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Wagner ER, Gasch AP. Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense. J Fungi (Basel) 2023; 9:786. [PMID: 37623557 PMCID: PMC10455348 DOI: 10.3390/jof9080786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay's controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
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Affiliation(s)
- Ellen R. Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
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2
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Yao W, Li Y, Chen Y, Chen Y, Xie Y, Ye M, Zhang Y, Chen X, Wu X, Feng Y, Hong Z, Wang Y, Liu W, Yi C. Atg1-mediated Atg11 phosphorylation is required for selective autophagy by regulating its association with receptor proteins. Autophagy 2023; 19:180-188. [PMID: 35427192 PMCID: PMC9809958 DOI: 10.1080/15548627.2022.2063494] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Atg11 is an adaptor protein required for the induction of selective autophagy via receptor binding. However, our understanding of the molecular mechanisms by which it regulates selective autophagy remains incomplete. Here, we show that Atg11 is phosphorylated by Atg1. Rapamycin treatment or starvation conditions induced slower electrophoretic mobility of Atg11 in an Atg1 kinase activity-dependent manner. Through in vitro kinase assays combined with mutagenesis, we determined that Atg1 phosphorylates S949, S1057, and S1064 residues in CC4 domain of Atg11. Replacing the three residues with alanine suppressed the cleavage of selective autophagy substrates for the cytoplasm-to-vacuole targeting (Cvt) pathway, mitophagy, reticulophagy, and pexophagy. The Atg11 mutant was defective in binding to related selective autophagy receptors. These results demonstrate a previously unknown function of Atg1 in regulation of selective autophagy via Atg11 phosphorylation.Abbreviations: AMPK: AMP-activated protein kinase; ATG: autophagy-related; Cvt: cytoplasm-to-vacuole targeting; FUNDC1: FUN14 domain-containing protein 1; GFP: green fluorescent protein; MTOR: mechanistic target of rapamycin kinase; PAS: phagophore assembly site; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PRKAC/PKA: protein kinase cAMP-activated; SD-G: glucose starvation; SD-N: nitrogen starvation; ULK1: unc-51 like autophagy activating kinase 1; λ-PPase: lambda protein phosphatase.
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Affiliation(s)
- Weijing Yao
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yixing Li
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingcong Chen
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuting Chen
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Xie
- College of Chemistry and Bio-Engineering, Yichun University, Yichun, China
| | - Miaojuan Ye
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ying Zhang
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, Jiefang Road, Hangzhou, China,Institute of Translational Medicine, Zhejiang University School of Medicine, Kaixuan Road, Hangzhou, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, Jiefang Road, Hangzhou, China,Institute of Translational Medicine, Zhejiang University School of Medicine, Kaixuan Road, Hangzhou, China
| | - Xiaoyong Wu
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuyao Feng
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Hong
- ZJU-UoE Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Yigang Wang
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wei Liu
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Cong Yi
- Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,CONTACT Cong Yi Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang310058, China
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3
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Mameri A, Côté J. JAZF1: A metabolic actor subunit of the NuA4/TIP60 chromatin modifying complex. Front Cell Dev Biol 2023; 11:1134268. [PMID: 37091973 PMCID: PMC10119425 DOI: 10.3389/fcell.2023.1134268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
The multisubunit NuA4/TIP60 complex is a lysine acetyltransferase, chromatin modifying factor and gene co-activator involved in diverse biological processes. The past decade has seen a growing appreciation for its role as a metabolic effector and modulator. However, molecular insights are scarce and often contradictory, underscoring the need for further mechanistic investigation. A particularly exciting route emerged with the recent identification of a novel subunit, JAZF1, which has been extensively linked to metabolic homeostasis. This review summarizes the major findings implicating NuA4/TIP60 in metabolism, especially in light of JAZF1 as part of the complex.
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4
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Qu X, Han Y, Chen X, Lv Y, Zhang Y, Cao L, Zhang J, Jin Y. Inhibition of 26 S Proteasome Enhances AKAP3-mediated cAMP-PKA Signaling During Boar Sperm Capacitation. Anim Reprod Sci 2022; 247:107079. [DOI: 10.1016/j.anireprosci.2022.107079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/20/2022] [Accepted: 09/21/2022] [Indexed: 11/01/2022]
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5
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Guerra P, Vuillemenot LAPE, van Oppen YB, Been M, Milias-Argeitis A. TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle. J Cell Sci 2022; 135:276358. [PMID: 35975715 DOI: 10.1242/jcs.260378] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 10/15/2022] Open
Abstract
Recent studies have revealed that the growth rate of budding yeast and mammalian cells varies during the cell cycle. By linking a multitude of signals to cell growth, the highly conserved Target of Rapamycin Complex 1 (TORC1) and Protein Kinase A (PKA) pathways are prime candidates for mediating the dynamic coupling between growth and division. However, measurements of TORC1 and PKA activity during the cell cycle are still lacking. Following the localization dynamics of two TORC1 and PKA targets via time-lapse microscopy in hundreds of yeast cells, we found that the activity of these pathways towards ribosome biogenesis fluctuates in synchrony with the cell cycle even under constant external conditions. Mutations of upstream TORC1 and PKA regulators suggested that internal metabolic signals partially mediate these activity changes. Our study reveals a new aspect of TORC1 and PKA signaling, which will be important for understanding growth regulation during the cell cycle.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Luc-Alban P E Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Yulan B van Oppen
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Marije Been
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Netherlands
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6
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Jin JX, Sun JT, Jiang CQ, Cui HD, Bian Y, Lee S, Zhang L, Lee BC, Liu ZH. Melatonin Regulates Lipid Metabolism in Porcine Cumulus–Oocyte Complexes via the Melatonin Receptor 2. Antioxidants (Basel) 2022; 11:antiox11040687. [PMID: 35453372 PMCID: PMC9027243 DOI: 10.3390/antiox11040687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022] Open
Abstract
Previous studies suggest that the inclusion of melatonin (MTn) in in vitro maturation protocols improves the developmental competence of oocytes by scavenging reactive oxygen species (ROS). However, the molecular mechanisms integrating melatonin receptor (MT)-mediated lipid metabolism and redox signaling during in vitro cumulus–oocyte complex (COC) development still remain unclear. Here, we aimed to elucidate the potential role of MTn receptors in lipid metabolic adjustments during in vitro porcine COC development. We observed that MTn-mediated Gsα–cAMP/PKA signaling facilitated lipolysis primarily through the MT2 receptor and subsequently increased fatty acid (FA) release by hydrolyzing intracellular triglycerides (TGs) in cumulus cells. Furthermore, CD36 was a critical FA transporter that transported available FAs from cumulus cells to oocytes and promoted de novo TG synthesis in the latter. In addition, MTn regulated lipogenesis and intracellular lipolysis to maintain lipid homeostasis and limit ROS production, thereby supporting oocyte cytoplasmic maturation and the subsequent embryo development. Taken together, these findings provide insight into the possible mechanism integrating MT2-mediated lipid homeostasis and redox signaling, which limits ROS production during in vitro COC development. Therefore, understanding the dynamics of the interactions between lipid homeostasis and redox signaling driven by MT2 is necessary in order to predict drug targets and the effects of therapeutics used to improve female reproductive health.
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Affiliation(s)
- Jun-Xue Jin
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China; (J.-T.S.); (C.-Q.J.); (H.-D.C.); (Y.B.)
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.L.); (B.C.L.)
- Correspondence: (J.-X.J.); (Z.-H.L.)
| | - Jing-Tao Sun
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China; (J.-T.S.); (C.-Q.J.); (H.-D.C.); (Y.B.)
| | - Chao-Qian Jiang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China; (J.-T.S.); (C.-Q.J.); (H.-D.C.); (Y.B.)
| | - Hong-Di Cui
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China; (J.-T.S.); (C.-Q.J.); (H.-D.C.); (Y.B.)
| | - Ya Bian
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China; (J.-T.S.); (C.-Q.J.); (H.-D.C.); (Y.B.)
| | - Sanghoon Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.L.); (B.C.L.)
