1
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Otto TA, Bergsma T, Dekker M, Mouton SN, Gallardo P, Wolters JC, Steen A, Onck PR, Veenhoff LM. Nucleoporin Nsp1 surveils the phase state of FG-Nups. Cell Rep 2024; 43:114793. [PMID: 39356635 DOI: 10.1016/j.celrep.2024.114793] [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: 05/17/2023] [Revised: 06/21/2024] [Accepted: 09/07/2024] [Indexed: 10/04/2024] Open
Abstract
Transport through the nuclear pore complex (NPC) relies on intrinsically disordered FG-nucleoporins (FG-Nups) forming a selective barrier. Away from the NPC, FG-Nups readily form condensates and aggregates, and we address how this behavior is surveilled in cells. FG-Nups, including Nsp1, together with the nuclear transport receptor Kap95, form a native daughter cell-specific cytosolic condensate in yeast. In aged cells, this condensate disappears as cytosolic Nsp1 levels decline. Biochemical assays and modeling show that Nsp1 is a modulator of FG-Nup condensates, promoting a liquid-like state. Nsp1's presence in the cytosol and condensates is critical, as a reduction of cytosolic levels in young cells induces NPC defects and a general decline in protein quality control that quantitatively mimics aging phenotypes. These phenotypes can be rescued by a cytosolic form of Nsp1. We conclude that Nsp1 is a phase state regulator that surveils FG-Nups and impacts general protein homeostasis.
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Affiliation(s)
- Tegan A Otto
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Tessa Bergsma
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Maurice Dekker
- Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands
| | - Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Justina C Wolters
- Laboratory of Pediatrics, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands.
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2
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Ramakrishnan P, Keeney J. The yeast gene ECM9 regulates cell wall maintenance and cell division in stress conditions. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001313. [PMID: 39415825 PMCID: PMC11480822 DOI: 10.17912/micropub.biology.001313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/26/2024] [Accepted: 09/23/2024] [Indexed: 10/19/2024]
Abstract
Saccharomyces cerevisiae , Baker's yeast, is a well-studied model eukaryotic organism. Much of our knowledge about eukaryotic cell function comes from yeast studies, though nearly 10% of yeast genes remain uncharacterized. This study focuses on YKR004C, a verified gene of unknown function named ECM9 , predicted to be involved in cell division and cell wall maintenance or composition based on previous studies. We investigated the sensitivity in stress conditions of an ECM9 deletion strain, compared to wild-type, to cell wall integrity. These results suggest that ECM9 is involved in cell wall maintenance and the regulatory pathway determining cell division readiness under stress.
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Affiliation(s)
| | - Jill Keeney
- Biology, Juniata College, Huntingdon, Pennsylvania, United States
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3
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Tran KD, Le-Thi L, Vo HH, Dinh-Thi TV, Nguyen-Thi T, Phan NH, Nguyen KU. Probiotic Properties and Safety Evaluation in the Invertebrate Model Host Galleria mellonella of the Pichia kudriavzevii YGM091 Strain Isolated from Fermented Goat Milk. Probiotics Antimicrob Proteins 2024; 16:1288-1303. [PMID: 37368223 DOI: 10.1007/s12602-023-10114-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2023] [Indexed: 06/28/2023]
Abstract
Potential probiotic yeast strains isolated from fermented food need to meet safe and beneficial conditions for the host's health. The Pichia kudriavzevii YGM091 strain isolated from fermented goat milk has outstanding probiotic characteristics, including: the high survival percentage in digestive system conditions (reaching up 247.13 ± 0.12 and 145.03 ± 0.06% at pH 3.0 and bile salt 0.5%, respectively); good tolerance to temperature, salt, phenol, ethanol; good surface properties such as high hydrophobicity percentage (> 60%), the high auto-aggregation percentage rate (66.56 ± 1.45% after 45 min of incubation) and the high co-aggregation percentage rate with pathogenic bacteria in a short time (> 40% after 2 h of incubation); biofilm forming after 24 h of incubation on abiotic surfaces; antioxidant activity reached excellent level after only 24 h of incubation (The percentage free radical scavenging and the Trolox equivalent reaching up 79.86 ± 0.70% and 92.09 ± 0.75 µg/mL after 72 h of incubation); extracellular enzymes production protease and cellulase with high activity, amylase and pectinase with moderate activity and non-lipase activity. Simultaneously, the YGM091 strain is the in vitro safety yeast: insensitive to antibiotics and fluconazole, negative for gelatinase, phospholipase, coagulase, and non-hemolysis activities. Furthermore, this strain is in vivo safety yeast with the dosages below 106 CFU/larva in the Galleria mellonella model with over 90% survival larvae and the yeast density reduced to just 102-103 CFU/larva after 72 h post-injection. Research results have demonstrated that the Pichia kudriavzevii YGM091 strain is a safe potential probiotic yeast and could become a candidate probiotic food to be used in the future.
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Affiliation(s)
- Kim-Diep Tran
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Da Lat, Vietnam.
- Yersin University, Da Lat, Vietnam.
| | | | | | | | | | - Nha-Hoa Phan
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Da Lat, Vietnam
| | - Khanh-Uyen Nguyen
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Da Lat, Vietnam
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4
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Kuo ME, Parish M, Jonatzke KE, Antonellis A. Comprehensive assessment of recessive, pathogenic AARS1 alleles in a humanized yeast model reveals loss-of-function and dominant-negative effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599900. [PMID: 38979321 PMCID: PMC11230197 DOI: 10.1101/2024.06.20.599900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Alanyl-tRNA synthetase 1 (AARS1) encodes the enzyme that ligates tRNA molecules to alanine in the cytoplasm, which is required for protein translation. Variants in AARS1 have been implicated in early-onset, multi-system recessive phenotypes and in later-onset dominant peripheral neuropathy; to date, no single variant has been associated with both dominant and recessive diseases raising questions about shared mechanisms between the two inheritance patterns. AARS1 variants associated with recessive disease are predicted to result in null or hypomorphic alleles and this has been demonstrated, in part, via yeast complementation assays. However, pathogenic alleles have not been assessed in a side-by-side manner to carefully scrutinize the strengths and limitations of this model system. To address this, we employed a humanized yeast model to evaluate the functional consequences of all AARS1 missense variants reported in recessive disease. The majority of variants showed variable loss-of-function effects, ranging from no growth to significantly reduced growth. These data deem yeast a reliable model to test the functional consequences of human AARS1 variants; however, our data indicate that this model is prone to false-negative results and is not informative for genotype-phenotype studies. We next tested missense variants associated with no growth for dominant-negative effects. Interestingly, K81T AARS1, a variant implicated in recessive disease, demonstrated loss-of-function and dominant-negative effects, indicating that certain AARS1 variants may be capable of causing both dominant and recessive disease phenotypes.
