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Conacher CG, Watson BW, Bauer FF. Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community. FEMS Microbiol Ecol 2024; 100:fiae080. [PMID: 38777744 PMCID: PMC11212668 DOI: 10.1093/femsec/fiae080] [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: 01/23/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
Microbial communities are vital to our lives, yet their ecological functioning and dynamics remain poorly understood. This understanding is crucial for assessing threats to these systems and leveraging their biotechnological applications. Given that temporal dynamics are linked to community functioning, this study investigated the drivers of community succession in the wine yeast community. We experimentally generated population dynamics data and used it to create an interpretable model with a gradient boosted regression tree approach. The model was trained on temporal data of viable species populations in various combinations, including pairs, triplets, and quadruplets, and was evaluated for predictive accuracy and input feature importance. Key findings revealed that the inoculation dosage of non-Saccharomyces species significantly influences their performance in mixed cultures, while Saccharomyces cerevisiae consistently dominates regardless of initial abundance. Additionally, we observed multispecies interactions where the dynamics of Wickerhamomyces anomalus were influenced by Torulaspora delbrueckii in pairwise cultures, but this interaction was altered by the inclusion of S. cerevisiae. This study provides insights into yeast community succession and offers valuable machine learning-based analysis techniques applicable to other microbial communities, opening new avenues for harnessing microbial communities.
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Affiliation(s)
- Cleo Gertrud Conacher
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa
- Centre for Artificial Intelligence Research (CAIR), School for Data-Science & Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Bruce William Watson
- Centre for Artificial Intelligence Research (CAIR), School for Data-Science & Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Florian Franz Bauer
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa
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2
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Manzoor Y, Aouida M, Ramadoss R, Moovarkumudalvan B, Ahmed N, Sulaiman AA, Mohanty A, Ali R, Mifsud B, Ramotar D. Loss of the yeast transporter Agp2 upregulates the pleiotropic drug-resistant pump Pdr5 and confers resistance to the protein synthesis inhibitor cycloheximide. PLoS One 2024; 19:e0303747. [PMID: 38776347 PMCID: PMC11111045 DOI: 10.1371/journal.pone.0303747] [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: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/24/2024] Open
Abstract
The transmembrane protein Agp2, initially shown as a transporter of L-carnitine, mediates the high-affinity transport of polyamines and the anticancer drug bleomycin-A5. Cells lacking Agp2 are hyper-resistant to polyamine and bleomycin-A5. In these earlier studies, we showed that the protein synthesis inhibitor cycloheximide blocked the uptake of bleomycin-A5 into the cells suggesting that the drug uptake system may require de novo synthesis. However, our recent findings demonstrated that cycloheximide, instead, induced rapid degradation of Agp2, and in the absence of Agp2 cells are resistant to cycloheximide. These observations raised the possibility that the degradation of Agp2 may allow the cell to alter its drug resistance network to combat the toxic effects of cycloheximide. In this study, we show that membrane extracts from agp2Δ mutants accentuated several proteins that were differentially expressed in comparison to the parent. Mass spectrometry analysis of the membrane extracts uncovered the pleiotropic drug efflux pump, Pdr5, involved in the efflux of cycloheximide, as a key protein upregulated in the agp2Δ mutant. Moreover, a global gene expression analysis revealed that 322 genes were differentially affected in the agp2Δ mutant versus the parent, including the prominent PDR5 gene and genes required for mitochondrial function. We further show that Agp2 is associated with the upstream region of the PDR5 gene, leading to the hypothesis that cycloheximide resistance displayed by the agp2Δ mutant is due to the derepression of the PDR5 gene.