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Lianjin Zhang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.L.); (B.C.L.)
| | - Zhong-Hua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin 150030, China; (J.-T.S.); (C.-Q.J.); (H.-D.C.); (Y.B.)
- Correspondence: (J.-X.J.); (Z.-H.L.)
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7
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Yan J, Fan YJ, Bao H, Li YG, Zhang SM, Yao QP, Huo YL, Jiang ZL, Qi YX, Han Y. Platelet-derived microvesicles regulate vascular smooth muscle cell energy metabolism via PRKAA after intimal injury. J Cell Sci 2022; 135:275043. [PMID: 35297486 DOI: 10.1242/jcs.259364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Vascular intimal injury initiates various cardiovascular disease processes. Exposure to subendothelial collagen can cause platelet activation, leading to platelet-derived microvesicles (aPMVs) secretion. In addition, vascular smooth muscle cells (VSMCs) exposed to large amounts of aPMVs undergo abnormal energy metabolism, they proliferate excessively and migrate after the loss of endothelium, eventually contributing to neointimal hyperplasia. However, the roles of aPMVs in VSMC energy metabolism are still unknown. Carotid artery intimal injury model indicated platelets adhered to injured blood vessels. In vitro, p-Pka content was increased in aPMVs. aPMVs significantly changed VSMC glycolysis and oxidative phosphorylation, and promoted VSMC migration and proliferation by upregulating p-PRKAA/p-FoxO1. Compound C, an inhibitor of PRKAA, effectively reversed the cell function and energy metabolism triggered by aPMVs in vitro and neointimal formation in vivo. Our data show that aPMVs can affect VSMC energy metabolism through the Pka/PRKAA/FoxO1 signaling pathway and ultimately affect VSMC function, indicating that VSMC metabolic phenotype shifted by aPMVs can be considered a potential target for the inhibition of hyperplasia and providing a new perspective for regulating the abnormal activity of VSMCs after injury.
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Affiliation(s)
- Jing Yan
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang-Jing Fan
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Han Bao
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yong-Guang Li
- Department of Cardiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shou-Min Zhang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Ping Yao
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun-Long Huo
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zong-Lai Jiang
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying-Xin Qi
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Han
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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8
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [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: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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9
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Chen K, Rong N, Wang S, Luo C. A novel two-layer-integrated microfluidic device for high-throughput yeast proteomic dynamics analysis at the single-cell level. Integr Biol (Camb) 2021; 12:241-249. [PMID: 32995887 DOI: 10.1093/intbio/zyaa018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/12/2020] [Accepted: 08/31/2020] [Indexed: 11/14/2022]
Abstract
Current microfluidic methods for studying multicell strains (e.g., m-types) with multienvironments (e.g., n-types) require large numbers of inlets/outlets (m*n), a complicated procedure or expensive machinery. Here, we developed a novel two-layer-integrated method to combine different PDMS microchannel layers with different functions into one chip by a PDMS through-hole array, which improved the design of a PDMS-based microfluidic system. Using this method, we succeeded in converting 2 × m × n inlets/outlets into m + n inlets/outlets and reduced the time cost of loading processing (from m × n to m) of the device for studying multicell strains (e.g., m-types) in varied multitemporal environments (i.e., n-types). Using this device, the dynamic behavior of the cell-stress-response proteins was studied when the glucose concentration decreased from 2% to a series of lower concentrations. Our device could also be widely used in high-throughput studies of various stress responses, and the new concept of a multilayer-integrated fabrication method could greatly improve the design of PDMS-based microfluidic systems.
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Affiliation(s)
- Kaiyue Chen
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Shujing Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
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10
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Grisan F, Iannucci LF, Surdo NC, Gerbino A, Zanin S, Di Benedetto G, Pozzan T, Lefkimmiatis K. PKA compartmentalization links cAMP signaling and autophagy. Cell Death Differ 2021; 28:2436-2449. [PMID: 33742135 PMCID: PMC8328970 DOI: 10.1038/s41418-021-00761-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Autophagy is a highly regulated degradative process crucial for maintaining cell homeostasis. This important catabolic mechanism can be nonspecific, but usually occurs with fine spatial selectivity (compartmentalization), engaging only specific subcellular sites. While the molecular machines driving autophagy are well understood, the involvement of localized signaling events in this process is not well defined. Among the pathways that regulate autophagy, the cyclic AMP (cAMP)/protein kinase A (PKA) cascade can be compartmentalized in distinct functional units called microdomains. However, while it is well established that, depending on the cell type, cAMP can inhibit or promote autophagy, the role of cAMP/PKA microdomains has not been tested. Here we show not only that the effects on autophagy of the same cAMP elevation differ in different cell types, but that they depend on a highly complex sub-compartmentalization of the signaling cascade. We show in addition that, in HT-29 cells, in which autophagy is modulated by cAMP rising treatments, PKA activity is strictly regulated in space and time by phosphatases, which largely prevent the phosphorylation of soluble substrates, while membrane-bound targets are less sensitive to the action of these enzymes. Interestingly, we also found that the subcellular distribution of PKA type-II regulatory PKA subunits hinders the effect of PKA on autophagy, while displacement of type-I regulatory PKA subunits has no effect. Our data demonstrate that local PKA activity can occur independently of local cAMP concentrations and provide strong evidence for a link between localized PKA signaling events and autophagy.
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Affiliation(s)
- Francesca Grisan
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Liliana F Iannucci
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nicoletta C Surdo
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Gerbino
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Sofia Zanin
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Giulietta Di Benedetto
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy
- Neuroscience Institute, National Research Council, Padua, Italy
| | - Tullio Pozzan
- Neuroscience Institute, National Research Council, Padua, Italy
| | - Konstantinos Lefkimmiatis
- Foundation for Advanced Biomedical Research, Veneto Institute of Molecular Medicine, Padua, Italy.
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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11
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Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
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12
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Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:1-53. [PMID: 34340765 DOI: 10.1016/bs.apcsb.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.
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13
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Andres-Alonso M, Kreutz MR, Karpova A. Autophagy and the endolysosomal system in presynaptic function. Cell Mol Life Sci 2020; 78:2621-2639. [PMID: 33340068 PMCID: PMC8004491 DOI: 10.1007/s00018-020-03722-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022]
Abstract
The complex morphology of neurons, the specific requirements of synaptic neurotransmission and the accompanying metabolic demands create a unique challenge for proteostasis. The main machineries for neuronal protein synthesis and degradation are localized in the soma, while synaptic junctions are found at vast distances from the cell body. Sophisticated mechanisms must, therefore, ensure efficient delivery of newly synthesized proteins and removal of faulty proteins. These requirements are exacerbated at presynaptic sites, where the demands for protein turnover are especially high due to synaptic vesicle release and recycling that induces protein damage in an intricate molecular machinery, and where replacement of material is hampered by the extreme length of the axon. In this review, we will discuss the contribution of the two major pathways in place, autophagy and the endolysosomal system, to presynaptic protein turnover and presynaptic function. Although clearly different in their biogenesis, both pathways are characterized by cargo collection and transport into distinct membrane-bound organelles that eventually fuse with lysosomes for cargo degradation. We summarize the available evidence with regard to their degradative function, their regulation by presynaptic machinery and the cargo for each pathway. Finally, we will discuss the interplay of both pathways in neurons and very recent findings that suggest non-canonical functions of degradative organelles in synaptic signalling and plasticity.
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Affiliation(s)
- Maria Andres-Alonso
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
- Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Michael R Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.
- Center for Behavioral Brain Sciences, Otto Von Guericke University, Magdeburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany.
| | - Anna Karpova
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Otto Von Guericke University, Magdeburg, Germany.
