1
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Pontisso I, Ornelas-Guevara R, Chevet E, Combettes L, Dupont G. Gradual ER calcium depletion induces a progressive and reversible UPR signaling. PNAS NEXUS 2024; 3:pgae229. [PMID: 38933930 PMCID: PMC11200134 DOI: 10.1093/pnasnexus/pgae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/29/2024] [Indexed: 06/28/2024]
Abstract
The unfolded protein response (UPR) is a widespread signal transduction pathway triggered by endoplasmic reticulum (ER) stress. Because calcium (Ca2+) is a key factor in the maintenance of ER homeostasis, massive Ca2+ depletion of the ER is a potent inducer of ER stress. Although moderate changes in ER Ca2+ drive the ubiquitous Ca2+ signaling pathways, a possible incremental relationship between UPR activation and Ca2+ changes has yet to be described. Here, we determine the sensitivity and time-dependency of activation of the three ER stress sensors, inositol-requiring protein 1 alpha (IRE1α), protein kinase R-like ER kinase (PERK), and activating transcription factor 6 alpha (ATF6α) in response to controlled changes in the concentration of ER Ca2+ in human cultured cells. Combining Ca2+ imaging, fluorescence recovery after photobleaching experiments, biochemical analyses, and mathematical modeling, we uncover a nonlinear rate of activation of the IRE1α branch of UPR, as compared to the PERK and ATF6α branches that become activated gradually with time and are sensitive to more important ER Ca2+ depletions. However, the three arms are all activated within a 1 h timescale. The model predicted the deactivation of PERK and IRE1α upon refilling the ER with Ca2+. Accordingly, we showed that ER Ca2+ replenishment leads to the complete reversion of IRE1α and PERK phosphorylation in less than 15 min, thus revealing the highly plastic character of the activation of the upstream UPR sensors. In conclusion, our results reveal a dynamic and dose-sensitive Ca2+-dependent activation/deactivation cycle of UPR induction, which could tightly control cell fate upon acute and/or chronic stress.
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Affiliation(s)
- Ilaria Pontisso
- U1282 “Calcium Signaling and Microbial Infections”, Institut de Biologie Intégrative de la Cellule (I2BC)—Université Paris-Saclay, Gif-Sur-Yvette 91190, France
| | - Roberto Ornelas-Guevara
- Unit of Theoretical Chronobiology, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Eric Chevet
- Inserm U1242 Université de Rennes, 35000 Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, 35042 Rennes, France
| | - Laurent Combettes
- U1282 “Calcium Signaling and Microbial Infections”, Institut de Biologie Intégrative de la Cellule (I2BC)—Université Paris-Saclay, Gif-Sur-Yvette 91190, France
| | - Geneviève Dupont
- Unit of Theoretical Chronobiology, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
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2
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Le Goupil S, Laprade H, Aubry M, Chevet E. Exploring the IRE1 interactome: From canonical signaling functions to unexpected roles. J Biol Chem 2024; 300:107169. [PMID: 38494075 PMCID: PMC11007444 DOI: 10.1016/j.jbc.2024.107169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
The unfolded protein response is a mechanism aiming at restoring endoplasmic reticulum (ER) homeostasis and is likely involved in other adaptive pathways. The unfolded protein response is transduced by three proteins acting as sensors and triggering downstream signaling pathways. Among them, inositol-requiring enzyme 1 alpha (IRE1α) (referred to as IRE1 hereafter), an endoplasmic reticulum-resident type I transmembrane protein, exerts its function through both kinase and endoribonuclease activities, resulting in both X-box binding protein 1 mRNA splicing and RNA degradation (regulated ire1 dependent decay). An increasing number of studies have reported protein-protein interactions as regulators of these signaling mechanisms, and additionally, driving other noncanonical functions. In this review, we deliver evolutive and structural insights on IRE1 and further describe how this protein interaction network (interactome) regulates IRE1 signaling abilities or mediates other cellular processes through catalytic-independent mechanisms. Moreover, we focus on newly discovered targets of IRE1 kinase activity and discuss potentially novel IRE1 functions based on the nature of the interactome, thereby identifying new fields to explore regarding this protein's biological roles.
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Affiliation(s)
- Simon Le Goupil
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France.
| | - Hadrien Laprade
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France
| | - Marc Aubry
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France; Centre de Lutte contre le cancer Eugène Marquis, Rennes, France
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3
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Mogre S, Blazanin N, Walsh H, Ibinson J, Minnich C, Andrew Hu CC, Glick AB. TGFβ1 regulates HRas-mediated activation of IRE1α through the PERK-RPAP2 axis in keratinocytes. Mol Carcinog 2022; 61:958-971. [PMID: 35975910 PMCID: PMC9486931 DOI: 10.1002/mc.23453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/25/2022] [Accepted: 06/08/2022] [Indexed: 11/08/2022]
Abstract
Transforming Growth Factor β1 (TGFβ1) is a critical regulator of tumor progression in response to HRas. Recently, TGFβ1 has been shown to trigger ER stress in many disease models; however, its role in oncogene-induced ER stress is unclear. Oncogenic HRas induces the unfolded protein response (UPR) predominantly via the Inositol-requiring enzyme 1α (IRE1α) pathway to initiate the adaptative responses to ER stress, with importance for both proliferation and senescence. Here, we show a role of the UPR sensor proteins IRE1α and (PKR)-like endoplasmic reticulum kinase (PERK) to mediate the tumor-suppressive roles of TGFβ1 in mouse keratinocytes expressing mutant forms of HRas. TGFβ1 suppressed IRE1α phosphorylation and activation by HRas both in in vitro and in vivo models while simultaneously activating the PERK pathway. However, the increase in ER stress indicated an uncoupling of ER stress and IRE1α activation by TGFβ1. Pharmacological and genetic approaches demonstrated that TGFβ1-dependent dephosphorylation of IRE1α was mediated by PERK through RNA Polymerase II Associated Protein 2 (RPAP2), a PERK-dependent IRE1α phosphatase. In addition, TGFβ1-mediated growth arrest in oncogenic HRas keratinocytes was partially dependent on PERK-induced IRE1α dephosphorylation and inactivation. Together, these results demonstrate a critical cross-talk between UPR proteins that is important for TGFβ1-mediated tumor suppressive responses.
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Affiliation(s)
- Saie Mogre
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Nicholas Blazanin
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Hailey Walsh
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Jack Ibinson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Chase Minnich
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Chih-Chi Andrew Hu
- Center for Translational Research in Hematologic Malignancies, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, Texas, USA
| | - Adam B Glick
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, Pennsylvania, USA
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4
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Fu F, Doroudgar S. IRE1/XBP1 and Endoplasmic Reticulum Signaling – From Basic to Translational Research for Cardiovascular Disease. CURRENT OPINION IN PHYSIOLOGY 2022; 28. [DOI: 10.1016/j.cophys.2022.100552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Licheva M, Raman B, Kraft C, Reggiori F. Phosphoregulation of the autophagy machinery by kinases and phosphatases. Autophagy 2021; 18:104-123. [PMID: 33970777 PMCID: PMC8865292 DOI: 10.1080/15548627.2021.1909407] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells use post-translational modifications to diversify and dynamically coordinate the function and properties of protein networks within various cellular processes. For example, the process of autophagy strongly depends on the balanced action of kinases and phosphatases. Highly conserved from the budding yeast Saccharomyces cerevisiae to humans, autophagy is a tightly regulated self-degradation process that is crucial for survival, stress adaptation, maintenance of cellular and organismal homeostasis, and cell differentiation and development. Many studies have emphasized the importance of kinases and phosphatases in the regulation of autophagy and identified many of the core autophagy proteins as their direct targets. In this review, we summarize the current knowledge on kinases and phosphatases acting on the core autophagy machinery and discuss the relevance of phosphoregulation for the overall process of autophagy.
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Affiliation(s)
- Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Babu Raman
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, AV Groningen, The Netherlands
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, AV Groningen, The Netherlands
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6
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The Unfolded Protein Response: An Overview. BIOLOGY 2021; 10:biology10050384. [PMID: 33946669 PMCID: PMC8146082 DOI: 10.3390/biology10050384] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022]
Abstract
Simple Summary The unfolded protein response (UPR) is the cells’ way of maintaining the balance of protein folding in the endoplasmic reticulum, which is the section of the cell designated for folding proteins with specific destinations such as other organelles or to be secreted by the cell. The UPR is activated when unfolded proteins accumulate in the endoplasmic reticulum. This accumulation puts a greater load on the molecules in charge of folding the proteins, and therefore the UPR works to balance this by lowering the number of unfolded proteins present in the cell. This is done in multiple ways, such as lowering the number of proteins that need to be folded; increasing the folding ability of the endoplasmic reticulum and by removing some of the unfolded proteins which take longer to fold. If the UPR is successful at reducing the number of unfolded proteins, the UPR is inactivated and the cells protein folding balance is returned to normal. However, if the UPR is unsuccessful, then this can lead to cell death. Abstract The unfolded protein response is the mechanism by which cells control endoplasmic reticulum (ER) protein homeostasis. Under normal conditions, the UPR is not activated; however, under certain stresses, such as hypoxia or altered glycosylation, the UPR can be activated due to an accumulation of unfolded proteins. The activation of the UPR involves three signaling pathways, IRE1, PERK and ATF6, which all play vital roles in returning protein homeostasis to levels seen in non-stressed cells. IRE1 is the best studied of the three pathways, as it is the only pathway present in Saccharomyces cerevisiae. This pathway involves spliceosome independent splicing of HAC1 or XBP1 in yeast and mammalians cells, respectively. PERK limits protein synthesis, therefore reducing the number of new proteins requiring folding. ATF6 is translocated and proteolytically cleaved, releasing a NH2 domain fragment which is transported to the nucleus and which affects gene expression. If the UPR is unsuccessful at reducing the load of unfolded proteins in the ER and the UPR signals remain activated, this can lead to programmed cell death.