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Affiliation(s)
- Yusra Manzoor
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ramya Ramadoss
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
| | - Balasubramanian Moovarkumudalvan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Nisar Ahmed
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Abdallah Alhaj Sulaiman
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ashima Mohanty
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Reem Ali
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Borbala Mifsud
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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3
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Lian F, Yang H, Hong R, Xu H, Yu T, Sun G, Zheng G, Xie B. Evaluation of the antitumor effect of neoantigen peptide vaccines derived from the translatome of lung cancer. Cancer Immunol Immunother 2024; 73:129. [PMID: 38744688 PMCID: PMC11093939 DOI: 10.1007/s00262-024-03670-0] [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: 11/27/2023] [Accepted: 03/08/2024] [Indexed: 05/16/2024]
Abstract
Emerging evidence suggests that tumor-specific neoantigens are ideal targets for cancer immunotherapy. However, how to predict tumor neoantigens based on translatome data remains obscure. Through the extraction of ribosome-nascent chain complexes (RNCs) from LLC cells, followed by RNC-mRNA extraction, RNC-mRNA sequencing, and comprehensive bioinformatic analysis, we successfully identified proteins undergoing translatome and exhibiting mutations in the cells. Subsequently, novel antigens identification was analyzed by the interaction between their high affinity and the Major Histocompatibility Complex (MHC). Neoantigens immunogenicity was analyzed by enzyme-linked immunospot assay (ELISpot). Finally, in vivo experiments in mice were conducted to evaluate the antitumor effects of translatome-derived neoantigen peptides on lung cancer. The results showed that ten neoantigen peptides were identified and synthesized by translatome data from LLC cells; 8 out of the 10 neoantigens had strong immunogenicity. The neoantigen peptide vaccine group exhibited significant tumor growth inhibition effect. In conclusion, neoantigen peptide vaccine derived from the translatome of lung cancer exhibited significant tumor growth inhibition effect.
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Affiliation(s)
- Fenbao Lian
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Haitao Yang
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Rujun Hong
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Hang Xu
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China
| | - Tingting Yu
- Department of Thoracic Oncology, The Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Gang Sun
- Department of Breast and Thyroid Surgery, The Affiliated Tumor Hospital of Xinjiang Medical University, 789 East Suzhou Street, Xinshi District, Urumqi, 830011, Xinjiang, China.
- Xinjiang Cancer Center/Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, Xinjiang, China.
| | - Guanying Zheng
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China.
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China.
| | - Baosong Xie
- Shengli Clinical Medical College, Fujian Medical University, No. 134 East Street, Fuzhou City, 350001, Fujian Province, China.
- Department of Respiratory Medicine and Critical Care Medicine, Fujian Provincial Hospital, No. 134 East Street, Fuzhou, 350001, China.
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Dean B, Scarr E. Common changes in rat cortical gene expression after antidepressant drug treatment: Impacts on metabolism of polyamines, mRNA splicing, regulation of RAS by GAPs, neddylation and GPCR ligand binding. World J Biol Psychiatry 2024; 25:200-213. [PMID: 38349617 DOI: 10.1080/15622975.2024.2312475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/27/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVES This study sought to identify pathways affected by rat cortical RNA that were changed after treatment with fluoxetine or imipramine. METHODS We measured levels of cortical RNA in male rats using GeneChip® Rat Exon 1.0 ST Array after treatment with vehicle (0.9% NaCl), fluoxetine (10 mg/kg/day) or imipramine (20 mg/kg/day) for 28 days. Levels of coding and non-coding RNA in vehicle treated rats were compared to those in treated rats using ANOVA in JMP Genomics 13 and the Panther Gene Ontology Classification System was used to identify pathways involving the changed RNAs. RESULTS 18,876 transcripts were detected; there were highly correlated changes in 1010 levels of RNA after both drug treatments that would principally affect the metabolism of polyamines, mRNA splicing, regulation of RAS by GAPs, neddylation and GPCR ligand binding. Using our previously published data, we compared changes in transcripts after treatment with antipsychotic and mood stabilising drugs. CONCLUSIONS Our study shows there are common, correlated, changes in coding and non-coding RNA in the rat cortex after treatment with fluoxetine or imipramine; we propose the pathways affected by these changes are involved in the therapeutic mechanisms of action of antidepressant drugs.