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14
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Baro Graf C, Ritagliati C, Stival C, Luque GM, Gentile I, Buffone MG, Krapf D. Everything you ever wanted to know about PKA regulation and its involvement in mammalian sperm capacitation. Mol Cell Endocrinol 2020; 518:110992. [PMID: 32853743 DOI: 10.1016/j.mce.2020.110992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
The 3', 5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase (PKA) is a tetrameric holoenzyme comprising a set of two regulatory subunits (PKA-R) and two catalytic (PKA-C) subunits. The PKA-R subunits act as sensors of cAMP and allow PKA-C activity. One of the first signaling events observed during mammalian sperm capacitation is PKA activation. Thus, understanding how PKA activity is restricted in space and time is crucial to decipher the critical steps of sperm capacitation. It is widely accepted that PKA specificity depends on several levels of regulation. Anchoring proteins play a pivotal role in achieving proper localization signaling, subcellular targeting and cAMP microdomains. These multi-factorial regulation steps are necessary for a precise spatio-temporal activation of PKA. Here we discuss recent understanding of regulatory mechanisms of PKA in mammalian sperm, such as post-translational modifications, in the context of its role as the master orchestrator of molecular events conducive to capacitation.
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Affiliation(s)
- Carolina Baro Graf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina; Laboratorio de Medicina Reproductiva (LMR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carla Ritagliati
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Cintia Stival
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Guillermina M Luque
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Iñaki Gentile
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Mariano G Buffone
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Dario Krapf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina; Laboratorio de Medicina Reproductiva (LMR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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15
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Molin M, Logg K, Bodvard K, Peeters K, Forsmark A, Roger F, Jörhov A, Mishra N, Billod JM, Amir S, Andersson M, Eriksson LA, Warringer J, Käll M, Blomberg A. Protein kinase A controls yeast growth in visible light. BMC Biol 2020; 18:168. [PMID: 33198745 PMCID: PMC7667738 DOI: 10.1186/s12915-020-00867-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 01/07/2023] Open
Abstract
Background A wide variety of photosynthetic and non-photosynthetic species sense and respond to light, having developed protective mechanisms to adapt to damaging effects on DNA and proteins. While the biology of UV light-induced damage has been well studied, cellular responses to stress from visible light (400–700 nm) remain poorly understood despite being a regular part of the life cycle of many organisms. Here, we developed a high-throughput method for measuring growth under visible light stress and used it to screen for light sensitivity in the yeast gene deletion collection. Results We found genes involved in HOG pathway signaling, RNA polymerase II transcription, translation, diphthamide modifications of the translational elongation factor eEF2, and the oxidative stress response to be required for light resistance. Reduced nuclear localization of the transcription factor Msn2 and lower glycogen accumulation indicated higher protein kinase A (cAMP-dependent protein kinase, PKA) activity in many light-sensitive gene deletion strains. We therefore used an ectopic fluorescent PKA reporter and mutants with constitutively altered PKA activity to show that repression of PKA is essential for resistance to visible light. Conclusion We conclude that yeast photobiology is multifaceted and that protein kinase A plays a key role in the ability of cells to grow upon visible light exposure. We propose that visible light impacts on the biology and evolution of many non-photosynthetic organisms and have practical implications for how organisms are studied in the laboratory, with or without illumination.
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Affiliation(s)
- Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. .,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Katarina Logg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristofer Bodvard
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Ken Peeters
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Annabelle Forsmark
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Friederike Roger
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Jörhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Neha Mishra
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Horizon Discovery, Cambridge, CB25 9TL, UK
| | - Jean-Marc Billod
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Bio-Me A/S, Oslo Science Park, Gaustadalléen, 210349, Oslo, Norway
| | - Sabiha Amir
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Käll
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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16
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Walden EA, Fong RY, Pham TT, Knill H, Laframboise SJ, Huard S, Harper ME, Baetz K. Phenomic screen identifies a role for the yeast lysine acetyltransferase NuA4 in the control of Bcy1 subcellular localization, glycogen biosynthesis, and mitochondrial morphology. PLoS Genet 2020; 16:e1009220. [PMID: 33253187 PMCID: PMC7728387 DOI: 10.1371/journal.pgen.1009220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/10/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cellular metabolism is tightly regulated by many signaling pathways and processes, including lysine acetylation of proteins. While lysine acetylation of metabolic enzymes can directly influence enzyme activity, there is growing evidence that lysine acetylation can also impact protein localization. As the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 has been implicated in a variety of metabolic processes, we have explored whether NuA4 controls the localization and/or protein levels of metabolic proteins. We performed a high-throughput microscopy screen of over 360 GFP-tagged metabolic proteins and identified 23 proteins whose localization and/or abundance changed upon deletion of the NuA4 scaffolding subunit, EAF1. Within this, three proteins were required for glycogen synthesis and 14 proteins were associated with the mitochondria. We determined that in eaf1Δ cells the transcription of glycogen biosynthesis genes is upregulated resulting in increased proteins and glycogen production. Further, in the absence of EAF1, mitochondria are highly fused, increasing in volume approximately 3-fold, and are chaotically distributed but remain functional. Both the increased glycogen synthesis and mitochondrial elongation in eaf1Δ cells are dependent on Bcy1, the yeast regulatory subunit of PKA. Surprisingly, in the absence of EAF1, Bcy1 localization changes from being nuclear to cytoplasmic and PKA activity is altered. We found that NuA4-dependent localization of Bcy1 is dependent on a lysine residue at position 313 of Bcy1. However, the glycogen accumulation and mitochondrial elongation phenotypes of eaf1Δ, while dependent on Bcy1, were not fully dependent on Bcy1-K313 acetylation state and subcellular localization of Bcy1. As NuA4 is highly conserved with the human Tip60 complex, our work may inform human disease biology, revealing new avenues to investigate the role of Tip60 in metabolic diseases.
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Affiliation(s)
- Elizabeth A. Walden
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Roger Y. Fong
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Trang T. Pham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Hana Knill
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sylvain Huard
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
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17
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Roger F, Picazo C, Reiter W, Libiad M, Asami C, Hanzén S, Gao C, Lagniel G, Welkenhuysen N, Labarre J, Nyström T, Grøtli M, Hartl M, Toledano MB, Molin M. Peroxiredoxin promotes longevity and H 2O 2-resistance in yeast through redox-modulation of protein kinase A. eLife 2020; 9:e60346. [PMID: 32662770 PMCID: PMC7392609 DOI: 10.7554/elife.60346] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022] Open
Abstract
Peroxiredoxins are H2O2 scavenging enzymes that also carry out H2O2 signaling and chaperone functions. In yeast, the major cytosolic peroxiredoxin, Tsa1 is required for both promoting resistance to H2O2 and extending lifespan upon caloric restriction. We show here that Tsa1 effects both these functions not by scavenging H2O2, but by repressing the nutrient signaling Ras-cAMP-PKA pathway at the level of the protein kinase A (PKA) enzyme. Tsa1 stimulates sulfenylation of cysteines in the PKA catalytic subunit by H2O2 and a significant proportion of the catalytic subunits are glutathionylated on two cysteine residues. Redox modification of the conserved Cys243 inhibits the phosphorylation of a conserved Thr241 in the kinase activation loop and enzyme activity, and preventing Thr241 phosphorylation can overcome the H2O2 sensitivity of Tsa1-deficient cells. Results support a model of aging where nutrient signaling pathways constitute hubs integrating information from multiple aging-related conduits, including a peroxiredoxin-dependent response to H2O2.