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Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up? Microorganisms 2021; 9:microorganisms9030620. [PMID: 33802931 PMCID: PMC8002603 DOI: 10.3390/microorganisms9030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
HAC1 encodes a key transcription factor that transmits the unfolded protein response (UPR) from the endoplasmic reticulum (ER) to the nucleus and regulates downstream UPR genes in Saccharomyces cerevisiae. In response to the accumulation of unfolded proteins in the ER, Ire1p oligomers splice HAC1 pre-mRNA (HAC1u) via a non-conventional process and allow the spliced HAC1 (HAC1i) to be translated efficiently. However, leaky splicing and translation of HAC1u may occur in non-UPR cells to induce undesirable UPR. To control accidental UPR activation, multiple fail-safe mechanisms have been proposed to prevent leaky HAC1 splicing and translation and to facilitate rapid degradation of translated Hac1up and Hac1ip. Among proposed regulatory mechanisms is a degron sequence encoded at the 5′ end of the HAC1 intron that silences Hac1up expression. To investigate the necessity of an intron-encoded degron sequence that specifically targets Hac1up for degradation, we employed publicly available transcriptomic data to quantify leaky HAC1 splicing and translation in UPR-induced and non-UPR cells. As expected, we found that HAC1u is only efficiently spliced into HAC1i and efficiently translated into Hac1ip in UPR-induced cells. However, our analysis of ribosome profiling data confirmed frequent occurrence of leaky translation of HAC1u regardless of UPR induction, demonstrating the inability of translation fail-safe to completely inhibit Hac1up production. Additionally, among 32 yeast HAC1 surveyed, the degron sequence is highly conserved by Saccharomyces yeast but is poorly conserved by all other yeast species. Nevertheless, the degron sequence is the most conserved HAC1 intron segment in yeasts. These results suggest that the degron sequence may indeed play an important role in mitigating the accumulation of Hac1up to prevent accidental UPR activation in the Saccharomyces yeast.
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8
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Gong P, Lei P, Wang S, Zeng A, Lou H. Post-Translational Modifications Aid Archaeal Survival. Biomolecules 2020; 10:biom10040584. [PMID: 32290118 PMCID: PMC7226565 DOI: 10.3390/biom10040584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high diversity, and ability to grow in special environments. Archaea often thrive in extreme conditions such as high temperature, high/low pH, high salinity, and anoxic ecosystems. All of these are threats to the stability and proper functioning of biological molecules, especially proteins and nucleic acids. Post-translational modifications (PTMs), such as phosphorylation, methylation, acetylation, and glycosylation, are reportedly widespread in Archaea and represent a critical adaptive mechanism to extreme habitats. Here, we summarize our current understanding of the contributions of PTMs to aid in extremophile survival, with a particular focus on the maintenance of genome stability.
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Affiliation(s)
- Ping Gong
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
- Correspondence: (P.G.); (H.L.)
| | - Ping Lei
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Shengping Wang
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Ao Zeng
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No.2 Yuan-Ming-Yuan West Road, Beijing 100193, China
- Correspondence: (P.G.); (H.L.)
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Telini BDP, Menoncin M, Bonatto D. Does Inter-Organellar Proteostasis Impact Yeast Quality and Performance During Beer Fermentation? Front Genet 2020; 11:2. [PMID: 32076433 PMCID: PMC7006503 DOI: 10.3389/fgene.2020.00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/06/2020] [Indexed: 02/02/2023] Open
Abstract
During beer production, yeast generate ethanol that is exported to the extracellular environment where it accumulates. Depending on the initial carbohydrate concentration in the wort, the amount of yeast biomass inoculated, the fermentation temperature, and the yeast attenuation capacity, a high concentration of ethanol can be achieved in beer. The increase in ethanol concentration as a consequence of the fermentation of high gravity (HG) or very high gravity (VHG) worts promotes deleterious pleiotropic effects on the yeast cells. Moderate concentrations of ethanol (5% v/v) change the enzymatic kinetics of proteins and affect biological processes, such as the cell cycle and metabolism, impacting the reuse of yeast for subsequent fermentation. However, high concentrations of ethanol (> 5% v/v) dramatically alter protein structure, leading to unfolded proteins as well as amorphous protein aggregates. It is noteworthy that the effects of elevated ethanol concentrations generated during beer fermentation resemble those of heat shock stress, with similar responses observed in both situations, such as the activation of proteostasis and protein quality control mechanisms in different cell compartments, including endoplasmic reticulum (ER), mitochondria, and cytosol. Despite the extensive published molecular and biochemical data regarding the roles of proteostasis in different organelles of yeast cells, little is known about how this mechanism impacts beer fermentation and how different proteostasis mechanisms found in ER, mitochondria, and cytosol communicate with each other during ethanol/fermentative stress. Supporting this integrative view, transcriptome data analysis was applied using publicly available information for a lager yeast strain grown under beer production conditions. The transcriptome data indicated upregulation of genes that encode chaperones, co-chaperones, unfolded protein response elements in ER and mitochondria, ubiquitin ligases, proteasome components, N-glycosylation quality control pathway proteins, and components of processing bodies (p-bodies) and stress granules (SGs) during lager beer fermentation. Thus, the main purpose of this hypothesis and theory manuscript is to provide a concise picture of how inter-organellar proteostasis mechanisms are connected with one another and with biological processes that may modulate the viability and/or vitality of yeast populations during HG/VHG beer fermentation and serial repitching.
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Affiliation(s)
- Bianca de Paula Telini
- Brewing Yeast Research Group, Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marcelo Menoncin
- Brewing Yeast Research Group, Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diego Bonatto
- Brewing Yeast Research Group, Centro de Biotecnologia da UFRGS, Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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10
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Xia X. Translation Control of HAC1 by Regulation of Splicing in Saccharomyces cerevisiae. Int J Mol Sci 2019; 20:ijms20122860. [PMID: 31212749 PMCID: PMC6627864 DOI: 10.3390/ijms20122860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/19/2022] Open
Abstract
Hac1p is a key transcription factor regulating the unfolded protein response (UPR) induced by abnormal accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER) in Saccharomyces cerevisiae. The accumulation of unfolded/misfolded proteins is sensed by protein Ire1p, which then undergoes trans-autophosphorylation and oligomerization into discrete foci on the ER membrane. HAC1 pre-mRNA, which is exported to the cytoplasm but is blocked from translation by its intron sequence looping back to its 5’UTR to form base-pair interaction, is transported to the Ire1p foci to be spliced, guided by a cis-acting bipartite element at its 3’UTR (3’BE). Spliced HAC1 mRNA can be efficiently translated. The resulting Hac1p enters the nucleus and activates, together with coactivators, a large number of genes encoding proteins such as protein chaperones to restore and maintain ER homeostasis and secretary protein quality control. This review details the translation regulation of Hac1p production, mediated by the nonconventional splicing, in the broad context of translation control and summarizes the evolution and diversification of the UPR signaling pathway among fungal, metazoan and plant lineages.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada.
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11
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Pinter N, Hach CA, Hampel M, Rekhter D, Zienkiewicz K, Feussner I, Poehlein A, Daniel R, Finkernagel F, Heimel K. Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis. PLoS Pathog 2019; 15:e1007734. [PMID: 30998787 PMCID: PMC6490947 DOI: 10.1371/journal.ppat.1007734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 03/27/2019] [Indexed: 11/18/2022] Open
Abstract
The corn smut fungus Ustilago maydis requires the unfolded protein response (UPR) to maintain homeostasis of the endoplasmic reticulum (ER) during the biotrophic interaction with its host plant Zea mays (maize). Crosstalk between the UPR and pathways controlling pathogenic development is mediated by protein-protein interactions between the UPR regulator Cib1 and the developmental regulator Clp1. Cib1/Clp1 complex formation results in mutual modification of the connected regulatory networks thereby aligning fungal proliferation in planta, efficient effector secretion with increased ER stress tolerance and long-term UPR activation in planta. Here we address UPR-dependent gene expression and its modulation by Clp1 using combinatorial RNAseq/ChIPseq analyses. We show that increased ER stress resistance is connected to Clp1-dependent alterations of Cib1 phosphorylation, protein stability and UPR gene expression. Importantly, we identify by deletion screening of UPR core genes the signal peptide peptidase Spp1 as a novel key factor that is required for establishing a compatible biotrophic interaction between U. maydis and its host plant maize. Spp1 is dispensable for ER stress resistance and vegetative growth but requires catalytic activity to interfere with the plant defense, revealing a novel virulence specific function for signal peptide peptidases in a biotrophic fungal/plant interaction. Biotrophic pathogens establish compatible interactions with their host to cause disease. A critical step in this process is the suppression of plant defense responses by secreted effector proteins. In the maize infecting fungus Ustilago maydis expression of effector encoding genes is coordinately upregulated at defined stages of pathogenic development in so-called effector waves. Efficient secretion of the multitude of effectors relies on the unfolded protein response (UPR) to maintain homeostasis of the endoplasmic reticulum. Activation of the UPR is connected to the control of fungal proliferation through direct protein-protein interactions between the UPR regulator Cib1 and the developmental regulator Clp1. Here, we show that this interaction leads to functional modification of Cib1 and modulation of UPR gene expression to adapt the UPR for long-term activity in the plant. Within a core set of UPR regulated genes we identify the signal peptide peptidase Spp1 as a key factor for fungal virulence. We show that Spp1 requires its conserved catalytic activity to suppress the plant defense and cause disease. The virulence specific function of Spp1 does not involve pathways previously known to be associated with Spp1-like proteins or plant defense suppression, suggesting a novel role for Spp1 substrates in biotrophic interactions.