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Affiliation(s)
- Molly E Kuo
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Maclaine Parish
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Kira E Jonatzke
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, USA
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
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5
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Separovich RJ, Karakatsanis NM, Gao K, Fuh D, Hamey JJ, Wilkins MR. Proline-directed yeast and human MAP kinases phosphorylate the Dot1p/DOT1L histone H3K79 methyltransferase. FEBS J 2024; 291:2590-2614. [PMID: 38270553 DOI: 10.1111/febs.17062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/24/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Disruptor of telomeric silencing 1 (Dot1p) is an exquisitely conserved histone methyltransferase and is the sole enzyme responsible for H3K79 methylation in the budding yeast Saccharomyces cerevisiae. It has been shown to be highly phosphorylated in vivo; however, the upstream kinases that act on Dot1p are almost entirely unknown in yeast and all other eukaryotes. Here, we used in vitro and in vivo kinase discovery approaches to show that mitogen-activated protein kinase HOG1 (Hog1p) is a bona fide kinase of the Dot1p methyltransferase. In vitro kinase assays showed that Hog1p phosphorylates Dot1p at multiple sites, including at several proline-adjacent sites that are consistent with known Hog1p substrate preferences. The activity of Hog1p was specifically enhanced at these proline-adjacent sites on Dot1p upon Hog1p activation by the osmostress-responsive MAP kinase kinase PBS2 (Pbs2p). Genomic deletion of HOG1 reduced phosphorylation at specific sites on Dot1p in vivo, providing further evidence for Hog1p kinase activity on Dot1p in budding yeast cells. Phenotypic analysis of knockout and phosphosite mutant yeast strains revealed the importance of Hog1p-catalysed phosphorylation of Dot1p for cellular responses to ultraviolet-induced DNA damage. In mammalian systems, this kinase-substrate relationship was found to be conserved: human DOT1L (the ortholog of yeast Dot1p) can be phosphorylated by the proline-directed kinase p38β (also known as MAPK11; the ortholog of yeast Hog1p) at multiple sites in vitro. Taken together, our findings establish Hog1p and p38β as newly identified upstream kinases of the Dot1p/DOT1L H3K79 methyltransferase enzymes in eukaryotes.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Nicola M Karakatsanis
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Kelley Gao
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - David Fuh
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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6
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Li Y, Gong JY, Wang P, Fu H, Yousef F, Xie R, Wang W, Liu Z, Pan DW, Ju XJ, Chu LY. Dissolving microneedle system containing Ag nanoparticle-decorated silk fibroin microspheres and antibiotics for synergistic therapy of bacterial biofilm infection. J Colloid Interface Sci 2024; 661:123-138. [PMID: 38295695 DOI: 10.1016/j.jcis.2024.01.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/11/2024] [Accepted: 01/21/2024] [Indexed: 02/27/2024]
Abstract
Most cases of delayed wound healing are associated with bacterial biofilm infections due to high antibiotic resistance. To improve patient compliance and recovery rates, it is critical to develop minimally invasive and efficient methods to eliminate bacterial biofilms as an alternative to clinical debridement techniques. Herein, we develop a dissolving microneedle system containing Ag nanoparticles (AgNPs)-decorated silk fibroin microspheres (SFM-AgNPs) and antibiotics for synergistic treatment of bacterial biofilm infection. Silk fibroin microspheres (SFM) are controllably prepared in an incompatible system formed by a mixture of protein and carbohydrate solutions by using a mild all-aqueous phase method and serve as biological templates for the synthesis of AgNPs. The SFM-AgNPs exert dose- and time-dependent broad-spectrum antibacterial effects by inducing bacterial adhesion. The combination of SFM-AgNPs with antibiotics breaks the limitation of the antibacterial spectrum and achieves better efficacy with reduced antibiotic dosage. Using hyaluronic acid (HA) as the soluble matrix, the microneedle system containing SFM-AgNPs and anti-Gram-positive coccus drug (Mupirocin) inserts into the bacterial biofilms with sufficient strength, thereby effectively delivering the antibacterial agents and realizing good antibiofilm effect on Staphylococcus aureus-infected wounds. This work demonstrates the great potential for the development of novel therapeutic systems for eradicating bacterial biofilm infections.
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Affiliation(s)
- Yao Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jue-Ying Gong
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Po Wang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Han Fu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Faraj Yousef
- Department of Chemical Engineering, University of Chester, Chester CH1 4BJ, United Kingdom
| | - Rui Xie
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Wei Wang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Zhuang Liu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Da-Wei Pan
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Xiao-Jie Ju
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China.
| | - Liang-Yin Chu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
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7
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Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H. Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature 2024; 628:212-220. [PMID: 38509361 PMCID: PMC10990931 DOI: 10.1038/s41586-024-07196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs)1,2. However, the mechanism by which RAD51 functions at DSB sites in chromatin has remained elusive. Here we report the cryo-electron microscopy structures of human RAD51-nucleosome complexes, in which RAD51 forms ring and filament conformations. In the ring forms, the N-terminal lobe domains (NLDs) of RAD51 protomers are aligned on the outside of the RAD51 ring, and directly bind to the nucleosomal DNA. The nucleosomal linker DNA that contains the DSB site is recognized by the L1 and L2 loops-active centres that face the central hole of the RAD51 ring. In the filament form, the nucleosomal DNA is peeled by the RAD51 filament extension, and the NLDs of RAD51 protomers proximal to the nucleosome bind to the remaining nucleosomal DNA and histones. Mutations that affect nucleosome-binding residues of the RAD51 NLD decrease nucleosome binding, but barely affect DNA binding in vitro. Consistently, yeast Rad51 mutants with the corresponding mutations are substantially defective in DNA repair in vivo. These results reveal an unexpected function of the RAD51 NLD, and explain the mechanism by which RAD51 associates with nucleosomes, recognizes DSBs and forms the active filament in chromatin.
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Affiliation(s)
- Takuro Shioi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Eriko Oya
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wataru Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mitsuo Ogasawara
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takehiko Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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8
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Soong TH, Hotze C, Khandelwal NK, Tomasiak TM. Structural Basis for Oxidized Glutathione Recognition by the Yeast Cadmium Factor 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578287. [PMID: 38352558 PMCID: PMC10862839 DOI: 10.1101/2024.01.31.578287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Transporters from the ABCC family have an essential role in detoxifying electrophilic compounds including metals, drugs, and lipids, often through conjugation with glutathione complexes. The Yeast Cadmium Factor 1 (Ycf1) transports glutathione alone as well as glutathione conjugated to toxic heavy metals including Cd2+, Hg2+, and As3+. To understand the complicated selectivity and promiscuity of heavy metal substrate binding, we determined the cryo-EM structure of Ycf1 bound to the substrate, oxidized glutathione. We systematically tested binding determinants with cellular survival assays against cadmium to determine how the substrate site accommodates different-sized metal complexes. We identify a "flex-pocket" for substrate binding that binds glutathione complexes asymmetrically and flexes to accommodate different size complexes.