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Affiliation(s)
- Friederike Roger
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Cecilia Picazo
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburgSweden
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenterViennaAustria
| | - Marouane Libiad
- Oxidative Stress and Cancer Laboratory, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif sur YvetteFrance
| | - Chikako Asami
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Sarah Hanzén
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Chunxia Gao
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Gilles Lagniel
- Oxidative Stress and Cancer Laboratory, Integrative Biology and Molecular Genetics Unit (SBIGEM)CEA SaclayFrance
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, Chalmers University of Technology and University of GothenburgGothenburgSweden
| | - Jean Labarre
- Oxidative Stress and Cancer Laboratory, Integrative Biology and Molecular Genetics Unit (SBIGEM)CEA SaclayFrance
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Markus Hartl
- Mass Spectrometry Facility, Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenterViennaAustria
| | - Michel B Toledano
- Oxidative Stress and Cancer Laboratory, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif sur YvetteFrance
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburgSweden
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18
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Borisov N, Sorokin M, Garazha A, Buzdin A. Quantitation of Molecular Pathway Activation Using RNA Sequencing Data. Methods Mol Biol 2020; 2063:189-206. [PMID: 31667772 DOI: 10.1007/978-1-0716-0138-9_15] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intracellular molecular pathways (IMPs) control all major events in the living cell. IMPs are considered hotspots in biomedical sciences and thousands of IMPs have been discovered for humans and model organisms. Knowledge of IMPs activation is essential for understanding biological functions and differences between the biological objects at the molecular level. Here we describe the Oncobox system for accurate quantitative scoring activities of up to several thousand molecular pathways based on high throughput molecular data. Although initially designed for gene expression and mainly RNA sequencing data, Oncobox is now also applicable for quantitative proteomics, microRNA and transcription factor binding sites mapping data. The Oncobox system includes modules of gene expression data harmonization, aggregation and comparison and a recursive algorithm for automatic annotation of molecular pathways. The universal rationale of Oncobox enables scoring of signaling, metabolic, cytoskeleton, immunity, DNA repair, and other pathways in a multitude of biological objects. The Oncobox system can be helpful to all those working in the fields of genetics, biochemistry, interactomics, and big data analytics in molecular biomedicine.
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Affiliation(s)
- Nicolas Borisov
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Omicsway Corp., Walnut, CA, USA
| | - Maxim Sorokin
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Omicsway Corp., Walnut, CA, USA
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Anton Buzdin
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
- Omicsway Corp., Walnut, CA, USA.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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19
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Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomyces cerevisiae. Genetics 2018; 211:531-547. [PMID: 30546002 DOI: 10.1534/genetics.118.301727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
The Dam1 complex is an essential component of the outer kinetochore that mediates attachments between spindle microtubules and chromosomes. Dam1p, a subunit of the Dam1 complex, binds to microtubules and is regulated by Aurora B/Ipl1p phosphorylation. We find that overexpression of cAMP-dependent protein kinase (PKA) catalytic subunits (i.e., TPK1, TPK2, TPK3) is lethal in DAM1 mutants and increases the rate of chromosome loss in wild-type cells. Replacing an evolutionarily conserved PKA site (S31) in Dam1p with a nonphosphorylatable alanine suppressed the high-copy PKA dosage lethality in dam1-1 Consistent with Dam1p as a target of PKA, we find that in vitro PKA can directly phosphorylate S31 in Dam1p and we observed phosphorylation of S31 in Dam1p purified from asynchronously growing yeast cells. Cells carrying high-copy TPK2 or a Dam1p phospho-mimetic S31D mutant displayed a reduction in Dam1p localization at the kinetochore, suggesting that PKA phosphorylation plays a role in assembly and/or stability of the Dam1 complex. Furthermore, we observed spindle defects associated with S31 phosphorylation. Finally, we find that phosphorylation of Dam1p on S31 is reduced when glucose is limiting as well as during α-factor arrest, conditions that inhibit PKA activity. These observations suggest that the PKA site of Dam1p participates in regulating kinetochore activity. While PKA is a well-established effector of glucose signaling, our work shows for the first time that glucose-dependent PKA activity has an important function in chromosome segregation.
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20
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Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs. Semin Cancer Biol 2018; 53:110-124. [DOI: 10.1016/j.semcancer.2018.06.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 02/06/2023]
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21
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Stynen B, Abd-Rabbo D, Kowarzyk J, Miller-Fleming L, Aulakh SK, Garneau P, Ralser M, Michnick SW. Changes of Cell Biochemical States Are Revealed in Protein Homomeric Complex Dynamics. Cell 2018; 175:1418-1429.e9. [PMID: 30454649 PMCID: PMC6242466 DOI: 10.1016/j.cell.2018.09.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 01/22/2023]
Abstract
We report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins, or other small molecules based on "homomer dynamics" protein-fragment complementation assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating the confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health span-affecting drugs, the immunosuppressant rapamycin and the type 2 diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency and includes a change in protein-bound iron levels. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatment of diabetes, cancers, and other chronic diseases of aging.
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Affiliation(s)
- Bram Stynen
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Diala Abd-Rabbo
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC H3C 3J7, Canada
| | - Jacqueline Kowarzyk
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Leonor Miller-Fleming
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Garneau
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada; Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC H3C 3J7, Canada.
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22
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Li S, Giardina DM, Siegal ML. Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors. PLoS Genet 2018; 14:e1007744. [PMID: 30388117 PMCID: PMC6241136 DOI: 10.1371/journal.pgen.1007744] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 11/14/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023] Open
Abstract
Genetically identical cells exhibit extensive phenotypic variation even under constant and benign conditions. This so-called nongenetic heterogeneity has important clinical implications: within tumors and microbial infections, cells show nongenetic heterogeneity in growth rate and in susceptibility to drugs or stress. The budding yeast, Saccharomyces cerevisiae, shows a similar form of nongenetic heterogeneity in which growth rate correlates positively with susceptibility to acute heat stress at the single-cell level. Using genetic and chemical perturbations, combined with high-throughput single-cell assays of yeast growth and gene expression, we show here that heterogeneity in intracellular cyclic AMP (cAMP) levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies this nongenetic heterogeneity. Lower levels of cAMP correspond to slower growth, as shown by direct comparison of cAMP concentration in subpopulations enriched for slower vs. faster growing cells. Concordantly, an endogenous reporter of this pathway’s activity correlates with growth in individual cells. The paralogs Msn2 and Msn4 differ in their roles in nongenetic heterogeneity in a way that demonstrates slow growth and stress tolerance are not inevitably linked. Heterogeneity in growth rate requires each, whereas only Msn2 is required for heterogeneity in expression of Tsl1, a subunit of trehalose synthase that contributes to acute-stress tolerance. Perturbing nongenetic heterogeneity by mutating genes in this pathway, or by culturing wild-type cells with the cell-permeable cAMP analog 8-bromo-cAMP or the PKA inhibitor H89, significantly impacts survival of acute heat stress. Perturbations that increase intracellular cAMP levels reduce the slower-growing subpopulation and increase susceptibility to acute heat stress, whereas PKA inhibition slows growth and decreases susceptibility to acute heat stress. Loss of Msn2 reduces, but does not completely eliminate, the correlation in individual cells between growth rate and acute-stress survival, suggesting a major role for the Msn2 pathway in nongenetic heterogeneity but also a residual benefit of slow growth. Our results shed light on the genetic control of nongenetic heterogeneity and suggest a possible means of defeating bet-hedging pathogens or tumor cells by making them more uniformly susceptible to treatment. Nongenetic heterogeneity exists when a trait differs among individuals that have identical genotypes and environments. A clonal population can maximize its long-term success in an uncertain environment by diversifying its phenotypes via nongenetic heterogeneity: the currently unfavored ones may become the favored ones when conditions change. Nongenetic heterogeneity has clinical relevance. For example, populations of tumor cells or infectious microbes show cell-to-cell differences in growth and in drug or stress tolerance. This heterogeneity hampers efficient treatment and can potentiate harmful evolution of a tumor or pathogen. We show that in budding yeast, heterogeneity in intracellular cyclic AMP levels acting through the conserved Ras/cAMP/protein kinase A (PKA) pathway and its target transcription factors, Msn2 and Msn4, underlies the nongenetic heterogeneity of both single-cell growth rate and acute heat-stress tolerance. Perturbations of this pathway significantly affect population survival upon acute heat stress. These results illuminate a mechanism of nongenetic heterogeneity and suggest the potential value of antitumor or antifungal treatment strategies that target nongenetic heterogeneity to render the tumor or pathogen population more uniformly susceptible to a second drug that aims to kill.