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Affiliation(s)
- Niko Pinter
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Christina Andrea Hach
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Martin Hampel
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Dmitrij Rekhter
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Krzysztof Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Florian Finkernagel
- Center for Tumor Biology and Immunology (ZTI), Institute of Molecular Biology and Tumor Research (IMT), Marburg, Germany
| | - Kai Heimel
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
- * E-mail:
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12
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Chang TK, Lawrence DA, Lu M, Tan J, Harnoss JM, Marsters SA, Liu P, Sandoval W, Martin SE, Ashkenazi A. Coordination between Two Branches of the Unfolded Protein Response Determines Apoptotic Cell Fate. Mol Cell 2019; 71:629-636.e5. [PMID: 30118681 DOI: 10.1016/j.molcel.2018.06.038] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/16/2018] [Accepted: 06/25/2018] [Indexed: 12/31/2022]
Abstract
The kinases PERK and IRE1 alleviate endoplasmic reticulum (ER) stress by orchestrating the unfolded protein response (UPR). If stress mitigation fails, PERK promotes cell death by activating pro-apoptotic genes, including death receptor 5 (DR5). Conversely, IRE1-which harbors both kinase and endoribonuclease (RNase) modules-blocks apoptosis through regulated IRE1-dependent decay (RIDD) of DR5 mRNA. Under irresolvable ER stress, PERK activity persists, whereas IRE1 paradoxically attenuates, by mechanisms that remain obscure. Here, we report that PERK governs IRE1's attenuation through a phosphatase known as RPAP2 (RNA polymerase II-associated protein 2). RPAP2 reverses IRE1 phosphorylation, oligomerization, and RNase activation. This inhibits IRE1-mediated adaptive events, including activation of the cytoprotective transcription factor XBP1s, and ER-associated degradation of unfolded proteins. Furthermore, RIDD termination by RPAP2 unleashes DR5-mediated caspase activation and drives cell death. Thus, PERK attenuates IRE1 via RPAP2 to abort failed ER-stress adaptation and trigger apoptosis.
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Affiliation(s)
- Tsun-Kai Chang
- Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - David A Lawrence
- Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Min Lu
- Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Jenille Tan
- Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Scot A Marsters
- Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Peter Liu
- Microchemistry Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wendy Sandoval
- Microchemistry Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Scott E Martin
- Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Avi Ashkenazi
- Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080, USA.
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PP2C phosphatases promote autophagy by dephosphorylation of the Atg1 complex. Proc Natl Acad Sci U S A 2019; 116:1613-1620. [PMID: 30655342 DOI: 10.1073/pnas.1817078116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Macroautophagy is orchestrated by the Atg1-Atg13 complex in budding yeast. Under nutrient-rich conditions, Atg13 is maintained in a hyperphosphorylated state by the TORC1 kinase. After nutrient starvation, Atg13 is dephosphorylated, triggering Atg1 kinase activity and macroautophagy induction. The phosphatases that dephosphorylate Atg13 remain uncharacterized. Here, we show that two redundant PP2C phosphatases, Ptc2 and Ptc3, regulate macroautophagy by dephosphorylating Atg13 and Atg1. In the absence of these phosphatases, starvation-induced macroautophagy and the cytoplasm-to-vacuole targeting pathway are inhibited, and the recruitment of the essential autophagy machinery to the phagophore assembly site is impaired. Expressing a genomic ATG13 -8SA allele lacking key TORC1 phosphorylation sites partially bypasses the macroautophagy defect in ptc2Δ ptc3Δ strains. Moreover, Ptc2 and Ptc3 interact with the Atg1-Atg13 complex. Taken together, these results suggest that PP2C-type phosphatases promote macroautophagy by regulating the Atg1 complex.
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CO 2 Signaling through the Ptc2-Ssn3 Axis Governs Sustained Hyphal Development of Candida albicans by Reducing Ume6 Phosphorylation and Degradation. mBio 2019; 10:mBio.02320-18. [PMID: 30647154 PMCID: PMC6336421 DOI: 10.1128/mbio.02320-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Candida albicans is the most common cause of invasive fungal infections in humans. Its ability to sense and adapt to changing carbon dioxide levels is crucial for its pathogenesis. Carbon dioxide promotes hyphal development. The hypha-specific transcription factor Ume6 is rapidly degraded in air, but is stable under physiological CO2 and hypoxia to sustain hyphal elongation. Here, we show that Ume6 stability is regulated by two parallel E3 ubiquitin ligases, SCFGrr1 and Ubr1, in response to CO2 and O2, respectively. To uncover the CO2 signaling pathway that regulates Ume6 stability, we performed genetic screens for mutants unable to respond to CO2 for sustained filamentation. We find that the type 2C protein phosphatase Ptc2 is specifically required for CO2-induced stabilization of Ume6 and hyphal elongation. In contrast, the cyclin-dependent kinase Ssn3 is found to be required for Ume6 phosphorylation and degradation in atmospheric CO2 Furthermore, we find that Ssn3 is dephosphorylated in 5% CO2 in a Ptc2-dependent manner, whereas deletion of PTC2 has no effect on Ssn3 phosphorylation in air. Our study uncovers the Ptc2-Ssn3 axis as a new CO2 signaling pathway that controls hyphal elongation by regulating Ume6 stability in C. albicans IMPORTANCE The capacity to sense and adapt to changing carbon dioxide levels is crucial for all organisms. In fungi, CO2 is a key determinant involved in fundamental biological processes, including growth, morphology, and virulence. In the pathogenic fungus Candida albicans, high CO2 is directly sensed by adenylyl cyclase to promote hyphal growth. However, little is known about the mechanism by which hyphal development is maintained in response to physiological levels of CO2 Here we report that a signal transduction system mediated by a phosphatase-kinase pair controls CO2-responsive Ume6 phosphorylation and stability that in turn dictate hyphal elongation. Our results unravel a new regulatory mechanism of CO2 signaling in fungi.
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Welihinda AA, Tirasophon W, Kaufman RJ. The cellular response to protein misfolding in the endoplasmic reticulum. Gene Expr 2018; 7:293-300. [PMID: 10440230 PMCID: PMC6174664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
In eukaryotic cells, accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) leads to a stress response. Cells respond to ER stress by upregulating the synthesis of ER resident protein chaperones, thus increasing the folding capacity in this organelle. In addition, this response also activates pathways to induce programmed cell death. The stress-induced chaperone synthesis is regulated at the level of transcription. In Saccharomyces cerevisiae, the transmembrane protein, Ire1p, with both serine/threonine kinase and site-specific endoribonuclease activities is implicated as the sensor of unfolded proteins in the ER that transmits the signal from the ER to activate transcription in the nucleus. Activation of the unfolded protein response (UPR) pathway also requires the bZIP transcription factor, Haclp. Although HACl is transcribed constitutively, the mRNA is poorly translated. Upon accumulation of unfolded proteins, Ire1p generates a new processed form of HACl mRNA that is efficiently translated by removal of a 252 base sequence. Using the yeast-interaction trap system we identified additional components of the UPR. A yeast transcriptional coactivator complex, Gcn5p/Ada, which is composed of Gcn5p, Ada2p, Ada3p, and Ada5p, was identified that interacts with Ire1p and Hac1p. Deletion of GCN5, ADA2, and/or ADA3 reduces, and deletion of ADA5 completely abrogates, the transcriptional induction in response to misfolded protein in the ER. A protein phosphatase, Ptc2p, was also identified as a negative regulator of the UPR that directly interacts with and dephosphorylates activated Ire1p. Recently, two mammalian homologues of Ire1p, IRE1 and IRE2, were identified. hIre1p, is preferentially localized to the nuclear envelope and requires a functional nuclease activity to transmit the UPR. These results indicate that some features of the UPR are conserved from yeast to humans and may be composed of a multicomponent complex that is regulated by phosphorylation status and is associated with the nuclear envelope to regulate processes including transcriptional induction and mRNA processing. We propose that activation of Ire1p induces splicing of HACl mRNA as well as engages and targets the Gcn5/Ada/Hac1 protein complex to genes that are transcriptionally activated in response to unfolded protein in the ER. The transcriptional activation is facilitated by targeting the histone acetylase, Gcn5p in yeast, to promote histone acetylation at chromatin encoding ER stress-responsive genes. In addition, activation of Ire1p leads to increased lipid biosynthesis, thereby allowing ER expansion to accommodate increasing lumenal constituents. Under conditions of more severe stress, cells activate an Ire1p-dependent death pathway that is mediated through induction of GADD153/CHOP.
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Affiliation(s)
- Ajith A. Welihinda
- *Department of Biological Chemistry, The University of Michigan Medical Center, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-0650
| | - Witoon Tirasophon
- *Department of Biological Chemistry, The University of Michigan Medical Center, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-0650
| | - Randal J. Kaufman
- *Department of Biological Chemistry, The University of Michigan Medical Center, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-0650
- †Howard Hughes Medical Institute, The University of Michigan Medical Center, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-0650
- Address correspondence to Dr. Randal J. Kaufman, Howard Hughes Medical Institute, The University of Michigan Medical Center, MSRB II Room 4570, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-0650. Tel: (734) 763-9037; Fax: (734) 763-9323; E-mail:
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16
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Tavernier Q, Bennana E, Poindessous V, Schaeffer C, Rampoldi L, Pietrancosta N, Pallet N. Regulation of IRE1 RNase activity by the Ribonuclease inhibitor 1 (RNH1). Cell Cycle 2018; 17:1901-1916. [PMID: 30109813 DOI: 10.1080/15384101.2018.1506655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Adaptation to endoplasmic reticulum (ER) stress depends on the activation of the sensor inositol-requiring enzyme 1α (IRE1), an endoribonuclease that splices the mRNA of the transcription factor XBP1 (X-box-binding protein 1). To better understand the protein network that regulates the activity of the IRE1 pathway, we systematically screened the proteins that interact with IRE1 and identified a ribonuclease inhibitor called ribonuclease/angiogenin inhibitor 1 (RNH1). RNH1 is a leucine-rich repeat domains-containing protein that binds to and inhibits ribonucleases. Immunoprecipitation experiments confirmed this interaction. Docking experiments indicated that RNH1 physically interacts with IRE1 through its cytosolic RNase domain. Upon ER stress, the interaction of RNH1 with IRE1 in the ER increased at the expense of the nuclear pool of RNH1. Inhibition of RNH1 expression using siRNA mediated RNA interference upon ER stress led to an increased splicing activity of XBP1. Modulation of IRE1 RNase activity by RNH1 was recapitulated in a cell-free system, suggesting direct regulation of IRE1 by RNH. We conclude that RNH1 attenuates the activity of IRE1 by interacting with its ribonuclease domain. These findings have implications for understanding the molecular mechanism by which IRE1 signaling is attenuated upon ER stress.