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Affiliation(s)
- Tik Hang Soong
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Clare Hotze
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Nitesh Kumar Khandelwal
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Biochemistry and Physics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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9
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Wahid E, Ocheja OB, Guaragnella N, Guaragnella C. A Matlab-based application for quantification of yeast cell growth on solid media. J R Soc Interface 2024; 21:20230695. [PMID: 38503339 PMCID: PMC10950458 DOI: 10.1098/rsif.2023.0695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Quantitative assessment of growth and survival is a suitable technique in studying biochemical, genetic and physiological processes in the cells. The budding yeast Saccharomyces cerevisiae is one of the most widely used eukaryotic model organisms for studying cellular mechanisms and processes in evolutionarily distant species, including humans. Yeast growth can be evaluated on both liquid and solid media by measuring cell suspension turbidity and colony forming units, respectively. Several software tools utilizing different parameters have been proposed to quantify yeast growth on solid media. Here, we developed a Matlab-based application which provides a rapid and robust quantitative yeast growth analysis from spot plating assay. Spot plating assay is a typical procedure to evaluate yeast growth in low-throughput laboratory settings, including growth on different nutrient sources or treatment with specific stressors. The app has a one-step installation process, a self-explanatory interface and shorter analysis steps compared with previous established methods, providing a useful tool for both expert and non-expert yeast researchers.
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Affiliation(s)
- Ehtisham Wahid
- Department of Electrical and Information Engineering, Politecnico di Bari, Bari, Puglia 70125, Italy
| | - Ohiemi Benjamin Ocheja
- Department of Biosciences, Biotechnologies and Environment, University of Bari ‘Aldo Moro’, Puglia 70125, Italy
| | - Nicoletta Guaragnella
- Department of Biosciences, Biotechnologies and Environment, University of Bari ‘Aldo Moro’, Puglia 70125, Italy
| | - Cataldo Guaragnella
- Department of Electrical and Information Engineering, Politecnico di Bari, Bari, Puglia 70125, Italy
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10
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Librais GMN, Jiang Y, Razzaq I, Brandl CJ, Shapiro RS, Lajoie P. Evolutionary diversity of the control of the azole response by Tra1 across yeast species. G3 (BETHESDA, MD.) 2024; 14:jkad250. [PMID: 37889998 PMCID: PMC10849324 DOI: 10.1093/g3journal/jkad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/16/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
Tra1 is an essential coactivator protein of the yeast SAGA and NuA4 acetyltransferase complexes that regulate gene expression through multiple mechanisms including the acetylation of histone proteins. Tra1 is a pseudokinase of the PIKK family characterized by a C-terminal PI3K domain with no known kinase activity. However, mutations of specific arginine residues to glutamine in the PI3K domains (an allele termed tra1Q3) result in reduced growth and increased sensitivity to multiple stresses. In the opportunistic fungal pathogen Candida albicans, the tra1Q3 allele reduces pathogenicity and increases sensitivity to the echinocandin antifungal drug caspofungin, which disrupts the fungal cell wall. Here, we found that compromised Tra1 function, in contrast to what is seen with caspofungin, increases tolerance to the azole class of antifungal drugs, which inhibits ergosterol synthesis. In C. albicans, tra1Q3 increases the expression of genes linked to azole resistance, such as ERG11 and CDR1. CDR1 encodes a multidrug ABC transporter associated with efflux of multiple xenobiotics, including azoles. Consequently, cells carrying tra1Q3 show reduced intracellular accumulation of fluconazole. In contrast, a tra1Q3 Saccharomyces cerevisiae strain displayed opposite phenotypes: decreased tolerance to azole, decreased expression of the efflux pump PDR5, and increased intracellular accumulation of fluconazole. Therefore, our data provide evidence that Tra1 differentially regulates the antifungal response across yeast species.
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Affiliation(s)
| | - Yuwei Jiang
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Iqra Razzaq
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
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11
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Maniero RA, Koltun A, Vitti M, Factor BG, de Setta N, Câmara AS, Lima JE, Figueira A. Identification and functional characterization of the sugarcane ( Saccharum spp.) AMT2-type ammonium transporter ScAMT3;3 revealed a presumed role in shoot ammonium remobilization. FRONTIERS IN PLANT SCIENCE 2023; 14:1299025. [PMID: 38098795 PMCID: PMC10720369 DOI: 10.3389/fpls.2023.1299025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023]
Abstract
Sugarcane (Saccharum spp.) is an important crop for sugar and bioethanol production worldwide. To maintain and increase sugarcane yields in marginal areas, the use of nitrogen (N) fertilizers is essential, but N overuse may result in the leaching of reactive N to the natural environment. Despite the importance of N in sugarcane production, little is known about the molecular mechanisms involved in N homeostasis in this crop, particularly regarding ammonium (NH4 +), the sugarcane's preferred source of N. Here, using a sugarcane bacterial artificial chromosome (BAC) library and a series of in silico analyses, we identified an AMMONIUM TRANSPORTER (AMT) from the AMT2 subfamily, sugarcane AMMONIUM TRANSPORTER 3;3 (ScAMT3;3), which is constitutively and highly expressed in young and mature leaves. To characterize its biochemical function, we ectopically expressed ScAMT3;3 in heterologous systems (Saccharomyces cerevisiae and Arabidopsis thaliana). The complementation of triple mep mutant yeast demonstrated that ScAMT3;3 is functional for NH3/H+ cotransport at high availability of NH4 + and under physiological pH conditions. The ectopic expression of ScAMT3;3 in the Arabidopsis quadruple AMT knockout mutant restored the transport capacity of 15N-NH4 + in roots and plant growth under specific N availability conditions, confirming the role of ScAMT3;3 in NH4 + transport in planta. Our results indicate that ScAMT3;3 belongs to the low-affinity transport system (Km 270.9 µM; Vmax 209.3 µmol g-1 root DW h-1). We were able to infer that ScAMT3;3 plays a presumed role in NH4 + source-sink remobilization in the shoots via phloem loading. These findings help to shed light on the functionality of a novel AMT2-type protein and provide bases for future research focusing on the improvement of sugarcane yield and N use efficiency.
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Affiliation(s)
- Rodolfo A. Maniero
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Alessandra Koltun
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Marielle Vitti
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Bruna G. Factor
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Amanda S. Câmara
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Joni E. Lima
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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12
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Meyer-Schuman R, Marte S, Smith TJ, Feely SME, Kennerson M, Nicholson G, Shy ME, Koutmou KS, Antonellis A. A humanized yeast model reveals dominant-negative properties of neuropathy-associated alanyl-tRNA synthetase mutations. Hum Mol Genet 2023; 32:2177-2191. [PMID: 37010095 PMCID: PMC10281750 DOI: 10.1093/hmg/ddad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/04/2023] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes that ligate tRNA molecules to cognate amino acids. Heterozygosity for missense variants or small in-frame deletions in six ARS genes causes dominant axonal peripheral neuropathy. These pathogenic variants reduce enzyme activity without significantly decreasing protein levels and reside in genes encoding homo-dimeric enzymes. These observations raise the possibility that neuropathy-associated ARS variants exert a dominant-negative effect, reducing overall ARS activity below a threshold required for peripheral nerve function. To test such variants for dominant-negative properties, we developed a humanized yeast assay to co-express pathogenic human alanyl-tRNA synthetase (AARS1) mutations with wild-type human AARS1. We show that multiple loss-of-function AARS1 mutations impair yeast growth through an interaction with wild-type AARS1, but that reducing this interaction rescues yeast growth. This suggests that neuropathy-associated AARS1 variants exert a dominant-negative effect, which supports a common, loss-of-function mechanism for ARS-mediated dominant peripheral neuropathy.