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Affiliation(s)
- Shuang Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Daniella M. Giardina
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Mark L. Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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23
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N'guyen GQ, Martin N, Jain M, Lagacé L, Landry CR, Filteau M. A systems biology approach to explore the impact of maple tree dormancy release on sap variation and maple syrup quality. Sci Rep 2018; 8:14658. [PMID: 30279486 PMCID: PMC6168607 DOI: 10.1038/s41598-018-32940-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
Abstract
Maple sap is a complex nutrient matrix collected during spring to produce maple syrup. The characteristics of sap change over the production period and its composition directly impacts syrup quality. This variability could in part be attributed to changes in tree metabolism following dormancy release, but little is known about these changes in deciduous trees. Therefore, understanding the variation in sap composition associated with dormancy release could help pinpoint the causes of some defects in maple syrup. In particular, a defect known as "buddy", is an increasing concern for the industry. This off-flavor appears around the time of bud break, hence its name. To investigate sap variation related to bud break and the buddy defect, we monitored sap variation with respect to a dormancy release index (Sbb) and syrup quality. First, we looked at variation in amino acid content during this period. We observed a shift in amino acid relative proportions associated with dormancy release and found that most of them increase rapidly near the point of bud break, correlating with changes in syrup quality. Second, we identified biological processes that respond to variation in maple sap by performing a competition assay using the barcoded Saccharomyces cerevisiae prototroph deletion collection. This untargeted approach revealed that the organic sulfur content may be responsible for the development of the buddy off-flavor, and that dormancy release is necessary for the appearance of the defect, but other factors such as microbial activity may also be contributing.
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Affiliation(s)
- Guillaume Quang N'guyen
- Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Québec, Québec, G1V 0A6, Canada.,Département de Biologie, Département de Biochimie, Microbiologie et Bio-informatique, PROTEO, Centre de recherche en données massives and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Nathalie Martin
- Centre de recherche, de développement et de transfert technologique acéricole Inc., Saint-Norbert-d'Arthabaska, Québec, G0P 1B0, Canada
| | - Mani Jain
- Département de Biologie, Département de Biochimie, Microbiologie et Bio-informatique, PROTEO, Centre de recherche en données massives and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Luc Lagacé
- Centre de recherche, de développement et de transfert technologique acéricole Inc., Saint-Norbert-d'Arthabaska, Québec, G0P 1B0, Canada
| | - Christian R Landry
- Département de Biologie, Département de Biochimie, Microbiologie et Bio-informatique, PROTEO, Centre de recherche en données massives and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Québec, Québec, G1V 0A6, Canada.
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Ritagliati C, Luque GM, Stival C, Baro Graf C, Buffone MG, Krapf D. Lysine acetylation modulates mouse sperm capacitation. Sci Rep 2018; 8:13334. [PMID: 30190490 PMCID: PMC6127136 DOI: 10.1038/s41598-018-31557-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022] Open
Abstract
Mammalian sperm are unable to fertilize the egg immediately after ejaculation. To gain fertilization competence, they need to undergo a series of modifications inside the female reproductive tract, known as capacitation. Capacitation involves several molecular events such as phosphorylation cascades, hyperpolarization of the plasma membrane and intracellular Ca2+ changes, which prepare the sperm to develop two essential features for fertilization competence: hyperactivation and acrosome reaction. Since sperm cells lack new protein biosynthesis, post-translational modification of existing proteins plays a crucial role to obtain full functionality. Here, we show the presence of acetylated proteins in murine sperm, which increase during capacitation. Pharmacological hyperacetylation of lysine residues in non-capacitated sperm induces activation of PKA, hyperpolarization of the sperm plasma membrane, CatSper opening and Ca2+ influx, all capacitation-associated molecular events. Furthermore, hyperacetylation of non-capacitated sperm promotes hyperactivation and prepares the sperm to undergo acrosome reaction. Together, these results indicate that acetylation could be involved in the acquisition of fertilization competence of mammalian sperm.
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Affiliation(s)
- Carla Ritagliati
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, 2000, Argentina
| | - Guillermina M Luque
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, C1428ADN, Argentina
| | - Cintia Stival
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, 2000, Argentina
| | - Carolina Baro Graf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, 2000, Argentina
| | - Mariano G Buffone
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, C1428ADN, Argentina
| | - Dario Krapf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, 2000, Argentina.
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Hyndman KA, Yang CR, Jung HJ, Umejiego EN, Chou CL, Knepper MA. Proteomic determination of the lysine acetylome and phosphoproteome in the rat native inner medullary collecting duct. Physiol Genomics 2018; 50:669-679. [PMID: 29932826 DOI: 10.1152/physiolgenomics.00029.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phosphorylation and lysine (K)-acetylation are dynamic posttranslational modifications of proteins. Previous proteomic studies have identified over 170,000 phosphorylation sites and 15,000 K-acetylation sites in mammals. We recently reported that the inner medullary collecting duct (IMCD), which functions in the regulation of water-reabsorption, via the actions of vasopressin, expresses many of the enzymes that can modulated K-acetylation. The purpose of this study was to determine the K-acetylated or phosphorylated proteins expressed in IMCD cells. Second we questioned whether vasopressin V2 receptor activation significantly affects the IMCD acetylome or phosphoproteome? K-acetylated or serine-, threonine-, or tyrosine-phosphorylated peptides were identified from native rat IMCDs by proteomic analysis with four different enzymes (trypsin, chymotrypsin, ASP-N, or Glu-C) to generate a high-resolution proteome. K-acetylation was identified in 431 unique proteins, and 64% of the K-acetylated sites were novel. The acetylated proteins were expressed in all compartments of the cell and were enriched in pathways including glycolysis and vasopressin-regulated water reabsorption. In the vasopressin-regulated water reabsorption pathway, eight proteins were acetylated, including the novel identification of the basolateral water channel, AQP3, acetylated at K282; 215 proteins were phosphorylated in this IMCD cohort, including AQP2 peptides that were phosphorylated at four serines: 256, 261, 264, and 269. Acute dDAVP did not significantly affect the IMCD acetylome; however, it did significantly affect previously known vasopressin-regulated phosphorylation sites. In conclusion, presence of K-acetylated proteins involved in metabolism, ion, and water transport in the IMCD points to multiple roles of K-acetylation beyond its canonical role in transcriptional regulation.
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Affiliation(s)
- Kelly A Hyndman
- Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham , Birmingham, Alabama
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
| | - Hyun Jun Jung
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
| | - Ezigbobiara N Umejiego
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
| | - Chung-Ling Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
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26
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Distributed and dynamic intracellular organization of extracellular information. Proc Natl Acad Sci U S A 2018; 115:6088-6093. [PMID: 29784812 DOI: 10.1073/pnas.1716659115] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.
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27
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MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 2018; 13:e1006088. [PMID: 29738528 PMCID: PMC5940180 DOI: 10.1371/journal.pcbi.1006088] [Citation(s) in RCA: 18] [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: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress. Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response. Much of this response is controlled by post-translational protein phosphorylation. Although many regulators that mediate changes in protein phosphorylation are known, how these regulators inter-connect in a single regulatory network that can transmit cellular signals is not known. It is also unclear how regulators that promote growth and regulators that activate the stress response interconnect to reorganize resource allocation during stress. Here, we developed an integrated experimental and computational workflow to infer the signaling network that regulates phosphorylation changes during osmotic stress in the budding yeast Saccharomyces cerevisiae. The workflow integrates data measuring protein phosphorylation changes in response to osmotic stress with known physical interactions between yeast proteins from large-scale datasets, along with other information about how regulators recognize their targets. The resulting network suggested new signaling connections between regulators and pathways, including those involved in regulating growth and defense, and predicted new regulators involved in stress defense. Our work highlights the power of using network inference to deliver new insight on how cells coordinate a diverse adaptive strategy to stress.
