mating. The results have shown some remarkable characteristics of mating adhesins and add knowledge about the design and evolution of mating adhesins. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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45 pages, 6063 KiB

Open AccessReview

D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

by Daniel P. Brink, Celina Borgström, Viktor C. Persson, Karen Ofuji Osiro and Marie F. Gorwa-Grauslund

Int. J. Mol. Sci. 2021, 22(22), 12410; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212410 - 17 Nov 2021

Cited by 17 | Viewed by 3808

Abstract

Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker’s yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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12 pages, 1858 KiB

Open AccessReview

Using Budding Yeast to Identify Molecules That Block Cancer Cell ‘Mitotic Slippage’ Only in the Presence of Mitotic Poisons

by Scott C. Schuyler and Hsin-Yu Chen

Int. J. Mol. Sci. 2021, 22(15), 7985; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22157985 - 26 Jul 2021

Cited by 1 | Viewed by 2323

Abstract

Research on the budding yeast Saccharomyces cerevisiae has yielded fundamental discoveries on highly conserved biological pathways and yeast remains the best-studied eukaryotic cell in the world. Studies on the mitotic cell cycle and the discovery of cell cycle checkpoints in budding yeast has led to a detailed, although incomplete, understanding of eukaryotic cell cycle progression. In multicellular eukaryotic organisms, uncontrolled aberrant cell division is the defining feature of cancer. Some of the most successful classes of anti-cancer chemotherapeutic agents are mitotic poisons. Mitotic poisons are thought to function by inducing a mitotic spindle checkpoint-dependent cell cycle arrest, via the assembly of the highly conserved mitotic checkpoint complex (MCC), leading to apoptosis. Even in the presence of mitotic poisons, some cancer cells continue cell division via ‘mitotic slippage’, which may correlate with a cancer becoming refractory to mitotic poison chemotherapeutic treatments. In this review, knowledge about budding yeast cell cycle control is explored to suggest novel potential drug targets, namely, specific regions in the highly conserved anaphase-promoting complex/cyclosome (APC/C) subunits Apc1 and/or Apc5, and in a specific N-terminal region in the APC/C co-factor cell division cycle 20 (Cdc20), which may yield molecules which block ‘mitotic slippage’ only in the presence of mitotic poisons. Full article

(This article belongs to the Special Issue Yeast Cell Signalling Pathways)

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