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Affiliation(s)
- Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sheila Marte
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tyler J Smith
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shawna M E Feely
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
- Molecular Medicine Laboratory, Concord General Repatriation Hospital, Sydney, NSW 2139, Australia
| | - Garth Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
- Molecular Medicine Laboratory, Concord General Repatriation Hospital, Sydney, NSW 2139, Australia
| | - Mike E Shy
- Department of Neurology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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13
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Mercier R, Yama D, LaPointe P, Johnson JL. Hsp90 mutants with distinct defects provide novel insights into cochaperone regulation of the folding cycle. PLoS Genet 2023; 19:e1010772. [PMID: 37228112 DOI: 10.1371/journal.pgen.1010772] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Molecular chaperones play a key role in maintaining proteostasis and cellular health. The abundant, essential, cytosolic Hsp90 (Heat shock protein, 90 kDa) facilitates the folding and activation of hundreds of newly synthesized or misfolded client proteins in an ATP-dependent folding pathway. In a simplified model, Hsp70 first helps load client onto Hsp90, ATP binding results in conformational changes in Hsp90 that result in the closed complex, and then less defined events result in nucleotide hydrolysis, client release and return to the open state. Cochaperones bind and assist Hsp90 during this process. We previously identified a series of yeast Hsp90 mutants that appear to disrupt either the 'loading', 'closing' or 'reopening' events, and showed that the mutants had differing effects on activity of some clients. Here we used those mutants to dissect Hsp90 and cochaperone interactions. Overexpression or deletion of HCH1 had dramatically opposing effects on the growth of cells expressing different mutants, with a phenotypic shift coinciding with formation of the closed conformation. Hch1 appears to destabilize Hsp90-nucleotide interaction, hindering formation of the closed conformation, whereas Cpr6 counters the effects of Hch1 by stabilizing the closed conformation. Hch1 and the homologous Aha1 share some functions, but the role of Hch1 in inhibiting progression through the early stages of the folding cycle is unique. Sensitivity to the Hsp90 inhibitor NVP-AUY922 also correlates with the conformational cycle, with mutants defective in the loading phase being most sensitive and those defective in the reopening phase being most resistant to the drug. Overall, our results indicate that the timing of transition into and out of the closed conformation is tightly regulated by cochaperones. Further analysis will help elucidate additional steps required for progression through the Hsp90 folding cycle and may lead to new strategies for modulating Hsp90 function.
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Affiliation(s)
- Rebecca Mercier
- Department of Cell Biology, Faculty of Medicine and Dentistry, the University of Alberta, Edmonton, Alberta, Canada
| | - Danielle Yama
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, the University of Alberta, Edmonton, Alberta, Canada
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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14
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Di Noia MA, Scarcia P, Agrimi G, Ocheja OB, Wahid E, Pisano I, Paradies E, Palmieri L, Guaragnella C, Guaragnella N. Inactivation of HAP4 Accelerates RTG-Dependent Osmoadaptation in Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065320. [PMID: 36982394 PMCID: PMC10049445 DOI: 10.3390/ijms24065320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Mitochondrial RTG (an acronym for ReTroGrade) signaling plays a cytoprotective role under various intracellular or environmental stresses. We have previously shown its contribution to osmoadaptation and capacity to sustain mitochondrial respiration in yeast. Here, we studied the interplay between RTG2, the main positive regulator of the RTG pathway, and HAP4, encoding the catalytic subunit of the Hap2-5 complex required for the expression of many mitochondrial proteins that function in the tricarboxylic acid (TCA) cycle and electron transport, upon osmotic stress. Cell growth features, mitochondrial respiratory competence, retrograde signaling activation, and TCA cycle gene expression were comparatively evaluated in wild type and mutant cells in the presence and in the absence of salt stress. We showed that the inactivation of HAP4 improved the kinetics of osmoadaptation by eliciting both the activation of retrograde signaling and the upregulation of three TCA cycle genes: citrate synthase 1 (CIT1), aconitase 1 (ACO1), and isocitrate dehydrogenase 1 (IDH1). Interestingly, their increased expression was mostly dependent on RTG2. Impaired respiratory competence in the HAP4 mutant does not affect its faster adaptive response to stress. These findings indicate that the involvement of the RTG pathway in osmostress is fostered in a cellular context of constitutively reduced respiratory capacity. Moreover, it is evident that the RTG pathway mediates peroxisomes–mitochondria communication by modulating the metabolic function of mitochondria in osmoadaptation.
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Affiliation(s)
- Maria Antonietta Di Noia
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Ohiemi Benjamin Ocheja
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Ehtisham Wahid
- Department of Electrical and Information Engineering, Politecnico di Bari, 70125 Bari, Italy
| | - Isabella Pisano
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Eleonora Paradies
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 70126 Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Cataldo Guaragnella
- Department of Electrical and Information Engineering, Politecnico di Bari, 70125 Bari, Italy
| | - Nicoletta Guaragnella
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
- Correspondence:
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15
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Qiu Y, Kenana R, Beharry A, Wilhelm SDP, Hsu SY, Siu VM, Duennwald M, Heinemann IU. Histidine supplementation can escalate or rescue HARS deficiency in a Charcot-Marie-Tooth disease model. Hum Mol Genet 2023; 32:810-824. [PMID: 36164730 PMCID: PMC9941834 DOI: 10.1093/hmg/ddac239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases are essential enzymes responsible for charging amino acids onto cognate tRNAs during protein synthesis. In histidyl-tRNA synthetase (HARS), autosomal dominant mutations V133F, V155G, Y330C and S356N in the HARS catalytic domain cause Charcot-Marie-Tooth disease type 2 W (CMT2W), while tRNA-binding domain mutation Y454S causes recessive Usher syndrome type IIIB. In a yeast model, all human HARS variants complemented a genomic deletion of the yeast ortholog HTS1 at high expression levels. CMT2W associated mutations, but not Y454S, resulted in reduced growth. We show mistranslation of histidine to glutamine and threonine in V155G and S356N but not Y330C mutants in yeast. Mistranslating V155G and S356N mutants lead to accumulation of insoluble proteins, which was rescued by histidine. Mutants V133F and Y330C showed the most significant growth defect and decreased HARS abundance in cells. Here, histidine supplementation led to insoluble protein aggregation and further reduced viability, indicating histidine toxicity associated with these mutants. V133F proteins displayed reduced thermal stability in vitro, which was rescued by tRNA. Our data will inform future treatment options for HARS patients, where histidine supplementation may either have a toxic or compensating effect depending on the nature of the causative HARS variant.