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Affiliation(s)
- Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin -Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, Madison, WI, United States of America
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- * E-mail:
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28
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Ignatius Pang CN, Goel A, Wilkins MR. Investigating the Network Basis of Negative Genetic Interactions in Saccharomyces cerevisiae with Integrated Biological Networks and Triplet Motif Analysis. J Proteome Res 2018; 17:1014-1030. [DOI: 10.1021/acs.jproteome.7b00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Chi Nam Ignatius Pang
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Apurv Goel
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Marc R. Wilkins
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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29
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A Lipid Transfer Protein Signaling Axis Exerts Dual Control of Cell-Cycle and Membrane Trafficking Systems. Dev Cell 2018; 44:378-391.e5. [PMID: 29396115 DOI: 10.1016/j.devcel.2017.12.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 09/24/2017] [Accepted: 12/28/2017] [Indexed: 11/21/2022]
Abstract
Kes1/Osh4 is a member of the conserved, but functionally enigmatic, oxysterol binding protein-related protein (ORP) superfamily that inhibits phosphatidylinositol transfer protein (Sec14)-dependent membrane trafficking through the trans-Golgi (TGN)/endosomal network. We now report that Kes1, and select other ORPs, execute cell-cycle control activities as functionally non-redundant inhibitors of the G1/S transition when cells confront nutrient-poor environments and promote replicative aging. Kes1-dependent cell-cycle regulation requires the Greatwall/MASTL kinase ortholog Rim15, and is opposed by Sec14 activity in a mechanism independent of Kes1/Sec14 bulk membrane-trafficking functions. Moreover, the data identify Kes1 as a non-histone target for NuA4 through which this lysine acetyltransferase co-modulates membrane-trafficking and cell-cycle activities. We propose the Sec14/Kes1 lipid-exchange protein pair constitutes part of the mechanism for integrating TGN/endosomal lipid signaling with cell-cycle progression and hypothesize that ORPs define a family of stage-specific cell-cycle control factors that execute tumor-suppressor-like functions.
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30
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Tyler JK, Johnson JE. The role of autophagy in the regulation of yeast life span. Ann N Y Acad Sci 2018; 1418:31-43. [PMID: 29363766 DOI: 10.1111/nyas.13549] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/13/2017] [Accepted: 10/18/2017] [Indexed: 01/07/2023]
Abstract
The goal of the aging field is to develop novel therapeutic interventions that extend human health span and reduce the burden of age-related disease. While organismal aging is a complex, multifactorial process, a popular theory is that cellular aging is a significant contributor to the progressive decline inherent to all multicellular organisms. To explore the molecular determinants that drive cellular aging, as well as how to retard them, researchers have utilized the highly genetically tractable budding yeast Saccharomyces cerevisiae. Indeed, every intervention known to extend both cellular and organismal health span was identified in yeast, underlining the power of this approach. Importantly, a growing body of work has implicated the process of autophagy as playing a critical role in the delay of aging. This review summarizes recent reports that have identified a role for autophagy, or autophagy factors in the extension of yeast life span. These studies demonstrate (1) that yeast remains an invaluable tool for the identification and characterization of conserved mechanisms that promote cellular longevity and are likely to be relevant to humans, and (2) that the process of autophagy has been implicated in nearly all known longevity-promoting manipulations and thus represents an ideal target for interventions aimed at improving human health span.
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Affiliation(s)
- Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Jay E Johnson
- Department of Biology, Orentreich Foundation for the Advancement of Science, Cold Spring, New York
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31
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Stynen B, Abd-rabbo D, Kowarzyk J, Miller-fleming L, Ralser M, Michnick S. A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State.. [DOI: 10.1101/190389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractWe report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins or other small molecules based on “homomer dynamics” Protein-fragment Complementation Assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health-span-affecting drugs, immunosuppressant rapamycin and type II diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatments of diabetes, cancers and other chronic diseases of aging.
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32
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Torres-Quesada O, Mayrhofer JE, Stefan E. The many faces of compartmentalized PKA signalosomes. Cell Signal 2017; 37:1-11. [PMID: 28528970 DOI: 10.1016/j.cellsig.2017.05.012] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 01/03/2023]
Abstract
Cellular signal transmission requires the dynamic formation of spatiotemporally controlled molecular interactions. At the cell surface information is received by receptor complexes and relayed through intracellular signaling platforms which organize the actions of functionally interacting signaling enzymes and substrates. The list of hormone or neurotransmitter pathways that utilize the ubiquitous cAMP-sensing protein kinase A (PKA) system is expansive. This requires that the specificity, duration, and intensity of PKA responses are spatially and temporally restricted. Hereby, scaffolding proteins take the center stage for ensuring proper signal transmission. They unite second messenger sensors, activators, effectors, and kinase substrates within cellular micro-domains to precisely control and route signal propagation. A-kinase anchoring proteins (AKAPs) organize such subcellular signalosomes by tethering the PKA holoenzyme to distinct cell compartments. AKAPs differ in their modular organization showing pathway specific arrangements of interaction motifs or domains. This enables the cell- and compartment- guided assembly of signalosomes with unique enzyme composition and function. The AKAP-mediated clustering of cAMP and other second messenger sensing and interacting signaling components along with functional successive enzymes facilitates the rapid and precise dissemination of incoming signals. This review article delineates examples for different means of PKA regulation and for snapshots of compartmentalized PKA signalosomes.
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Affiliation(s)
- Omar Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johanna E Mayrhofer
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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33
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Torres-Quesada O, Röck R, Stefan E. Systematic Quantification of GPCR/cAMP-Controlled Protein Kinase A Interactions. Horm Metab Res 2017; 49:240-249. [PMID: 28427097 DOI: 10.1055/s-0042-110791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The diffusible second messenger cyclic AMP (cAMP) originates from multiple G protein-coupled receptor (GPCR) cascades activating the intracellular key effector protein kinase A (PKA). Spatially and temporally restricted cAMP-fluxes are directly sensed by macromolecular PKA complexes. The consequences are alterations of molecular interactions, which lead to activation of compartmentalized PKA phosphotransferase activities, regulating a vast array of cellular functions. To decode cell-type and cell-compartment specific PKA functions, the spatio-temporal dynamics of small molecule:protein interactions, protein:protein interactions (PPIs), cAMP-mobilization, and phosphotransferase activities need to be determined directly in the appropriate cellular context. A collection of cell-based reporters has been developed to either visualize or quantitatively measure kinase activities or PKA complex formation/dissociation. In this review, we list a collection of unimolecular and bimolecular PKA biosensors, followed by the specification of the modular design of a Renilla luciferase based protein-fragment complementation assay (PCA) platform for measuring PKA network interactions. We discuss the application spectrum of the PCA reporter to identify, quantify, and dissect dynamic and transient PKA complexes downstream of specific GPCR activities. We specify the implementation of a PCA PKA platform to systematically quantify the concurrent involvement of receptor-cAMP signaling, post-translational modifications, and kinase subunit mutations/perturbations in PKA activation. The systematic quantification of transient PKA network interactions will contribute to a better understanding how GPCR-recognized input signals are streamlined through the compartmentalized and cAMP-interacting PKA signalosome.