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Affiliation(s)
- Quentin Tavernier
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France
| | - Evangeline Bennana
- b Paris Descartes University , Paris , France.,c 3P5 Proteomic facility, COMUE Sorbonne Paris Cité , Université Paris Descartes , Paris , France
| | - Virginie Poindessous
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France
| | - Celine Schaeffer
- d Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology , IRCCS San Raffaele Scientific Institute , Milan , Italy
| | - Luca Rampoldi
- d Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology , IRCCS San Raffaele Scientific Institute , Milan , Italy
| | - Nicolas Pietrancosta
- b Paris Descartes University , Paris , France.,e Centre National pour la Recherche Scientifique (CNRS) U8601 , Paris , France.,f Team Chemistry and Biology, Modeling & Immunology for Therapy , CBMIT, 2MI Platform , Paris , France
| | - Nicolas Pallet
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France.,g Clinical Chemistry Department , Hôpital Européen Gorges Pompidou, APHP , Paris , France.,h Plate-forme Proteomique 3P5 , Universite Paris Descartes, Sorbonne Paris Cite , Paris , France
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17
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Bypass of Activation Loop Phosphorylation by Aspartate 836 in Activation of the Endoribonuclease Activity of Ire1. Mol Cell Biol 2017; 37:MCB.00655-16. [PMID: 28559428 PMCID: PMC5533888 DOI: 10.1128/mcb.00655-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/22/2017] [Indexed: 12/18/2022] Open
Abstract
The bifunctional protein kinase-endoribonuclease Ire1 initiates splicing of the mRNA for the transcription factor Hac1 when unfolded proteins accumulate in the endoplasmic reticulum. Activation of Saccharomyces cerevisiae Ire1 coincides with autophosphorylation of its activation loop at S840, S841, T844, and S850. Mass spectrometric analysis of Ire1 expressed in Escherichia coli identified S837 as another potential phosphorylation site in vivo. Mutation of all five potential phosphorylation sites in the activation loop decreased, but did not completely abolish, splicing of HAC1 mRNA, induction of KAR2 and PDI1 mRNAs, and expression of a β-galactosidase reporter activated by Hac1i. Phosphorylation site mutants survive low levels of endoplasmic reticulum stress better than IRE1 deletions strains. In vivo clustering and inactivation of Ire1 are not affected by phosphorylation site mutants. Mutation of D836 to alanine in the activation loop of phosphorylation site mutants nearly completely abolished HAC1 splicing, induction of KAR2, PDI1, and β-galactosidase reporters, and survival of ER stress, but it had no effect on clustering of Ire1. By itself, the D836A mutation does not confer a phenotype. These data argue that D836 can partially substitute for activation loop phosphorylation in activation of the endoribonuclease domain of Ire1.
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18
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Impairment of both IRE1 expression and XBP1 activation is a hallmark of GCB DLBCL and contributes to tumor growth. Blood 2017; 129:2420-2428. [PMID: 28167662 DOI: 10.1182/blood-2016-09-741348] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/31/2017] [Indexed: 12/12/2022] Open
Abstract
The endoplasmic reticulum kinase inositol-requiring enzyme 1 (IRE1) and its downstream target X-box-binding protein 1 (XBP1) drive B-cell differentiation toward plasma cells and have been shown to contribute to multiple myeloma development; yet, little is known of the role of this pathway in diffuse large B-cell lymphoma (DLBCL). Here, we show that in the germinal center B-cell-like (GCB) DLBCL subtype, IRE1 expression is reduced to a level that prevents XBP1 activation. Gene expression profiles indicated that, in GCB DLBCL cancer samples, expression of IRE1 messenger RNA was inversely correlated with the levels and activity of the epigenetic repressor, histone methyltransferase enhancer of zeste homolog 2 (EZH2). Correspondingly, in GCB-derived cell lines, the IRE1 promoter carried increased levels of the repressive epigenetic mark histone 3 lysine 27 trimethylation. Pharmacological inhibition of EZH2 erased those marks and restored IRE1 expression and function in vitro and in vivo. Moreover, reconstitution of the IRE1-signaling pathway, by expression of the XBP1-active form, compromised GCB DLBCL tumor growth in a mouse xenograft cancer model. These findings indicate that IRE1-XBP1 downregulation distinguishes GCB DLBCL from other DLBCL subtypes and contributes to tumor growth.
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Protein kinase Snf1 is involved in the proper regulation of the unfolded protein response in Saccharomyces cerevisiae. Biochem J 2015; 468:33-47. [PMID: 25730376 DOI: 10.1042/bj20140734] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glc7 is the only catalytic subunit of the protein phosphatase type 1 in the yeast S. cerevisiae and, together with its regulatory subunits, is involved in many essential processes. Analysis of the non-essential mutants in the regulatory subunits of Glc7 revealed that the lack of Reg1, and no other subunit, causes hypersensitivity to unfolded protein response (UPR)-inducers, which was concomitant with an augmented UPR element-dependent transcriptional response. The Glc7-Reg1 complex takes part in the regulation of the yeast AMP-activated serine/threonine protein kinase Snf1 in response to glucose. We demonstrate in the present study that the observed phenotypes of reg1 mutant cells are attributable to the inappropriate activation of Snf1. Indeed, growth in the presence of limited concentrations of glucose, where Snf1 is active, or expression of active forms of Snf1 in a wild-type strain increased the sensitivity to the UPR-inducer tunicamycin. Furthermore, reg1 mutant cells showed a sustained HAC1 mRNA splicing and KAR2 mRNA levels during the recovery phase of the UPR, and dysregulation of the Ire1-oligomeric equilibrium. Finally, overexpression of protein phosphatases Ptc2 and Ptc3 alleviated the growth defect of reg1 cells under endoplasmic reticulum (ER) stress conditions. Altogether, our results reveal that Snf1 plays an important role in the attenuation of the UPR, as well as identifying the protein kinase and its effectors as possible pharmacological targets for human diseases that are associated with insufficient UPR activation.
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20
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Montenegro-Montero A, Goity A, Larrondo LF. The bZIP Transcription Factor HAC-1 Is Involved in the Unfolded Protein Response and Is Necessary for Growth on Cellulose in Neurospora crassa. PLoS One 2015; 10:e0131415. [PMID: 26132395 PMCID: PMC4488935 DOI: 10.1371/journal.pone.0131415] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/02/2015] [Indexed: 12/15/2022] Open
Abstract
High protein secretion capacity in filamentous fungi requires an extremely efficient system for protein synthesis, folding and transport. When the folding capacity of the endoplasmic reticulum (ER) is exceeded, a pathway known as the unfolded protein response (UPR) is triggered, allowing cells to mitigate and cope with this stress. In yeast, this pathway relies on the transcription factor Hac1, which mediates the up-regulation of several genes required under these stressful conditions. In this work, we identified and characterized the ortholog of the yeast HAC1 gene in the filamentous fungus Neurospora crassa. We show that its mRNA undergoes an ER stress-dependent splicing reaction, which in N. crassa removes a 23 nt intron and leads to a change in the open reading frame. By disrupting the N. crassa hac-1 gene, we determined it to be crucial for activating UPR and for proper growth in the presence of ER stress-inducing chemical agents. Neurospora is naturally found growing on dead plant material, composed primarily by lignocellulose, and is a model organism for the study of plant cell wall deconstruction. Notably, we found that growth on cellulose, a substrate that requires secretion of numerous enzymes, imposes major demands on ER function and is dramatically impaired in the absence of hac-1, thus broadening the range of physiological functions of the UPR in filamentous fungi. Growth on hemicellulose however, another carbon source that necessitates the secretion of various enzymes for its deconstruction, is not impaired in the mutant nor is the amount of proteins secreted on this substrate, suggesting that secretion, as a whole, is unaltered in the absence of hac-1. The characterization of this signaling pathway in N. crassa will help in the study of plant cell wall deconstruction by fungi and its manipulation may result in important industrial biotechnological applications.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandra Goity
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F. Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail:
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21
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Puf4 regulates both splicing and decay of HXL1 mRNA encoding the unfolded protein response transcription factor in Cryptococcus neoformans. EUKARYOTIC CELL 2015; 14:385-95. [PMID: 25681267 DOI: 10.1128/ec.00273-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/30/2015] [Indexed: 11/20/2022]
Abstract
The endoplasmic reticulum (ER) responds to errors in protein folding or processing by induction of the unfolded protein response (UPR). During conditions of ER stress, unconventional splicing of an mRNA encoding the UPR-responsive transcription factor occurs at the ER surface, resulting in activation of the UPR. UPR activation is necessary for adaptation to ER stress and for the pathogenic fungus Cryptococcus neoformans is an absolute requirement for temperature adaptation and virulence. In this study, we have determined that C. neoformans has co-opted a conserved PUF RNA binding protein to regulate the posttranscriptional processing of the HXL1 mRNA encoding the UPR transcription factor. PUF elements were identified in both the 5' and 3' untranslated regions of the HXL1 transcript, and both elements bound Puf4. Deletion of PUF4 resulted in delayed unconventional splicing of HXL1 mRNA and delayed induction of Hxl1 target genes. In addition, the HXL1 transcript was stabilized in the absence of Puf4. The puf4Δ mutant exhibited temperature sensitivity but was as virulent as the wild type, despite a reduction in fungal burden in the brains of infected mice. Our results reveal a novel regulatory role in which a PUF protein influences the unconventional splicing of the mRNA encoding the UPR-responsive transcription factor. These data suggest a unique role for a PUF protein in controlling UPR kinetics via the posttranscriptional regulation of the mRNA encoding the UPR transcription factor Hxl1.