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Affiliation(s)
- Yi Qiu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rosan Kenana
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sarah D P Wilhelm
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sung Yuan Hsu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Victoria M Siu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Martin Duennwald
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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16
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Shi C, Murphy CT. piRNAs regulate a Hedgehog germline-to-soma pro-aging signal. NATURE AGING 2023; 3:47-63. [PMID: 37118518 PMCID: PMC10154208 DOI: 10.1038/s43587-022-00329-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2022] [Indexed: 04/30/2023]
Abstract
The reproductive system regulates somatic aging through competing anti- and pro-aging signals. Germline removal extends somatic lifespan through conserved pathways including insulin and mammalian target-of-rapamycin signaling, while germline hyperactivity shortens lifespan through unknown mechanisms. Here we show that mating-induced germline hyperactivity downregulates piRNAs, in turn desilencing their targets, including the Hedgehog-like ligand-encoding genes wrt-1 and wrt-10, ultimately causing somatic collapse and death. Germline-produced Hedgehog signals require PTR-6 and PTR-16 receptors for mating-induced shrinking and death. Our results reveal an unconventional role of the piRNA pathway in transcriptional regulation of Hedgehog signaling and a new role of Hedgehog signaling in the regulation of longevity and somatic maintenance: Hedgehog signaling is controlled by the tunable piRNA pathway to encode the previously unknown germline-to-soma pro-aging signal. Mating-induced piRNA downregulation in the germline and subsequent Hedgehog signaling to the soma enable the animal to tune somatic resource allocation to germline needs, optimizing reproductive timing and survival.
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Affiliation(s)
- Cheng Shi
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA.
| | - Coleen T Murphy
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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17
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Taguchi S, Suda Y, Irie K, Ozaki H. Automation of yeast spot assays using an affordable liquid handling robot. SLAS Technol 2022; 28:55-62. [PMID: 36503082 DOI: 10.1016/j.slast.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.
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18
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Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P. Tra1 controls the transcriptional landscape of the aging cell. G3 (BETHESDA, MD.) 2022; 13:6782959. [PMID: 36315064 PMCID: PMC9836359 DOI: 10.1093/g3journal/jkac287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
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Affiliation(s)
- Khaleda Afrin Bari
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Present address for Matthew D Berg: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada,Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Corresponding author: Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada.
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19
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Kuramata M, Abe T, Tanikawa H, Sugimoto K, Ishikawa S. A weak allele of OsNRAMP5 confers moderate cadmium uptake while avoiding manganese deficiency in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6475-6489. [PMID: 35788288 DOI: 10.1093/jxb/erac302] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Decreasing cadmium (Cd) concentrations in rice grains can effectively reduce potential risks to human health because rice is the major contributor to Cd intake in many diets. Among several genes involved in rice Cd accumulation, the loss of function of OsNRAMP5 is known to be effective in reducing grain concentration by inhibiting root uptake. However, disruption of this gene simultaneously decreases manganese (Mn) uptake because OsNRAMP5 is a major Mn transporter. With the aim of improving Mn uptake in OsNRAMP5 mutants while still restricting the grain Cd concentration below the upper limit of international standards, we identified a novel OsNRAMP5 allele encoding a protein in which glutamine (Q) at position 337 was replaced by lysine (K). The mutant carrying the OsNRAMP5-Q337K allele showed intermediate Cd and Mn accumulation between that of the wild-type and OsNRAMP5-knockout lines, and exhibited more resistance to Mn deficiency than the knockout lines. Different amino acid substitutions at position Q337 significantly affected the Cd and Mn transport activity in yeast cells, indicating that it is one of the crucial sites for OsNRAMP5 function. Our results suggest that the OsNRAMP5-Q337K allele might be useful for reducing grain Cd concentrations without causing severe Mn deficiency in rice cultivars through DNA marker-assisted breeding.
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Affiliation(s)
- Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Tadashi Abe
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | | | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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20
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Koike A, Becker F, Sennhenn P, Kim J, Zhang J, Hannus S, Brehm K. Targeting Echinococcus multilocularis PIM kinase for improving anti-parasitic chemotherapy. PLoS Negl Trop Dis 2022; 16:e0010483. [PMID: 36190997 PMCID: PMC9560627 DOI: 10.1371/journal.pntd.0010483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/13/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The potentially lethal zoonosis alveolar echinococcosis (AE) is caused by the metacestode larval stage of the tapeworm Echinococcus multilocularis. Current AE treatment options are limited and rely on surgery as well as on chemotherapy involving benzimidazoles (BZ). BZ treatment, however, is mostly parasitostatic only, must be given for prolonged time periods, and is associated with adverse side effects. Novel treatment options are thus urgently needed. METHODOLOGY/PRINCIPAL FINDINGS By applying a broad range of kinase inhibitors to E. multilocularis stem cell cultures we identified the proto-oncogene PIM kinase as a promising target for anti-AE chemotherapy. The gene encoding the respective E. multilocularis ortholog, EmPim, was characterized and in situ hybridization assays indicated its expression in parasite stem cells. By yeast two-hybrid assays we demonstrate interaction of EmPim with E. multilocularis CDC25, indicating an involvement of EmPim in parasite cell cycle regulation. Small molecule compounds SGI-1776 and CX-6258, originally found to effectively inhibit human PIM kinases, exhibited detrimental effects on in vitro cultured parasite metacestode vesicles and prevented the formation of mature vesicles from parasite stem cell cultures. To improve compound specificity for EmPim, we applied a high throughput in silico modelling approach, leading to the identification of compound Z196138710. When applied to in vitro cultured metacestode vesicles and parasite cell cultures, Z196138710 proved equally detrimental as SGI-1776 and CX-6258 but displayed significantly reduced toxicity towards human HEK293T and HepG2 cells. CONCLUSIONS/SIGNIFICANCE Repurposing of kinase inhibitors initially designed to affect mammalian kinases for helminth disease treatment is often hampered by adverse side effects of respective compounds on human cells. Here we demonstrate the utility of high throughput in silico approaches to design small molecule compounds of higher specificity for parasite cells. We propose EmPim as a promising target for respective approaches towards AE treatment.