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Affiliation(s)
- O Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - R Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - E Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
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34
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Altshuler-Keylin S, Kajimura S. Mitochondrial homeostasis in adipose tissue remodeling. Sci Signal 2017; 10:10/468/eaai9248. [PMID: 28246203 DOI: 10.1126/scisignal.aai9248] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial homeostasis is regulated by a balance between mitochondrial biogenesis and degradation. Emerging evidence suggests that mitophagy, a selective form of autophagy that degrades mitochondria, plays a key role in the physiology and pathophysiology of mitochondria-enriched cells, such as brown and beige adipocytes. This review discusses findings regarding the roles of autophagy and mitophagy in cellular development, maintenance, and functions of metabolic organs, including adipose tissue, liver, and pancreas. A better understanding of the molecular links between mitophagy and energy metabolism will help to identify promising targets for the treatment of obesity and obesity-associated disorders.
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Affiliation(s)
- Svetlana Altshuler-Keylin
- UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA 94143-0669, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143-0669, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143-0669, USA
| | - Shingo Kajimura
- UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA 94143-0669, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143-0669, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143-0669, USA
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35
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Kong D, Shen Y, Liu G, Zuo S, Ji Y, Lu A, Nakamura M, Lazarus M, Stratakis CA, Breyer RM, Yu Y. PKA regulatory IIα subunit is essential for PGD2-mediated resolution of inflammation. J Exp Med 2016; 213:2209-26. [PMID: 27621415 PMCID: PMC5030806 DOI: 10.1084/jem.20160459] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/12/2016] [Indexed: 12/28/2022] Open
Abstract
The kinetic participation of macrophages is critical for inflammatory resolution and recovery from myocardial infarction (MI), particularly with respect to the transition from the M1 to the M2 phenotype; however, the underlying mechanisms are poorly understood. In this study, we found that the deletion of prostaglandin (PG) D2 receptor subtype 1 (DP1) in macrophages retarded M2 polarization, antiinflammatory cytokine production, and resolution in different inflammatory models, including the MI model. DP1 deletion up-regulated proinflammatory genes expression via JAK2/STAT1 signaling in macrophages, whereas its activation facilitated binding of the separated PKA regulatory IIα subunit (PRKAR2A) to the transmembrane domain of IFN-γ receptor, suppressed JAK2-STAT1 axis-mediated M1 polarization, and promoted resolution. PRKAR2A deficiency attenuated DP1 activation-mediated M2 polarization and resolution of inflammation. Collectively, PGD2-DP1 axis-induced M2 polarization facilitates resolution of inflammation through the PRKAR2A-mediated suppression of JAK2/STAT1 signaling. These observations indicate that macrophage DP1 activation represents a promising strategy in the management of inflammation-associated diseases, including post-MI healing.
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Affiliation(s)
- Deping Kong
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yujun Shen
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Guizhu Liu
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengkai Zuo
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Ji
- The Key Laboratory of Cardiovascular Disease and Molecular Intervention, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ankang Lu
- Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Masataka Nakamura
- Human Gene Sciences Center, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Michael Lazarus
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba City, Ibaraki 305-8575, Japan
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 Pediatric Endocrinology Inter-institute Training Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Richard M Breyer
- Department of Veterans Affairs, Tennessee Valley Health Authority, Nashville, TN 37212 Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Ying Yu
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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36
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Rajan MR, Nyman E, Kjølhede P, Cedersund G, Strålfors P. Systems-wide Experimental and Modeling Analysis of Insulin Signaling through Forkhead Box Protein O1 (FOXO1) in Human Adipocytes, Normally and in Type 2 Diabetes. J Biol Chem 2016; 291:15806-19. [PMID: 27226562 DOI: 10.1074/jbc.m116.715763] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 01/31/2023] Open
Abstract
Insulin resistance is a major aspect of type 2 diabetes (T2D), which results from impaired insulin signaling in target cells. Signaling to regulate forkhead box protein O1 (FOXO1) may be the most important mechanism for insulin to control transcription. Despite this, little is known about how insulin regulates FOXO1 and how FOXO1 may contribute to insulin resistance in adipocytes, which are the most critical cell type in the development of insulin resistance. We report a detailed mechanistic analysis of insulin control of FOXO1 in human adipocytes obtained from non-diabetic subjects and from patients with T2D. We show that FOXO1 is mainly phosphorylated through mTORC2-mediated phosphorylation of protein kinase B at Ser(473) and that this mechanism is unperturbed in T2D. We also demonstrate a cross-talk from the MAPK branch of insulin signaling to stimulate phosphorylation of FOXO1. The cellular abundance and consequently activity of FOXO1 are halved in T2D. Interestingly, inhibition of mTORC1 with rapamycin reduces the abundance of FOXO1 to the levels in T2D. This suggests that the reduction of the concentration of FOXO1 is a consequence of attenuation of mTORC1, which defines much of the diabetic state in human adipocytes. We integrate insulin control of FOXO1 in a network-wide mathematical model of insulin signaling dynamics based on compatible data from human adipocytes. The diabetic state is network-wide explained by attenuation of an mTORC1-to-insulin receptor substrate-1 (IRS1) feedback and reduced abundances of insulin receptor, GLUT4, AS160, ribosomal protein S6, and FOXO1. The model demonstrates that attenuation of the mTORC1-to-IRS1 feedback is a major mechanism of insulin resistance in the diabetic state.
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Affiliation(s)
| | - Elin Nyman
- Biomedical Engineering, Linköping University, SE58185 Linköping, Sweden and Cardiovascular and Metabolic Diseases, Innovative Medicines, and Drug Metabolism and Pharmacokinetics, AstraZeneca Research and Development, 43150 Gothenburg, Sweden
| | - Preben Kjølhede
- From the Departments of Clinical and Experimental Medicine and
| | - Gunnar Cedersund
- From the Departments of Clinical and Experimental Medicine and Biomedical Engineering, Linköping University, SE58185 Linköping, Sweden and
| | - Peter Strålfors
- From the Departments of Clinical and Experimental Medicine and
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37
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Pautasso C, Reca S, Chatfield-Reed K, Chua G, Galello F, Portela P, Zaremberg V, Rossi S. Identification of novel transcriptional regulators of PKA subunits inSaccharomyces cerevisiaeby quantitative promoter–reporter screening. FEMS Yeast Res 2016; 16:fow046. [DOI: 10.1093/femsyr/fow046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 01/22/2023] Open
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38
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Tan X, Lambert PF, Rapraeger AC, Anderson RA. Stress-Induced EGFR Trafficking: Mechanisms, Functions, and Therapeutic Implications. Trends Cell Biol 2016; 26:352-366. [PMID: 26827089 PMCID: PMC5120732 DOI: 10.1016/j.tcb.2015.12.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/27/2015] [Accepted: 12/31/2015] [Indexed: 12/13/2022]
Abstract
Epidermal growth factor receptor (EGFR) has fundamental roles in normal physiology and cancer, making it a rational target for cancer therapy. Surprisingly, however, inhibitors that target canonical, ligand-stimulated EGFR signaling have proven to be largely ineffective in treating many EGFR-dependent cancers. Recent evidence indicates that both intrinsic and therapy-induced cellular stress triggers robust, noncanonical pathways of ligand-independent EGFR trafficking and signaling, which provides cancer cells with a survival advantage and resistance to therapeutics. Here, we review the mechanistic regulation of noncanonical EGFR trafficking and signaling, and the pathological and therapeutic stresses that activate it. We also discuss the implications of this pathway in clinical treatment of EGFR-overexpressing cancers.
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Affiliation(s)
- Xiaojun Tan
- Program in Molecular and Cellular Pharmacology, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Paul F Lambert
- Department of Oncology, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Alan C Rapraeger
- Department of Human Oncology, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Richard A Anderson
- Program in Molecular and Cellular Pharmacology, University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA.