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22
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Sharmin D, Sasano Y, Sugiyama M, Harashima S. Effects of deletion of different PP2C protein phosphatase genes on stress responses in Saccharomyces cerevisiae. Yeast 2014; 31:393-409. [PMID: 25088474 DOI: 10.1002/yea.3032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 06/02/2014] [Accepted: 07/12/2014] [Indexed: 11/06/2022] Open
Abstract
A key mechanism of signal transduction in eukaryotes is reversible protein phosphorylation, mediated through protein kinases and protein phosphatases (PPases). Modulation of signal transduction by this means regulates many biological processes. Saccharomyces cerevisiae has 40 PPases, including seven protein phosphatase 2C (PP2C PPase) genes (PTC1-PTC7). However, their precise functions remain poorly understood. To elucidate their cellular functions and to identify those that are redundant, we constructed 127 strains with deletions of all possible combinations of the seven PP2C PPase genes. All 127 disruptants were viable under nutrient-rich conditions, demonstrating that none of the combinations induced synthetic lethality under these conditions. However, several combinations exhibited novel phenotypes, e.g. the Δptc5Δptc7 double disruptant and the Δptc2Δptc3Δptc5Δptc7 quadruple disruptant exhibited low (13°C) and high (37°C) temperature-sensitive growth, respectively. Interestingly, the septuple disruptant Δptc1Δptc2Δptc3Δptc4Δptc5Δptc6Δptc7 showed an essentially normal growth phenotype at 37°C. The Δptc2Δptc3Δptc5Δptc7 quadruple disruptant was sensitive to LiCl (0.4 m). Two double disruptants, Δptc1Δptc2 and Δptc1Δptc4, displayed slow growth and Δptc1Δptc2Δptc4 could not grow on medium containing 1.5 m NaCl. The Δptc1Δptc6 double disruptant showed increased sensitivity to caffeine, congo red and calcofluor white compared to each single deletion. Our observations indicate that S. cerevisiae PP2C PPases have a shared and important role in responses to environmental stresses. These disruptants also provide a means for exploring the molecular mechanisms of redundant PTC gene functions under defined conditions.
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Affiliation(s)
- Dilruba Sharmin
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
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23
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Eletto D, Eletto D, Dersh D, Gidalevitz T, Argon Y. Protein disulfide isomerase A6 controls the decay of IRE1α signaling via disulfide-dependent association. Mol Cell 2014; 53:562-576. [PMID: 24508390 DOI: 10.1016/j.molcel.2014.01.004] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/25/2013] [Accepted: 01/03/2014] [Indexed: 11/29/2022]
Abstract
The response to endoplasmic reticulum (ER) stress relies on activation of unfolded protein response (UPR) sensors, and the outcome of the UPR depends on the duration and strength of signal. Here, we demonstrate a mechanism that attenuates the activity of the UPR sensor inositol-requiring enzyme 1α (IRE1α). A resident ER protein disulfide isomerase, PDIA6, limits the duration of IRE1α activity by direct binding to cysteine 148 in the lumenal domain of the sensor, which is oxidized when IRE1 is activated. PDIA6-deficient cells hyperrespond to ER stress with sustained autophosphorylation of IRE1α and splicing of XBP1 mRNA, resulting in exaggerated upregulation of UPR target genes and increased apoptosis. In vivo, PDIA6-deficient C. elegans exhibits constitutive UPR and fails to complete larval development, a program that normally requires the UPR. Thus, PDIA6 activity provides a mechanism that limits UPR signaling and maintains it within a physiologically appropriate range.
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Affiliation(s)
- Davide Eletto
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniela Eletto
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Devin Dersh
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tali Gidalevitz
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Yair Argon
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA 19104, USA
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24
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Pluquet O, Dejeans N, Bouchecareilh M, Lhomond S, Pineau R, Higa A, Delugin M, Combe C, Loriot S, Cubel G, Dugot-Senant N, Vital A, Loiseau H, Gosline SJC, Taouji S, Hallett M, Sarkaria JN, Anderson K, Wu W, Rodriguez FJ, Rosenbaum J, Saltel F, Fernandez-Zapico ME, Chevet E. Posttranscriptional regulation of PER1 underlies the oncogenic function of IREα. Cancer Res 2013; 73:4732-43. [PMID: 23752693 DOI: 10.1158/0008-5472.can-12-3989] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Growing evidence supports a role for the unfolded protein response (UPR) in carcinogenesis; however, the precise molecular mechanisms underlying this phenomenon remain elusive. Herein, we identified the circadian clock PER1 mRNA as a novel substrate of the endoribonuclease activity of the UPR sensor IRE1α. Analysis of the mechanism shows that IRE1α endoribonuclease activity decreased PER1 mRNA in tumor cells without affecting PER1 gene transcription. Inhibition of IRE1α signaling using either siRNA-mediated silencing or a dominant-negative strategy prevented PER1 mRNA decay, reduced tumorigenesis, and increased survival, features that were reversed upon PER1 silencing. Clinically, patients showing reduced survival have lower levels of PER1 mRNA expression and increased splicing of XBP1, a known IRE-α substrate, thereby pointing toward an increased IRE1α activity in these patients. Hence, we describe a novel mechanism connecting the UPR and circadian clock components in tumor cells, thereby highlighting the importance of this interplay in tumor development.
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Affiliation(s)
- Olivier Pluquet
- Inserm U1053, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux Cedex, France
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Feng J, Zhao Y, Duan Y, Jiang L. Genetic interactions between protein phosphatases CaPtc2p and CaPph3p in response to genotoxins and rapamycin inCandida albicans. FEMS Yeast Res 2013; 13:85-96. [DOI: 10.1111/1567-1364.12012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 10/11/2012] [Accepted: 10/12/2012] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jinrong Feng
- Department of Pathogen Biology; School of Medicine; Nantong University; Nantong; China
| | | | - Yinong Duan
- Department of Pathogen Biology; School of Medicine; Nantong University; Nantong; China
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26
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Deng Y, Srivastava R, Howell SH. Endoplasmic reticulum (ER) stress response and its physiological roles in plants. Int J Mol Sci 2013; 14:8188-212. [PMID: 23591838 PMCID: PMC3645738 DOI: 10.3390/ijms14048188] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/19/2013] [Accepted: 04/01/2013] [Indexed: 01/29/2023] Open
Abstract
The endoplasmic reticulum (ER) stress response is a highly conserved mechanism that results from the accumulation of unfolded or misfolded proteins in the ER. The response plays an important role in allowing plants to sense and respond to adverse environmental conditions, such as heat stress, salt stress and pathogen infection. Since the ER is a well-controlled microenvironment for proper protein synthesis and folding, it is highly susceptible to stress conditions. Accumulation of unfolded or misfolded proteins activates a signaling pathway, called the unfolded protein response (UPR), which acts to relieve ER stress and, if unsuccessful, leads to cell death. Plants have two arms of the UPR signaling pathway, an arm involving the proteolytic processing of membrane-associated basic leucine zipper domain (bZIP) transcription factors and an arm involving RNA splicing factor, IRE1, and its mRNA target. These signaling pathways play an important role in determining the cell's fate in response to stress conditions.
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Affiliation(s)
- Yan Deng
- Plant Sciences Institute and Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; E-Mails: (Y.D.); (R.S.)
| | - Renu Srivastava
- Plant Sciences Institute and Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; E-Mails: (Y.D.); (R.S.)
| | - Stephen H. Howell
- Plant Sciences Institute and Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; E-Mails: (Y.D.); (R.S.)
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Unfolded protein responses with or without unfolded proteins? Cells 2012; 1:926-50. [PMID: 24710536 PMCID: PMC3901143 DOI: 10.3390/cells1040926] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/15/2012] [Accepted: 10/22/2012] [Indexed: 01/08/2023] Open
Abstract
The endoplasmic reticulum (ER) is the site of secretory protein biogenesis. The ER quality control (QC) machinery, including chaperones, ensures the correct folding of secretory proteins. Mutant proteins and environmental stresses can overwhelm the available QC machinery. To prevent and resolve accumulation of misfolded secretory proteins in the ER, cells have evolved integral membrane sensors that orchestrate the Unfolded Protein Response (UPR). The sensors, Ire1p in yeast and IRE1, ATF6, and PERK in metazoans, bind the luminal ER chaperone BiP during homeostasis. As unfolded secretory proteins accumulate in the ER lumen, BiP releases, and the sensors activate. The mechanisms of activation and attenuation of the UPR sensors have exhibited unexpected complexity. A growing body of data supports a model in which Ire1p, and potentially IRE1, directly bind unfolded proteins as part of the activation process. However, evidence for an unfolded protein-independent mechanism has recently emerged, suggesting that UPR can be activated by multiple modes. Importantly, dysregulation of the UPR has been linked to human diseases including Type II diabetes, heart disease, and cancer. The existence of alternative regulatory pathways for UPR sensors raises the exciting possibility for the development of new classes of therapeutics for these medically important proteins.
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Zhao Y, Feng J, Li J, Jiang L. Mithochondrial type 2C protein phosphatases CaPtc5p, CaPtc6p, and CaPtc7p play vital roles in cellular responses to antifungal drugs and cadmium inCandida albicans. FEMS Yeast Res 2012; 12:897-906. [DOI: 10.1111/j.1567-1364.2012.00840.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 12/29/2022] Open
Affiliation(s)
- Yunying Zhao
- Department of Molecular and Cellular Pharmacology; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin; China
| | - Jinrong Feng
- Department of Pathogen Biology; School of Medicine; Nantong University; Nantong; China
| | - Jing Li
- Department of Molecular and Cellular Pharmacology; School of Pharmaceutical Science and Technology; Tianjin University; Tianjin; China
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Abstract
The endoplasmic reticulum (ER) controls many important aspects of cellular function, including processing of secreted and membrane proteins, synthesis of membranes, and calcium storage. Maintenance of ER function is controlled through a network of signaling pathways collectively known as the unfolded protein response (UPR). The UPR balances the load of incoming proteins with the folding capacity of the ER and allows cells to adapt to situations that disrupt this balance. This disruption is referred to as ER stress. Although ER stress often arises in pathological situations, the UPR plays a central role in the normal development and function of cells specializing in secretion. Many aspects of this response are conserved broadly across eukaryotes; most organisms use some subset of a group of ER transmembrane proteins to signal to the nucleus and induce a broad transcriptional upregulation of genes involved in ER function. However, new developments in metazoans, plants, and fungi illustrate interesting variations on this theme. Here, we summarize mechanisms for detecting and counteracting ER stress, the role of the UPR in normal secretory cell function, and how these pathways vary across organisms and among different tissues and cell types.