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Affiliation(s)
- Akito Koike
- University of Würzburg, Institute of Hygiene and Microbiology, Consultant Laboratory for Echinococcosis, Würzburg, Germany
| | | | | | - Jason Kim
- Immuneering Corporation, Cambridge, Massachusetts, United States of America
| | - Jenny Zhang
- Immuneering Corporation, Cambridge, Massachusetts, United States of America
| | | | - Klaus Brehm
- University of Würzburg, Institute of Hygiene and Microbiology, Consultant Laboratory for Echinococcosis, Würzburg, Germany
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21
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Bairwa NK, Shoket H, Pandita M, Sharma M. A Simple Assay for the Detection of Late-Stage Apoptosis Features in Saccharomyces cerevisiae. Curr Protoc 2022; 2:e525. [PMID: 36069669 DOI: 10.1002/cpz1.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Unicellular eukaryotic organisms such as yeast and protozoa serve as useful models for studying the impact of chemicals on cell physiology, cellular growth, and genome duplication. The yeast Saccharomyces cerevisiae has been widely used to assess apoptosis induced by chemicals due to its genetic tractability, ease of evaluation, and readily available impact assessment tools. Apoptosis in S. cerevisiae is characterized by many features, including increased cell death, loss of membrane integrity, release of caspases, chromatin condensation, and nuclear fragmentation, which are similar to the ones observed in mammalian cells. Current methods of apoptosis assessment typically require specialized equipment and reagents, which limits wide adoption. Here, we describe a rapid, inexpensive, and easy-to-perform assay in yeast for the analysis of late-stage apoptotic features in cells treated with a chemical. We describe a protocol for assessing loss of cell survival and changes in the nucleus. We demonstrate the approach by using acetic acid and hydrogen peroxide as test chemicals. This assay for the study of late-stage apoptotic features in S. cerevisiae can be performed reliably and rapidly by any laboratory with basic equipment and may be extended for studying apoptosis in similar single-cell organisms after treatment with toxicological agents. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Culture of Saccharomyces cerevisiae, treatment with acetic acid or hydrogen peroxide, and semi-quantitative growth assay Basic Protocol 2: DAPI staining and fluorescence microscopy for the assessment of change in nucleus-to-cytoplasm ratio and nuclear integrity.
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Affiliation(s)
- Narendra K Bairwa
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Heena Shoket
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Monika Pandita
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Meenu Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
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22
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Imre A, Kovács R, Tóth Z, Majoros L, Benkő Z, Pfliegler WP, Pócsi I. Heme Oxygenase-1 ( HMX1) Loss of Function Increases the In-Host Fitness of the Saccharomyces 'boulardii' Probiotic Yeast in a Mouse Fungemia Model. J Fungi (Basel) 2022; 8:522. [PMID: 35628777 PMCID: PMC9146039 DOI: 10.3390/jof8050522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
The use of yeast-containing probiotics is on the rise; however, these products occasionally cause fungal infections and possibly even fungemia among susceptible probiotic-treated patients. The incidence of such cases is probably underestimated, which is why it is important to delve deeper into the pathomechanism and the adaptive features of S. ‘boulardii’. Here in this study, the potential role of the gene heme oxygenase-1 (HMX1) in probiotic yeast bloodstream-derived infections was studied by generating marker-free HMX1 deletion mutants with CRISPR/Cas9 technology from both commercial and clinical S. ‘boulardii’ isolates. The six commercial and clinical yeasts used here represented closely related but different genetic backgrounds as revealed by comparative genomic analysis. We compared the wild-type isolates against deletion mutants for their tolerance of iron starvation, hemolytic activity, as well as kidney burden in immunosuppressed BALB/c mice after lateral tail vein injection. Our results reveal that the lack of HMX1 in S. ‘boulardii’ significantly (p < 0.0001) increases the kidney burden of the mice in most genetic backgrounds, while at the same time causes decreased growth in iron-deprived media in vitro. These findings indicate that even a single-gene loss-of-function mutation can, surprisingly, cause elevated fitness in the host during an opportunistic systemic infection. Our findings indicate that the safety assessment of S. ‘boulardii’ strains should not only take strain-to-strain variation into account, but also avoid extrapolating in vitro results to in vivo virulence factor determination.
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Affiliation(s)
- Alexandra Imre
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (A.I.); (Z.B.); (W.P.P.)
- Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary
| | - Renátó Kovács
- Department of Medical Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (R.K.); (Z.T.); (L.M.)
- Faculty of Pharmacy, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary
| | - Zoltán Tóth
- Department of Medical Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (R.K.); (Z.T.); (L.M.)
| | - László Majoros
- Department of Medical Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (R.K.); (Z.T.); (L.M.)
| | - Zsigmond Benkő
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (A.I.); (Z.B.); (W.P.P.)
| | - Walter P. Pfliegler
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (A.I.); (Z.B.); (W.P.P.)
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1., H4032 Debrecen, Hungary; (A.I.); (Z.B.); (W.P.P.)
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Shoket H, Parvez S, Sharma M, Pandita M, Sharma V, Kumar P, Bairwa NK. Deletion of autophagy related, ATG1 and F-box motif encoding YDR131C, together, lead to synthetic growth defects and flocculation behavior in Saccharomyces cerevisiae. J Biochem Mol Toxicol 2022; 36:e23064. [PMID: 35385166 DOI: 10.1002/jbt.23064] [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: 03/16/2021] [Revised: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 11/09/2022]
Abstract
Ubiquitin proteasome system (UPS) and autophagy both pathways are involved in clearing the nonessential cellular components and also crosstalk during cellular response to normal and stress conditions. The F-box motif proteins constitute the SCF-E3 ligase complex of the UPS pathway in Saccharomyces cerevisiae and are involved in the substrate recruitment for ubiquitination. The ATG1 encoded Atg1p, a conserved serine-threonine kinase is crucial for the autophagy process. Here in this study, we report that loss of F-box motif encoding YDR131C and ATG1 together results in growth defects, floc formation, sensitivity to hydroxyurea, methyl methanesulfonate, and hydrogen peroxide. Both the genes also interact with the flocculation-related genes (FLO) and associate with gene ontology terms "ubiquitin-protein transferase activity" and "cellular catabolic process." Based on in silico analysis and experimental evidence we conclude that YDR131C and ATG1 function in parallel pathways to regulate the growth, flocculation, and stress response.
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Affiliation(s)
- Heena Shoket
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Sadia Parvez
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Meenu Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Monika Pandita
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Vishali Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Prabhat Kumar
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Narendra K Bairwa
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
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Thayale Purayil F, Sudalaimuthuasari N, Li L, Aljneibi R, Al Shamsi AMK, David N, Kottackal M, AlZaabi M, Balan J, Kurup SS, Hazzouri KM, Amiri KMA. Transcriptome Profiling and Functional Validation of RING-Type E3 Ligases in Halophyte Sesuvium verrucosum under Salinity Stress. Int J Mol Sci 2022; 23:ijms23052821. [PMID: 35269961 PMCID: PMC8911510 DOI: 10.3390/ijms23052821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/19/2022] Open
Abstract
Owing to their sessile nature, plants have developed a tapestry of molecular and physiological mechanisms to overcome diverse environmental challenges, including abiotic stresses. Adaptive radiation in certain lineages, such as Aizoaceae, enable their success in colonizing arid regions and is driven by evolutionary selection. Sesuvium verrucosum (commonly known as Western sea-purslane) is a highly salt-tolerant succulent halophyte belonging to the Aizoaceae family; thus, it provides us with the model-platform for studying plant adaptation to salt stress. Various transcriptional and translational mechanisms are employed by plants to cope with salt stress. One of the systems, namely, ubiquitin-mediated post-translational modification, plays a vital role in plant tolerance to abiotic stress and other biological process. E3 ligase plays a central role in target recognition and protein specificity in ubiquitin-mediated protein degradation. Here, we characterize E3 ligases in Sesuvium verrucosum from transcriptome analysis of roots in response to salinity stress. Our de novo transcriptome assembly results in 131,454 transcripts, and the completeness of transcriptome was confirmed by BUSCO analysis (99.3% of predicted plant-specific ortholog genes). Positive selection analysis shows 101 gene families under selection; these families are enriched for abiotic stress (e.g., osmotic and salt) responses and proteasomal ubiquitin-dependent protein catabolic processes. In total, 433 E3 ligase transcripts were identified in S. verrucosum; among these transcripts, single RING-type classes were more abundant compared to multi-subunit RING-type E3 ligases. Additionally, we compared the number of single RING-finger E3 ligases with ten different plant species, which confirmed the abundance of single RING-type E3 ligases in different plant species. In addition, differential expression analysis showed significant changes in 13 single RING-type E3 ligases (p-value < 0.05) under salinity stress. Furthermore, the functions of the selected E3 ligases genes (12 genes) were confirmed by yeast assay. Among them, nine genes conferred salt tolerance in transgenic yeast. This functional assay supports the possible involvement of these E3 ligase in salinity stress. Our results lay a foundation for translational research in glycophytes to develop stress tolerant crops.