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Affiliation(s)
- Brian Dean
- The Molecular Psychiatry Laboratory, The Florey Institute for Neuroscience and Mental Health, Parkville, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Australia
| | - Elizabeth Scarr
- The Department of Psychiatry, The University of Melbourne, Parkville, Australia
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5
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Soto JS, Jami-Alahmadi Y, Wohlschlegel JA, Khakh BS. In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation. Nat Protoc 2024; 19:896-927. [PMID: 38062165 DOI: 10.1038/s41596-023-00923-7] [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: 08/03/2023] [Accepted: 10/03/2023] [Indexed: 02/08/2024]
Abstract
The central nervous system (CNS) comprises diverse and morphologically complex cells. To understand the molecular basis of their physiology, it is crucial to assess proteins expressed within intact cells. Commonly used methods utilize cell dissociation and sorting to isolate specific cell types such as neurons and astrocytes, the major CNS cells. Proteins purified from isolated cells are identified by mass spectrometry-based proteomics. However, dissociation and cell-sorting methods lead to near total loss of cellular morphology, thereby losing proteins from key relevant subcompartments such as processes, end feet, dendrites and axons. Here we provide a systematic protocol for cell- and subcompartment-specific labeling and identification of proteins found within intact astrocytes and neurons in vivo. This protocol utilizes the proximity-dependent biotinylation system BioID2, selectively expressed in either astrocytes or neurons, to label proximal proteins in a cell-specific manner. BioID2 is targeted genetically to assess the subproteomes of subcellular compartments such as the plasma membrane and sites of cell-cell contacts. We describe in detail the expression methods (variable timing), stereotaxic surgeries for expression (1-2 d and then 3 weeks), in vivo protein labeling (7 d), protein isolation (2-3 d), protein identification methods (2-3 d) and data analysis (1 week). The protocol can be applied to any area of the CNS in mouse models of physiological processes and for disease-related research.
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Affiliation(s)
- Joselyn S Soto
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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6
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Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
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Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
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7
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De Zoysa T, Hauke AC, Iyer NR, Marcus E, Ostrowski SM, Stegemann F, Ermolenko DN, Fay JC, Phizicky EM. A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay. PLoS Genet 2024; 20:e1011146. [PMID: 38295128 PMCID: PMC10861057 DOI: 10.1371/journal.pgen.1011146] [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: 09/18/2023] [Revised: 02/12/2024] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
tRNA modifications are crucial in all organisms to ensure tRNA folding and stability, and accurate translation. In both the yeast Saccharomyces cerevisiae and the evolutionarily distant yeast Schizosaccharomyces pombe, mutants lacking certain tRNA body modifications (outside the anticodon loop) are temperature sensitive due to rapid tRNA decay (RTD) of a subset of hypomodified tRNAs. Here we show that for each of two S. pombe mutants subject to RTD, mutations in ribosomal protein genes suppress the temperature sensitivity without altering tRNA levels. Prior work showed that S. pombe trm8Δ mutants, lacking 7-methylguanosine, were temperature sensitive due to RTD, and that one class of suppressors had mutations in the general amino acid control (GAAC) pathway, which was activated concomitant with RTD, resulting in further tRNA loss. We now find that another class of S. pombe trm8Δ suppressors have mutations in rpl genes, encoding 60S subunit proteins, and that suppression occurs with minimal restoration of tRNA levels and reduced GAAC activation. Furthermore, trm8Δ suppression extends to other mutations in the large or small ribosomal subunit. We also find that S. pombe tan1Δ mutants, lacking 4-acetylcytidine, are temperature sensitive due to RTD, that one class of suppressors have rpl mutations, associated with minimal restoration of tRNA levels, and that suppression extends to other rpl and rps mutations. However, although S. pombe tan1Δ temperature sensitivity is associated with some GAAC activation, suppression by an rpl mutation only modestly inhibits GAAC activation. We propose a model in which ribosomal protein mutations result in reduced ribosome concentrations, leading to both reduced ribosome collisions and a reduced requirement for tRNA, with these effects having different relative importance in trm8Δ and tan1Δ mutants. This model is consistent with our results in S. cerevisiae trm8Δ trm4Δ mutants, known to undergo RTD, fueling speculation that this model applies across eukaryotes.