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Affiliation(s)
- Kristin A Moore
- Department of Biology and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112-0840, USA
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Lajoie P, Moir RD, Willis IM, Snapp EL. Kar2p availability defines distinct forms of endoplasmic reticulum stress in living cells. Mol Biol Cell 2012; 23:955-64. [PMID: 22219379 PMCID: PMC3290652 DOI: 10.1091/mbc.e11-12-0995] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The endoplasmic reticulum (ER) unfolded protein response (UPR) is correlated with changes in unfolded secretory levels. A novel fluorescence biosensor now reports changes in the unfolded protein burden. This reporter reveals a form of ER stress—inositol withdrawal—that stimulates the UPR without changes in unfolded protein levels. Accumulation of misfolded secretory proteins in the endoplasmic reticulum (ER) activates the unfolded protein response (UPR) stress pathway. To enhance secretory protein folding and promote adaptation to stress, the UPR upregulates ER chaperone levels, including BiP. Here we describe chromosomal tagging of KAR2, the yeast homologue of BiP, with superfolder green fluorescent protein (sfGFP) to create a multifunctional endogenous reporter of the ER folding environment. Changes in Kar2p-sfGFP fluorescence levels directly correlate with UPR activity and represent a robust reporter for high-throughput analysis. A novel second feature of this reporter is that photobleaching microscopy (fluorescence recovery after photobleaching) of Kar2p-sfGFP mobility reports on the levels of unfolded secretory proteins in individual cells, independent of UPR status. Kar2p-sfGFP mobility decreases upon treatment with tunicamycin or dithiothreitol, consistent with increased levels of unfolded proteins and the incorporation of Kar2p-sfGFP into slower-diffusing complexes. During adaptation, we observe a significant lag between down-regulation of the UPR and resolution of the unfolded protein burden. Finally, we find that Kar2p-sfGFP mobility significantly increases upon inositol withdrawal, which also activates the UPR, apparently independent of unfolded protein levels. Thus Kar2p mobility represents a powerful new tool capable of distinguishing between the different mechanisms leading to UPR activation in living cells.
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Affiliation(s)
- Patrick Lajoie
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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31
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Dejeans N, Pluquet O, Lhomond S, Grise F, Bouchecareilh M, Juin A, Meynard-Cadars M, Bidaud-Meynard A, Gentil C, Moreau V, Saltel F, Chevet E. Autocrine control of glioma cells adhesion/migration through Inositol Requiring enzyme 1α (IRE1α)-mediated cleavage of Secreted Protein Acidic Rich in Cysteine (SPARC) mRNA. J Cell Sci 2012; 125:4278-87. [DOI: 10.1242/jcs.099291] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The endoplasmic reticulum (ER) is an organelle specialized for the folding and assembly of secretory and transmembrane proteins. ER homeostasis is often perturbed in tumor cells due to dramatic changes in solid tumor microenvironment, thereby leading to the activation of an adaptive mechanism named the Unfolded Protein Response (UPR). The activation of the UPR sensor IRE1α has been described to play an important role in tumor progression. However, the molecular events associated with this phenotype remain poorly characterized. In the present study, we examined the effects of IRE1α signaling on glioma cells adaptation to their microenvironment. We show that the characteristics of U87 cells migration are modified under conditions where IRE1α activity is impaired (DN_IRE1). This is linked to increased stress fiber formation and enhanced RhoA activity. Gene expression profiling also revealed that loss of functional IRE1α signaling mostly resulted in the up-regulation of genes encoding extracellular matrix proteins. Among these genes, SPARC, whose mRNA is a direct target of IRE1α endoribonuclease activity, was in part responsible for the phenotypic changes associated with IRE1α inactivation. Hence, our data demonstrate that IRE1α is a key regulator of SPARC expression in vitro in a glioma model. Our results also further support the critical role of IRE1α contribution to tumor growth and infiltration/invasion and extend the paradigm of secretome control in tumor microenvironment conditioning.
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Feng J, Zhao J, Li J, Zhang L, Jiang L. Functional characterization of the PP2C phosphatase CaPtc2p in the human fungal pathogen Candida albicans. Yeast 2010; 27:753-64. [PMID: 20641018 DOI: 10.1002/yea.1778] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Type 2C protein phosphatases (PP2C) are monomeric enzymes and their activities require the presence of magnesium or manganese ion. There are seven PP2C-like genes in Candida albicans. In this study, we demonstrate that CaPtc2p is a PP2C phosphatase. Surprisingly, in addition to the cytoplasmic localization, CaPtc2p is partially associated with mitochondria in yeast-form and filamentous cells of C. albicans. Expression of CaPTC2 is developmentally regulated during the serum-induced filamentation. Deletion of CaPTC2 renders C. albicans cells sensitive to SDS and azole antifungals, as well as the DNA methylation agent methylmethane sulphonate and the DNA synthesis inhibitor hydroxyurea. Therefore, CaPtc2p might fulfil multiple functions, including the regulation of mitochondrial physiology and checkpoint recovery from DNA damage in C. albicans cells.
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Affiliation(s)
- Jinrong Feng
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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33
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Abstract
Type 2C Ser/Thr phosphatases are a remarkable class of protein phosphatases, which are conserved in eukaryotes and involved in a large variety of functional processes. Unlike in other Ser/Thr phosphatases, the catalytic polypeptide is not usually associated with regulatory subunits, and functional specificity is achieved by encoding multiple isoforms. For fungi, most information comes from the study of type 2C protein phosphatase (PP2C) enzymes in Saccharomyces cerevisiae, where seven PP2C-encoding genes (PTC1 to -7) with diverse functions can be found. More recently, data on several Candida albicans PP2C proteins became available, suggesting that some of them can be involved in virulence. In this work we review the available literature on fungal PP2Cs and explore sequence databases to provide a comprehensive overview of these enzymes in fungi.
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Tomecki R, Dziembowski A. Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism. RNA (NEW YORK, N.Y.) 2010; 16:1692-1724. [PMID: 20675404 PMCID: PMC2924532 DOI: 10.1261/rna.2237610] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
For a long time it has been assumed that the decay of RNA in eukaryotes is mainly carried out by exoribonucleases, which is in contrast to bacteria, where endoribonucleases are well documented to initiate RNA degradation. In recent years, several as yet unknown endonucleases have been described, which has changed our view on eukaryotic RNA metabolism. Most importantly, it was shown that the primary eukaryotic 3' --> 5' exonuclease, the exosome complex has the ability to endonucleolytically cleave its physiological RNA substrates, and novel endonucleases involved in both nuclear and cytoplasmic RNA surveillance pathways were discovered concurrently. In addition, endoribonucleases responsible for long-known processing steps in the maturation pathways of various RNA classes were recently identified. Moreover, one of the most intensely studied RNA decay pathways--RNAi--is controlled and stimulated by the action of different endonucleases. Furthermore, endoribonucleolytic cleavages executed by various enzymes are also the hallmark of RNA degradation and processing in plant chloroplasts. Finally, multiple context-specific endoribonucleases control qualitative and/or quantitative changes of selected transcripts under particular conditions in different eukaryotic organisms. The aim of this review is to discuss the impact of all of these discoveries on our current understanding of eukaryotic RNA metabolism.
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Affiliation(s)
- Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, University of Warsaw, 02-106 Warsaw, Poland
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35
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Taylor EJ, Campbell SG, Griffiths CD, Reid PJ, Slaven JW, Harrison RJ, Sims PFG, Pavitt GD, Delneri D, Ashe MP. Fusel alcohols regulate translation initiation by inhibiting eIF2B to reduce ternary complex in a mechanism that may involve altering the integrity and dynamics of the eIF2B body. Mol Biol Cell 2010; 21:2202-16. [PMID: 20444979 PMCID: PMC2893985 DOI: 10.1091/mbc.e09-11-0962] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study highlights a connection between the eIF2B body and the regulation of translation initiation as a response to stress in Saccharomyces cerevisiae. Fusel alcohols are involved in signaling nitrogen scarcity to the cell and they inhibit protein synthesis by preventing the movement of the eIF2B body throughout the cell. Recycling of eIF2-GDP to the GTP-bound form constitutes a core essential, regulated step in eukaryotic translation. This reaction is mediated by eIF2B, a heteropentameric factor with important links to human disease. eIF2 in the GTP-bound form binds to methionyl initiator tRNA to form a ternary complex, and the levels of this ternary complex can be a critical determinant of the rate of protein synthesis. Here we show that eIF2B serves as the target for translation inhibition by various fusel alcohols in yeast. Fusel alcohols are endpoint metabolites from amino acid catabolism, which signal nitrogen scarcity. We show that the inhibition of eIF2B leads to reduced ternary complex levels and that different eIF2B subunit mutants alter fusel alcohol sensitivity. A DNA tiling array strategy was developed that overcame difficulties in the identification of these mutants where the phenotypic distinctions were too subtle for classical complementation cloning. Fusel alcohols also lead to eIF2α dephosphorylation in a Sit4p-dependent manner. In yeast, eIF2B occupies a large cytoplasmic body where guanine nucleotide exchange on eIF2 can occur and be regulated. Fusel alcohols impact on both the movement and dynamics of this 2B body. Overall, these results confirm that the guanine nucleotide exchange factor, eIF2B, is targeted by fusel alcohols. Moreover, they highlight a potential connection between the movement or integrity of the 2B body and eIF2B regulation.
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Affiliation(s)
- Eleanor J Taylor
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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36
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Qiu Y, Mao T, Zhang Y, Shao M, You J, Ding Q, Chen Y, Wu D, Xie D, Lin X, Gao X, Kaufman RJ, Li W, Liu Y. A crucial role for RACK1 in the regulation of glucose-stimulated IRE1alpha activation in pancreatic beta cells. Sci Signal 2010; 3:ra7. [PMID: 20103773 PMCID: PMC2940714 DOI: 10.1126/scisignal.2000514] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autophosphorylation of inositol-requiring enzyme 1alpha (IRE1alpha) is required for its activation, which elicits the cellular unfolded protein response (UPR) and is functionally connected with insulin biosynthesis in pancreatic beta cells. We found that the scaffold protein receptor for activated C-kinase 1 (RACK1) interacted with IRE1alpha in a glucose-stimulated or endoplasmic reticulum (ER) stress-responsive manner in pancreatic beta cells and primary islets. RACK1 mediated the glucose-inducible assembly of a complex containing IRE1alpha, RACK1, and protein phosphatase 2A (PP2A) to promote dephosphorylation of IRE1alpha by PP2A, thereby inhibiting glucose-stimulated IRE1alpha activation and attenuating IRE1alpha-dependent increases in insulin production. Moreover, IRE1alpha activation was increased and RACK1 abundance was decreased in a mouse model of diabetes. Thus, our findings demonstrate that RACK1 functions as a key component in regulating the IRE1alpha signaling pathway in pancreatic beta cells.