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Affiliation(s)
- Fayas Thayale Purayil
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Ling Li
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Ruwan Aljneibi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Aysha Mohammed Khamis Al Shamsi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Nelson David
- Center for Genomics and Systems Biology, New York University, Abu-Dhabi P.O. Box 129188, United Arab Emirates;
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Mariam AlZaabi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Jithin Balan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
| | - Shyam S. Kurup
- Department of Integrative Agriculture, College of Food and Agriculture, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates;
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
- Correspondence: (K.M.H.); (K.M.A.A.); Tel.: +971-37135624 (K.M.A.A.)
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates; (F.T.P.); (N.S.); (L.L.); (R.A.); (A.M.K.A.S.); (M.K.); (M.A.); (J.B.)
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.); Tel.: +971-37135624 (K.M.A.A.)
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25
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Separovich RJ, Wong MW, Bartolec TK, Hamey JJ, Wilkins MR. Site-specific phosphorylation of histone H3K36 methyltransferase Set2p and demethylase Jhd1p is required for stress responses in Saccharomyces cerevisiae. J Mol Biol 2022; 434:167500. [DOI: 10.1016/j.jmb.2022.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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26
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Mi C, Zhang L, Huang G, Shao G, Yang F, You X, Dong MQ, Sun S, Sui SF. Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32. SCIENCE ADVANCES 2022; 8:eabi5603. [PMID: 35080977 PMCID: PMC8791620 DOI: 10.1126/sciadv.abi5603] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast. Here, we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle-shaped monomers, while the monomer in the apo state exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both core TRAPP/TRAPPI and Trs120 via its nucleotide-binding domain and binds with Trs31 via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII.
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Affiliation(s)
- Chenchen Mi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li Zhang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangcan Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fan Yang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin You
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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27
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Ngo V, Brickenden A, Liu H, Yeung C, Choy WY, Duennwald ML. A novel yeast model detects Nrf2 and Keap1 interactions with Hsp90. Dis Model Mech 2022; 15:274138. [PMID: 35088844 PMCID: PMC9016900 DOI: 10.1242/dmm.049258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/11/2022] [Indexed: 11/20/2022] Open
Abstract
Nrf2 is the master transcriptional regulator of cellular responses against oxidative stress. It is chiefly regulated by Keap1, a substrate adaptor protein that mediates Nrf2 degradation. Nrf2 activity is also influenced by many other protein interactions that provide Keap1-independent regulation. To study Nrf2 regulation, we established and characterized yeast models expressing human Nrf2 (also known as NFE2L2), Keap1 and other proteins that interact with and regulate Nrf2. Yeast models have been well established as powerful tools to study protein function and genetic and physical protein-protein interactions. In this work, we recapitulate previously described Nrf2 interactions in yeast and discover that Nrf2 interacts with the molecular chaperone Hsp90. Our work establishes yeast as a useful tool to study Nrf2 interactions and provides new insight into the crosstalk between the antioxidant response and the heat shock response. Summary: We studied the interactions of human Nrf2 in a novel budding yeast model. We recapitulate previously described Nrf2 interactions and discover that Nrf2 interacts with Hsp90, establishing yeast as a useful tool to study Nrf2 interactions.
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Affiliation(s)
- Vy Ngo
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Anne Brickenden
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Hansen Liu
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Cynthia Yeung
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Martin L Duennwald
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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28
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Ngo V, Karunatilleke NC, Brickenden A, Choy WY, Duennwald ML. Oxidative Stress-Induced Misfolding and Inclusion Formation of Nrf2 and Keap1. Antioxidants (Basel) 2022; 11:antiox11020243. [PMID: 35204126 PMCID: PMC8868093 DOI: 10.3390/antiox11020243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Cells that experience high levels of oxidative stress respond by inducing antioxidant proteins through activation of the protein transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2). Nrf2 is negatively regulated by the E3 ubiquitin ligase Kelch-like ECH-associated protein 1 (Keap1), which binds to Nrf2 to facilitate its ubiquitination and ensuing proteasomal degradation under basal conditions. Here, we studied protein folding and misfolding in Nrf2 and Keap1 in yeast, mammalian cells, and purified proteins under oxidative stress conditions. Both Nrf2 and Keap1 are susceptible to protein misfolding and inclusion formation upon oxidative stress. We propose that the intrinsically disordered regions within Nrf2 and the high cysteine content of Keap1 contribute to their oxidation and the ensuing misfolding. Our work reveals previously unexplored aspects of Nrf2 and Keap1 regulation and/or dysregulation by oxidation-induced protein misfolding.
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Affiliation(s)
- Vy Ngo
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada;
| | - Nadun C. Karunatilleke
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada; (N.C.K.); (A.B.); (W.-Y.C.)
| | - Anne Brickenden
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada; (N.C.K.); (A.B.); (W.-Y.C.)
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada; (N.C.K.); (A.B.); (W.-Y.C.)
| | - Martin L. Duennwald
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada
- Correspondence:
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29
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Abstract
The use of DNA barcodes for determining changes in genotype frequencies has been instrumental to increase the scale at which we can phenotype strain libraries by using next-generation sequencing technologies. Here, we describe the determination of strain fitness for thousands of yeast strains simultaneously in a single assay using recent innovations that increase the precision of these measurements, such as the inclusion of unique-molecular identifiers (UMIs) and purification by solid-phase reverse immobilization (SPRI) beads.
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Affiliation(s)
- Claire A Chochinov
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Alex N Nguyen Ba
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON, Canada.