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39
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Li H, Li W, Liu F, Wang Z, Li G, Karamanos Y. Detection of Tumor Invasive Biomarker using a Peptamer of Signal Conversion and Signal Amplification. Anal Chem 2016; 88:3662-8. [PMID: 26938572 DOI: 10.1021/acs.analchem.5b04423] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inspired by the structural and functional features of proteins in cell signaling, a switchable peptide is designed in this work. This switchable peptide is named a "peptamer," and it can react to ligand binding with conformational change and activation/deactivation of catalytic ability. The peptamer is constructed by elaborately integrating several different peptide motifs with targeting and catalytic abilities. Thus, targeted binding of the peptamer to an integrin can be regulated by a synthetic ligand. Moreover, the conformational rearrangement of the peptamer induced by both integrin and the synthetic ligand can resolve in altered affinity of the peptamer for a catalytic cofactor, cupric ion. This leads to greatly contrasted efficiency of catalysis in the presence/absence of integrin. This distinct switching on/off of catalytic activity also enables a bioassay of tissue integrin expression in clinical samples of thyroid carcinoma. Experimental results reveal that the detected integrin level parallels the state of lymph node metastasis. Therefore, this simple peptide model may help to understand the structural reconfiguration of proteins involved in cellular signal transduction, as well as to provide a new means to assess protein activity under pathological conditions such as cancer.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, China
| | - Weiwei Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, China
| | - Fengzhen Liu
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University , Nanjing 210011, China
| | - Zhaoxia Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University , Nanjing 210011, China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, China.,Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University , Shanghai 200444, China
| | - Yannis Karamanos
- Laboratoire de la Barrière Hémato-encéphalique, Faculté des Sciences, Université d'Artois , rue Souvraz SP18, 62307 CEDEX Lens, France
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40
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Sample Preparation for Mass Spectrometry Analysis of Protein-Protein Interactions in Cancer Cell Lines and Tissues. Methods Mol Biol 2016; 1458:339-47. [PMID: 27581032 DOI: 10.1007/978-1-4939-3801-8_23] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A precisely controlled network of protein-protein interactions constitutes the basis for functional signaling pathways. This equilibrium is more often than not disrupted in cancer cells, by the aberrant expression or activation of oncogenic proteins. Therefore, the analysis of protein interaction networks in cancer cells has become crucial to expand our comprehension of the molecular underpinnings of tumor formation and progression. This protocol describes a sample preparation method for the analysis of signaling complexes by mass spectrometry (MS), following the affinity purification of a protein of interest from a cancer cell line or a solid tumor. In particular, we provide a spin tip-based protease digestion procedure that offers a more rapid and controlled alternative to other gel-based and gel-free methods. This sample preparation protocol represents a useful strategy to identify protein interactions and to gain insight into the molecular mechanisms that contribute to a given cancer phenotype.
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41
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Filteau M, Vignaud H, Rochette S, Diss G, Chrétien AÈ, Berger CM, Landry CR. Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps. Brief Funct Genomics 2015; 15:130-7. [PMID: 26476431 DOI: 10.1093/bfgp/elv043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cellular architectures and signaling machineries are organized through protein-protein interactions (PPIs). High-throughput methods to study PPIs in yeast have opened a new perspective on the organization of the cell by allowing the study of whole protein interactomes. Recent investigations have moved from the description of this organization to the analysis of its dynamics by experimenting how protein interaction networks (PINs) are rewired in response to perturbations. Here we review studies that have used the budding yeast as an experimental system to explore these altered networks. Given the large space of possible PPIs and the diversity of potential genetic and environmental perturbations, high-throughput methods are an essential requirement to survey PIN perturbations on a large scale. Network perturbations are typically conceptualized as the removal of entire proteins (nodes), the modification of single PPIs (edges) or changes in growth conditions. These studies have revealed mechanisms of PPI regulation, PIN architectural organization, robustness and sensitivity to perturbations. Despite these major advances, there are still inherent limits to current technologies that lead to a trade-off between the number of perturbations and the number of PPIs that can be considered simultaneously. Nevertheless, as we exemplify here, targeted approaches combined with the existing resources remain extremely powerful to explore the inner organization of cells and their responses to perturbations.
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42
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Röck R, Mayrhofer JE, Bachmann V, Stefan E. Impact of kinase activating and inactivating patient mutations on binary PKA interactions. Front Pharmacol 2015; 6:170. [PMID: 26347651 PMCID: PMC4539479 DOI: 10.3389/fphar.2015.00170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/30/2015] [Indexed: 11/13/2022] Open
Abstract
The second messenger molecule cAMP links extracellular signals to intracellular responses. The main cellular cAMP effector is the compartmentalized protein kinase A (PKA). Upon receptor initiated cAMP-mobilization, PKA regulatory subunits (R) bind cAMP thereby triggering dissociation and activation of bound PKA catalytic subunits (PKAc). Mutations in PKAc or RIa subunits manipulate PKA dynamics and activities which contribute to specific disease patterns. Mutations activating cAMP/PKA signaling contribute to carcinogenesis or hormone excess, while inactivating mutations cause hormone deficiency or resistance. Here we extended the application spectrum of a Protein-fragment Complementation Assay based on the Renilla Luciferase to determine binary protein:protein interactions (PPIs) of the PKA network. We compared time- and dose-dependent influences of cAMP-elevation on mutually exclusive PPIs of PKAc with the phosphotransferase inhibiting RIIb and RIa subunits and the protein kinase inhibitor peptide (PKI). We analyzed PKA dynamics following integration of patient mutations into PKAc and RIa. We observed that oncogenic modifications of PKAc(L206R) and RIa(Δ184-236) as well as rare disease mutations in RIa(R368X) affect complex formation of PKA and its responsiveness to cAMP elevation. With the cell-based PKA PPI reporter platform we precisely quantified the mechanistic details how inhibitory PKA interactions and defined patient mutations contribute to PKA functions.
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Affiliation(s)
| | | | | | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruck, Austria
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43
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Röck R, Bachmann V, Bhang HEC, Malleshaiah M, Raffeiner P, Mayrhofer JE, Tschaikner PM, Bister K, Aanstad P, Pomper MG, Michnick SW, Stefan E. In-vivo detection of binary PKA network interactions upon activation of endogenous GPCRs. Sci Rep 2015; 5:11133. [PMID: 26099953 PMCID: PMC4477410 DOI: 10.1038/srep11133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/14/2015] [Indexed: 12/21/2022] Open
Abstract
Membrane receptor-sensed input signals affect and modulate intracellular protein-protein interactions (PPIs). Consequent changes occur to the compositions of protein complexes, protein localization and intermolecular binding affinities. Alterations of compartmentalized PPIs emanating from certain deregulated kinases are implicated in the manifestation of diseases such as cancer. Here we describe the application of a genetically encoded Protein-fragment Complementation Assay (PCA) based on the Renilla Luciferase (Rluc) enzyme to compare binary PPIs of the spatially and temporally controlled protein kinase A (PKA) network in diverse eukaryotic model systems. The simplicity and sensitivity of this cell-based reporter allows for real-time recordings of mutually exclusive PPIs of PKA upon activation of selected endogenous G protein-coupled receptors (GPCRs) in cancer cells, xenografts of mice, budding yeast, and zebrafish embryos. This extends the application spectrum of Rluc PCA for the quantification of PPI-based receptor-effector relationships in physiological and pathological model systems.
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Affiliation(s)
- Ruth Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Verena Bachmann
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Hyo-Eun C Bhang
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical School, Baltimore, MD 21287, USA
| | - Mohan Malleshaiah
- Département de Biochimie, Université de Montréal, H3C 3J7 Montréal, Québec, Canada
| | - Philipp Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johanna E Mayrhofer
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Philipp M Tschaikner
- Institute of Molecular Biology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Pia Aanstad
- Institute of Molecular Biology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Martin G Pomper
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical School, Baltimore, MD 21287, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, H3C 3J7 Montréal, Québec, Canada
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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