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Affiliation(s)
- Yifu Qiu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Ting Mao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Yongliang Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Mengle Shao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Jia You
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Qiurong Ding
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Yan Chen
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Dongmei Wu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Dong Xie
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Xu Lin
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Xiang Gao
- Model Animal Research Center, Nanjing University, Nanjing 210093, China
| | - Randal J. Kaufman
- Department of Biological Chemistry and Internal Medicine, Howard Hughes Medical Institute, University of Michigan Medical Center, Ann Arbor, Michigan 48105, USA
| | - Wenjun Li
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
| | - Yong Liu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences; Shanghai 200031, China
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Yu L, Zhao J, Feng J, Fang J, Feng C, Jiang Y, Cao Y, Jiang L. Candida albicans CaPTC6 is a functional homologue for Saccharomyces cerevisiae ScPTC6 and encodes a type 2C protein phosphatase. Yeast 2009; 27:197-206. [PMID: 20033882 DOI: 10.1002/yea.1743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Type 2C protein phosphatases (PP2C) are monomeric enzymes and their activities require the presence of magnesium or manganese ions. There are seven PP2C genes, ScPTC1, ScPTC2, ScPTC3, ScPTC4, ScPTC5, ScPTC6 and ScPTC7, in Saccharomyces cerevisiae. PTC6 is highly conserved in pathogenic and nonpathogenic yeasts. In the current study we have demonstrated that the Candida albicans CaPTC6 gene could complement the functions of ScPTC6 in the rapamycin and caffeine sensitivities of S. cerevisiae cells, indicating that they are functional homologues. We have also demonstrated that the CaPTC6-encoded protein is a typical PP2C enzyme and that CaPtc6p is localized in the mitochondrion of yeast-form and hyphal cells. However, deletion of CaPTC6 neither affects cell and hyphal growth nor renders Candida cells sensitive to rapamycin and caffeine. Therefore, possibly with a functional redundancy to other mitochondrial phosphatases, CaPtc6p is likely to be involved in the regulation of a mitochondrial physiology.
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Affiliation(s)
- Liquan Yu
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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39
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Nagai A, Kadowaki H, Maruyama T, Takeda K, Nishitoh H, Ichijo H. USP14 inhibits ER-associated degradation via interaction with IRE1alpha. Biochem Biophys Res Commun 2009; 379:995-1000. [PMID: 19135427 DOI: 10.1016/j.bbrc.2008.12.182] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 12/31/2008] [Indexed: 01/18/2023]
Abstract
Accumulation of unfolded proteins within the endoplasmic reticulum (ER) lumen induces ER stress. Eukaryotic cells possess the ER quality control systems, the unfolded protein response (UPR), to adapt to ER stress. IRE1alpha is one of the ER stress receptors and mediates the UPR. Here, we identified ubiquitin specific protease (USP) 14 as a binding partner of IRE1alpha. USP14 interacted with the cytoplasmic region of IRE1alpha, and the endogenous interaction between USP14 and IRE1alpha was inhibited by ER stress. Overexpression of USP14 inhibited the ER-associated degradation (ERAD) pathway, and USP14 depletion by small interfering RNA effectively activated ERAD. These findings suggest that USP14 is a novel player in the UPR by serving as a physiological inhibitor of ERAD under the non-stressed condition.
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Affiliation(s)
- Atsushi Nagai
- Center of Excellence Program for Frontier Research on Molecular Destruction and Reconstruction of Tooth and Bone, Oral and Maxillofacial Surgery, Graduate School, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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40
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Lammers T, Lavi S. Role of type 2C protein phosphatases in growth regulation and in cellular stress signaling. Crit Rev Biochem Mol Biol 2008; 42:437-61. [PMID: 18066953 DOI: 10.1080/10409230701693342] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A number of interesting features, phenotypes, and potential clinical applications have recently been ascribed to the type 2C family of protein phosphatases. Thus far, 16 different PP2C genes have been identified in the human genome, encoding (by means of alternative splicing) for at least 22 different isozymes. Virtually ever since their discovery, type 2C phosphatases have been predominantly linked to cell growth and to cellular stress signaling. Here, we provide an overview of the involvement of type 2C phosphatases in these two processes, and we show that four of them (PP2Calpha, PP2Cbeta, ILKAP, and PHLPP) can be expected to function as tumor suppressor proteins, and one as an oncoprotein (PP2Cdelta /Wip1). In addition, we demonstrate that in virtually all cases in which they have been linked to the stress response, PP2Cs act as inhibitors of cellular stress signaling. Based on the vast amount of experimental evidence obtained thus far, it therefore seems justified to conclude that type 2C protein phosphatases are important physiological regulators of cell growth and of cellular stress signaling.
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Affiliation(s)
- Twan Lammers
- Department of Innovative Cancer Diagnosis and Therapy, German Cancer Research Center, Heidelberg, Germany.
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41
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Abstract
The endoplasmic reticulum (ER) is the first sub-cellular compartment encountered by secretory proteins en route to the plasma membrane. Newly synthesized secretory proteins translocate into the ER lumen and acquire their correct conformation prior to being exported to later compartments. When folding is not properly achieved, proteins accumulate in the ER due to resident quality control machineries and terminally misfolded proteins are ultimately degraded through the ER-associated degradation pathway. All these molecular machines function in a coordinated fashion to restore and maintain ER homeostasis. A fifth molecular machine plays a coordinating role in the ER. Indeed, the ER stress signaling machinery signals ER dysfunction to the rest of the cell and consequently integrates the functions of the four other molecular machines to improve their operation in stressful conditions. In this work, we have attempted to define the ER as a molecular biological system regulated by its own specific signaling pathways defined as the Unfolded Protein Response to delineate a systems biology approach of ER stress signaling.
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Abstract
Stress within the endoplasmic reticulum (ER) induces a sophisticated network of pathways termed the unfolded protein response (UPR), which is mediated through the ER transmembrane sensors PERK, ATF6, and IRE1. The UPR coordinates the temporary downregulation of protein translation, the upregulation of ER chaperones and folding machinery, and the enhanced expression of components necessary for ER-associated degradation (ERAD) essential for decreasing ER stress by clearing terminally misfolded proteins from the ER. Repetitive but futile folding attempts not only prolong ER stress but can also result in reactive oxygen species (ROS) generation, both of which may result in cell death. Additional mechanisms for decreasing stress and the protein load in the ER have been recently revealed. They include a newly identified function of IRE1 in degradation of select secretory protein mRNAs, a "preemptive" quality control responsible for averting translocation of select secretory proteins into the ER, upregulation of forward trafficking to allow misfolded proteins with intact exit signals to exit the ER, and upregulation of autophagy. The saturation or failure of some or all of these mechanisms can result in cell death and disease, including diabetes and a number of late-onset neurologic diseases.
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Affiliation(s)
- Margaret M Kincaid
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
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43
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Abstract
Cytoplasmic splicing is one of the major regulatory mechanisms of the unfolded protein response (UPR). The molecular mechanism of cytoplasmic splicing is unique and completely different from that of conventional nuclear splicing. The mammalian substrate of cytoplasmic splicing is XBP1 pre-mRNA, which is converted to spliced mRNA in response to UPR, leading to the production of an active transcription factor [pXBP1(S)] responsible for UPR. Interestingly, XBP1 pre-mRNA is also translated into a functional protein [pXBP1(U)] that negatively regulates the UPR. Thus, mammalian cells can quickly adapt to a change in conditions in the endoplasmic reticulum by switching proteins encoded in the mRNA from a negative regulator to an activator. This elaborate system contributes to various cellular functions, including plasma cell differentiation, viral infections, and carcinogenesis. In this short review, I briefly summarize research on cytoplasmic splicing and focus on current hot topics.
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Affiliation(s)
- Hiderou Yoshida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan., PRESTO-SORST, Japan Science and Technology Agency, Kyoto, Japan.
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Irsigler AST, Costa MDL, Zhang P, Reis PAB, Dewey RE, Boston RS, Fontes EPB. Expression profiling on soybean leaves reveals integration of ER- and osmotic-stress pathways. BMC Genomics 2007; 8:431. [PMID: 18036212 PMCID: PMC2242807 DOI: 10.1186/1471-2164-8-431] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 11/23/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the potential of the endoplasmic reticulum (ER) stress response to accommodate adaptive pathways, its integration with other environmental-induced responses is poorly understood in plants. We have previously demonstrated that the ER-stress sensor binding protein (BiP) from soybean exhibits an unusual response to drought. The members of the soybean BiP gene family are differentially regulated by osmotic stress and soybean BiP confers tolerance to drought. While these results may reflect crosstalk between the osmotic and ER-stress signaling pathways, the lack of mutants, transcriptional response profiles to stresses and genome sequence information of this relevant crop has limited our attempts to identify integrated networks between osmotic and ER stress-induced adaptive responses. As a fundamental step towards this goal, we performed global expression profiling on soybean leaves exposed to polyethylene glycol treatment (osmotic stress) or to ER stress inducers. RESULTS The up-regulated stress-specific changes unmasked the major branches of the ER-stress response, which include enhancing protein folding and degradation in the ER, as well as specific osmotically regulated changes linked to cellular responses induced by dehydration. However, a small proportion (5.5%) of total up-regulated genes represented a shared response that seemed to integrate the two signaling pathways. These co-regulated genes were considered downstream targets based on similar induction kinetics and a synergistic response to the combination of osmotic- and ER-stress-inducing treatments. Genes in this integrated pathway with the strongest synergistic induction encoded proteins with diverse roles, such as plant-specific development and cell death (DCD) domain-containing proteins, an ubiquitin-associated (UBA) protein homolog and NAC domain-containing proteins. This integrated pathway diverged further from characterized specific branches of ER-stress as downstream targets were inversely regulated by osmotic stress. CONCLUSION The present ER-stress- and osmotic-stress-induced transcriptional studies demonstrate a clear predominance of stimulus-specific positive changes over shared responses on soybean leaves. This scenario indicates that polyethylene glycol (PEG)-induced cellular dehydration and ER stress elicited very different up-regulated responses within a 10-h stress treatment regime. In addition to identifying ER-stress and osmotic-stress-specific responses in soybean (Glycine max), our global expression-profiling analyses provided a list of candidate regulatory components, which may integrate the osmotic-stress and ER-stress signaling pathways in plants.