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30
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Jethmalani Y, Tran K, Negesse MY, Sun W, Ramos M, Jaiswal D, Jezek M, Amos S, Garcia EJ, Park D, Green EM. Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres. Life Sci Alliance 2021; 4:e202101126. [PMID: 34625508 PMCID: PMC8507492 DOI: 10.26508/lsa.202101126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
The yeast chromatin protein Set4 is a member of the Set3-subfamily of SET domain proteins which play critical roles in the regulation of gene expression in diverse developmental and environmental contexts. We previously reported that Set4 promotes survival during oxidative stress and regulates expression of stress response genes via stress-dependent chromatin localization. In this study, global gene expression analysis and investigation of histone modification status identified a role for Set4 in maintaining gene repressive mechanisms within yeast subtelomeres under both normal and stress conditions. We show that Set4 works in a partially overlapping pathway to the SIR complex and the histone deacetylase Rpd3 to maintain proper levels of histone acetylation and expression of stress response genes encoded in subtelomeres. This role for Set4 is particularly critical for cells under hypoxic conditions, where the loss of Set4 decreases cell fitness and cell wall integrity. These findings uncover a new regulator of subtelomeric chromatin that is key to stress defense pathways and demonstrate a function for Set4 in regulating repressive, heterochromatin-like environments.
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Affiliation(s)
- Yogita Jethmalani
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Khoa Tran
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Maraki Y Negesse
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Winny Sun
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Mark Ramos
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Deepika Jaiswal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Shandon Amos
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Eric Joshua Garcia
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - DoHwan Park
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
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31
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Sharma M, Verma V, Bairwa NK. Genetic interaction between RLM1 and F-box motif encoding gene SAF1 contributes to stress response in Saccharomyces cerevisiae. Genes Environ 2021; 43:45. [PMID: 34627408 PMCID: PMC8501602 DOI: 10.1186/s41021-021-00218-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stress response is mediated by the transcription of stress-responsive genes. The F-box motif protein Saf1p is involved in SCF-E3 ligase mediated degradation of the adenine deaminase, Aah1p upon nutrient stress. The four transcription regulators, BUR6, MED6, SPT10, SUA7, are listed for SAF1 in the genome database of Saccharomyces cerevisiae. Here in this study, we carried out an in-silico analysis of gene expression and transcription factor databases to understand the regulation of SAF1 expression during stress for hypothesis and experimental analysis. RESULT An analysis of the GEO profile database indicated an increase in SAF1 expression when cells were treated with stress agents such as Clioquinol, Pterostilbene, Gentamicin, Hypoxia, Genotoxic, desiccation, and heat. The increase in expression of SAF1 during stress conditions correlated positively with the expression of RLM1, encoding the Rlm1p transcription factor. The expression of AAH1 encoding Aah1p, a Saf1p substrate for ubiquitination, appeared to be negatively correlated with the expression of RLM1 as revealed by an analysis of the Yeastract expression database. Based on analysis of expression profile and regulatory association of SAF1 and RLM1, we hypothesized that inactivation of both the genes together may contribute to stress tolerance. The experimental analysis of cellular growth response of cells lacking both SAF1 and RLM1 to selected stress agents such as cell wall and osmo-stressors, by spot assay indicated stress tolerance phenotype similar to parental strain however sensitivity to genotoxic and microtubule depolymerizing stress agents. CONCLUSIONS Based on in-silico and experimental data we suggest that SAF1 and RLM1 both interact genetically in differential response to genotoxic and general stressors.
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Affiliation(s)
- Meenu Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, 182320, India
| | - V Verma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, 182320, India
| | - Narendra K Bairwa
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, 182320, India.
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32
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Novačić A, Šupljika N, Bekavac N, Žunar B, Stuparević I. Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast. Microbiol Spectr 2021; 9:e0029521. [PMID: 34259554 PMCID: PMC8552689 DOI: 10.1128/spectrum.00295-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/18/2021] [Indexed: 11/20/2022] Open
Abstract
Yeast cell wall stability is important for cell division and survival under stress conditions. The expression of cell-wall-related proteins is regulated by several pathways involving RNA-binding proteins and RNases. The multiprotein RNA exosome complex provides the 3'→5' exoribonuclease activity that is critical for maintaining the stability and integrity of the yeast cell wall under stress conditions such as high temperatures. In this work, we show that the temperature sensitivity of RNA exosome mutants is most pronounced in the W303 genetic background due to the nonfunctional ssd1-d allele. This gene encodes the RNA-binding protein Ssd1, which is involved in the posttranscriptional regulation of cell-wall-related genes. Expression of the functional SSD1-V allele from its native genomic locus or from a centromeric plasmid suppresses the growth defects and aberrant morphology of RNA exosome mutant cells at high temperatures or upon treatment with cell wall stressors. Moreover, combined inactivation of the RNA exosome catalytic subunit Rrp6 and Ssd1 results in a synthetically sick phenotype of cell wall instability, as these proteins may function in parallel pathways (i.e., via different mRNA targets) to maintain cell wall stability. IMPORTANCE Stressful conditions such as high temperatures can compromise cellular integrity and cause bursting. In microorganisms surrounded by a cell wall, such as yeast, the cell wall is the primary shield that protects cells from environmental stress. Therefore, remodeling its structure requires inputs from multiple signaling pathways and regulators. In this work, we identify the interplay of the RNA exosome complex and the RNA-binding protein Ssd1 as an important factor in the yeast cell wall stress response. These proteins operate in independent pathways to support yeast cell wall stability. This work highlights the contribution of RNA-binding proteins in the regulation of yeast cell wall structure, providing new insights into yeast physiology.
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Affiliation(s)
- Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nada Šupljika
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nikša Bekavac
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Bojan Žunar
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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33
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Lin LTW, Razzaq A, Di Gregorio SE, Hong S, Charles B, Lopes MH, Beraldo F, Prado VF, Prado MAM, Duennwald ML. Hsp90 and its co-chaperone Sti1 control TDP-43 misfolding and toxicity. FASEB J 2021; 35:e21594. [PMID: 33908654 DOI: 10.1096/fj.202002645r] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/14/2022]
Abstract
Protein misfolding is a central feature of most neurodegenerative diseases. Molecular chaperones can modulate the toxicity associated with protein misfolding, but it remains elusive which molecular chaperones and co-chaperones interact with specific misfolded proteins. TDP-43 misfolding and inclusion formation are a hallmark of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. Using yeast and mammalian neuronal cells we find that Hsp90 and its co-chaperone Sti1 have the capacity to alter TDP-43 misfolding, inclusion formation, aggregation, and cellular toxicity. Our data also demonstrate that impaired Hsp90 function sensitizes cells to TDP-43 toxicity and that Sti1 specifically interacts with and strongly modulates TDP-43 toxicity in a dose-dependent manner. Our study thus uncovers a previously unrecognized tie between Hsp90, Sti1, TDP-43 misfolding, and cellular toxicity.
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Affiliation(s)
- Lilian Tsai-Wei Lin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Abdul Razzaq
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Sonja E Di Gregorio
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Soojie Hong
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Brendan Charles
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Marilene H Lopes
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Flavio Beraldo
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Vania F Prado
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Marco A M Prado
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Martin L Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
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