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Affiliation(s)
- André ST Irsigler
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
- Molecular Core Facility, Department of Biology, Florida State University, Tallahassee, FL 32306-4370, USA
| | - Maximiller DL Costa
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
| | - Ping Zhang
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Pedro AB Reis
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
| | - Ralph E Dewey
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca S Boston
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Elizabeth PB Fontes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, Universidade Federal de Viçosa, 36571.000 Viçosa, Minas Gerais, Brazil
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45
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Guillemain G, Ma E, Mauger S, Miron S, Thai R, Guérois R, Ochsenbein F, Marsolier-Kergoat MC. Mechanisms of checkpoint kinase Rad53 inactivation after a double-strand break in Saccharomyces cerevisiae. Mol Cell Biol 2007; 27:3378-89. [PMID: 17325030 PMCID: PMC1899965 DOI: 10.1128/mcb.00863-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, double-strand breaks (DSBs) activate DNA checkpoint pathways that trigger several responses including a strong G(2)/M arrest. We have previously provided evidence that the phosphatases Ptc2 and Ptc3 of the protein phosphatase 2C type are required for DNA checkpoint inactivation after a DSB and probably dephosphorylate the checkpoint kinase Rad53. In this article we have investigated further the interactions between Ptc2 and Rad53. We showed that forkhead-associated domain 1 (FHA1) of Rad53 interacts with a specific threonine of Ptc2, T376, located outside its catalytic domain in a TXXD motif which constitutes an optimal FHA1 binding sequence in vitro. Mutating T376 abolishes Ptc2 interaction with the Rad53 FHA1 domain and results in adaptation and recovery defects following a DSB. We found that Ckb1 and Ckb2, the regulatory subunits of the protein kinase CK2, are necessary for the in vivo interaction between Ptc2 and the Rad53 FHA1 domain, that Ckb1 binds Ptc2 in vitro and that ckb1Delta and ckb2Delta mutants are defective in adaptation and recovery after a DSB. Our data thus strongly suggest that CK2 is the kinase responsible for the in vivo phosphorylation of Ptc2 T376.
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Affiliation(s)
- Ghislaine Guillemain
- CEA, Direction des Sciences du Vivant, Institut de Biologie et de la Technologies de Saclay, 91191 Gif-sur-Yvette Cedex, France
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46
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Schröder M. The unfolded protein response. Mol Biotechnol 2007; 34:279-90. [PMID: 17172673 DOI: 10.1385/mb:34:2:279] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/11/2022]
Abstract
The unfolded protein response (UPR) is a signal transduction network activated by inhibition of protein folding in the endoplasmic reticulum (ER). The UPR coordinates adaptive responses to this stress situation, including induction of ER resident molecular chaperone and protein foldase expression to increase the protein folding capacity of the ER, induction of phospholipid synthesis, attenuation of general translation, and upregulation of ER-associated degradation to decrease the unfolded protein load of the ER, and an antioxidant response. Upon severe or prolonged ER stress the UPR induces apoptosis to eliminate unhealthy cells from an organism or a population. In this review, I will summarize our current knowledge about signal transduction pathways involved in transducing the unfolded protein signal from the ER to the nucleus or the cytosol.
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Affiliation(s)
- Martin Schröder
- School of Biological and Biomedical Sciences, University of Durham, Durham DH1 3LE, United Kingdom.
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Wang J, Yan Z, Shen SH, Whiteway M, Jiang L. Expression ofCaPTC7is developmentally regulated during serum-induced morphogenesis in the human fungal pathogen Candida albicans. Can J Microbiol 2007; 53:237-44. [PMID: 17496972 DOI: 10.1139/w06-125] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Type 2C protein phosphatases (PP2C) represent a diversified protein phosphatase family and play various roles in cells. We previously identified and characterized a novel PP2C phosphatase encoded by the CaPTC7 gene in the human fungal pathogen Candida albicans . The CaPtc7p has 365 amino acids with a PP2C core domain at the C terminus and an additional 116-residue N-terminal sequence containing a mitochondrion-targeting sequence. Here, we show that CaPtc7p is indeed localized in the mitochondrion, the only eukaryotic PP2C phosphatase that has been directly shown to reside in the mitochondrion, suggesting its potential role in the regulation of mitochondrial physiology. Furthermore, we show that the expression of CaPTC7 at both transcriptional and protein levels is developmentally regulated during the serum-induced morphogenesis of C. albicans cells. However, disruption of the two alleles of CaPTC7 does not affect cell viability or filamentous development in C. albicans.
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Affiliation(s)
- Jihong Wang
- Department of Molecular and Cellular Pharmacology, College of Pharmaceuticals and Biotechnology, Tianjin University, Tianjin 300072, China
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Grinyer J, Kautto L, Traini M, Willows RD, Te'o J, Bergquist P, Nevalainen H. Proteome mapping of the Trichoderma reesei 20S proteasome. Curr Genet 2006; 51:79-88. [PMID: 17119969 DOI: 10.1007/s00294-006-0108-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 10/28/2006] [Accepted: 10/31/2006] [Indexed: 10/23/2022]
Abstract
The 26S proteasome, a multicatalytic protease comprising the catalytic 20S core particle and the 19S regulatory particle has a crucial role in cellular protein quality control. We have used a chromatography-based approach to purify and map the protein content of the 20S core particle from the industrially-exploited filamentous fungus Trichoderma reesei. There are no previous reports on the isolation or proteomic mapping of the proteasome from any filamentous fungus. From the reference map, 13 of the 14 20S proteasome subunits and many related proteins that co-purified with the 20S proteasome have been identified. These include 78 kDa glucose-regulated protein (BIP) and several chaperones including heat shock proteins involved in the unfolded protein response (UPR). Some proteasome interacting proteins (PIPs) were also identified on the proteome map and included 14-3-3-like protein, glyceraldehyde-3-phosphate dehydrogenase, transaldolase, actin, translation elongation factor, enolase, ATPase in the ER (CDC48), and eukaryotic initiation factor. We present here a master map for the 20S catalytic core to pave the way for future differential display studies addressing intracellular degradation of endogenous and foreign proteins in filamentous fungi.
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Affiliation(s)
- Jasmine Grinyer
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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González A, Ruiz A, Serrano R, Ariño J, Casamayor A. Transcriptional Profiling of the Protein Phosphatase 2C Family in Yeast Provides Insights into the Unique Functional Roles of Ptc1. J Biol Chem 2006; 281:35057-69. [PMID: 16973600 DOI: 10.1074/jbc.m607919200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-5 and PTC7). To gain insight into the functions attributable to specific members of this gene family, we have investigated the transcriptional profiles of ptc1-5 mutants. Two main patterns were obtained as follows: the one generated by the ptc1 mutation and the one resulting from the lack of Ptc2-5. ptc4 and ptc5 profiles were quite similar, whereas that of ptc2 was less related to this group. Mutation of PTC1 resulted in increased expression of numerous genes that are also induced by cell wall damage, such as YKL161c, SED1, or CRH1, as well as in higher amounts of active Slt2 mitogen-activated protein kinase, indicating that lack of the phosphatase activates the cell wall integrity pathway. ptc1 cells were even more sensitive than slt2 mutants to a number of cell wall-damaging agents, and both mutations had additive effects. The sensitivity of ptc1 cells was not dependent on Hog1. Besides these phenotypes, we observed that calcineurin was hyperactivated in ptc1 cells, which were also highly sensitive to calcium ions, heavy metals, and alkaline pH, and exhibited a random haploid budding pattern. Remarkably, many of these traits are found in certain mutants with impaired vacuolar function. As ptc1 cells also display fragmented vacuoles, we hypothesized that lack of Ptc1 would primarily cause vacuolar malfunction, from which other phenotypes would derive. In agreement with this scenario, overexpression of VPS73, a gene of unknown function involved in vacuolar protein sorting, largely rescues not only vacuolar fragmentation but also sensitivity to cell wall damage, high calcium, alkaline pH, as well as other ptc1-specific phenotypes.
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Affiliation(s)
- Asier González
- Departament de Bioquímica i Biologia Molecular, Edificio V, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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50
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Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 2006; 103:14724-31. [PMID: 17003135 PMCID: PMC1595419 DOI: 10.1073/pnas.0508637103] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fundamental question in biology is how the cell uses transcription factors (TFs) to coordinate the expression of thousands of genes in response to various stimuli. The relationships between TFs and their target genes can be modeled in terms of directed regulatory networks. These relationships, in turn, can be readily compared with commonplace "chain-of-command" structures in social networks, which have characteristic hierarchical layouts. Here, we develop algorithms for identifying generalized hierarchies (allowing for various loop structures) and use these approaches to illuminate extensive pyramid-shaped hierarchical structures existing in the regulatory networks of representative prokaryotes (Escherichia coli) and eukaryotes (Saccharomyces cerevisiae), with most TFs at the bottom levels and only a few master TFs on top. These masters are situated near the center of the protein-protein interaction network, a different type of network from the regulatory one, and they receive most of the input for the whole regulatory hierarchy through protein interactions. Moreover, they have maximal influence over other genes, in terms of affecting expression-level changes. Surprisingly, however, TFs at the bottom of the regulatory hierarchy are more essential to the viability of the cell. Finally, one might think master TFs achieve their wide influence through directly regulating many targets, but TFs with most direct targets are in the middle of the hierarchy. We find, in fact, that these midlevel TFs are "control bottlenecks" in the hierarchy, and this great degree of control for "middle managers" has parallels in efficient social structures in various corporate and governmental settings.
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Affiliation(s)
- Haiyuan Yu
- Departments of Molecular Biophysics and Biochemistry and Computer Science and Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, P.O. Box 208114, New Haven, CT 06520
- *To whom correspondence may be addressed. E-mail:
or
| | - Mark Gerstein
- Departments of Molecular Biophysics and Biochemistry and Computer Science and Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, P.O. Box 208114, New Haven, CT 06520
- *To whom correspondence may be addressed. E-mail:
or
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