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Affiliation(s)
- Thareendra De Zoysa
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Alayna C. Hauke
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Nivedita R. Iyer
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Erin Marcus
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Sarah M. Ostrowski
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Franziska Stegemann
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Dmitri N. Ermolenko
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Justin C. Fay
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
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8
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Wang Z, Liu M, Ai Y, Zheng S, Chen Y, Du H, Yuan S, Guo X, Yuan Y, Li G, Song J, Deng C. The compound artemisinin-hydroxychloroquine ameliorates bleomycin-induced pulmonary fibrosis in rats by inhibiting TGF-β1/Smad2/3 signaling pathway. Pulm Pharmacol Ther 2023; 83:102268. [PMID: 37967761 DOI: 10.1016/j.pupt.2023.102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/27/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Pulmonary fibrosis (PF) is a lethal disease characterized by a progressive decline in lung function. Currently, lung transplantation remains the only available treatment for PF. However, both artemisinin (ART) and hydroxychloroquine (HCQ) possess potential antifibrotic properties. This study aimed to investigate the effects and mechanisms of a compound known as Artemisinin-Hydroxychloroquine (AH) in treating PF, specifically by targeting the TGF-β1/Smad2/3 pathway. To do this, we utilized an animal model of PF induced by a single tracheal drip of bleomycin (BLM) in Sprague-Dawley (SD) rats. The PF animal models were administered various doses of AH, and the efficacy and safety of AH were evaluated through pulmonary function testing, blood routine tests, serum biochemistry tests, organ index measurements, and pathological examinations. Additionally, Elisa, western blotting, and qPCR techniques were employed to explore the potential molecular mechanisms of AH in treating PF. Our findings reveal that AH effectively and safely alleviate PF by inhibiting BLM-induced specific inflammation, reducing extracellular matrix (ECM) deposition, and interfering with the TGF-β1/Smad2/3 signaling pathway. Notably, the windfall for this study is that the inhibition of ECM may initiate self-healing in the BLM-induced PF animal model. In conclusion, AH shows promise as a potential therapeutic drug for PF, as it inhibits disease progression through the TGF-β1/Smad2/3 signaling pathway.
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Affiliation(s)
- Zhaojia Wang
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Min Liu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Shaoqin Zheng
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China; Institute of Science and Technology, Guangzhou University of Chinese Medicine, 26 Chentai Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Yingyi Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Hujun Du
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Shijia Yuan
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Xueying Guo
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Yueming Yuan
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China; Institute of Science and Technology, Guangzhou University of Chinese Medicine, 26 Chentai Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Guoming Li
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Jianping Song
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China
| | - Changsheng Deng
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Airport Road, Baiyun District, Guangzhou, 510080, People's Republic of China.
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9
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Chaithanya KV, Sinha H. MKT1 alleles regulate stress responses through posttranscriptional modulation of Puf3 targets in budding yeast. Yeast 2023; 40:616-627. [PMID: 37990816 DOI: 10.1002/yea.3908] [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: 06/29/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 11/23/2023] Open
Abstract
MKT1 is a pleiotropic stress response gene identified by several quantitative trait studies with MKT189G as a causal variant, contributing to growth advantage in multiple stress environments. MKT1 has been shown to regulate HO endonuclease posttranscriptionally via the Pbp1-Pab1 complex. RNA-binding protein Puf3 modulates a set of nuclear-encoded mitochondrial transcripts whose expression was found to be affected by MKT1 alleles. This study attempts to relate the MKT1 allele-derived growth advantage with the stability of Puf3 targets during stress and elucidate the roles of Pbp1 and Puf3 in this mechanism. Our results showed that the growth advantage of the MKT189G allele in cycloheximide and H2 O2 was PBP1-dependent, whereas in 4-nitroquinoline 1-oxide, the growth advantage was dependent on both PUF3 and PBP1. We compared the messenger RNA decay kinetics of a set of Puf3 targets in multiple stress environments to understand the allele-specific regulation by MKT1. In oxidative stress, the MKT189G allele modulated the differential expression of nuclear-encoded mitochondrial genes in a PBP1- and PUF3-dependent manner. Additionally, MKT189G stabilised Puf3 targets, namely, COX17, MRS1 and RDL2, in an allele and stress-specific manner. Our results showed that COX17, MRS1 and RDL2 had a stress-specific response in stress environments, with the MKT189G allele contributing to better growth; this response was both PBP1- and PUF3-dependent. Our results indicate that the common allele, MKT189G , regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain's better growth in stress environments.
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Affiliation(s)
- Koppisetty Viswa Chaithanya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, Tamil Nadu, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, Tamil Nadu, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, Tamil Nadu, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, Tamil Nadu, India
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10
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Westbrook ER, Ford HZ, Antolović V, Chubb JR. Clearing the slate: RNA turnover to enable cell state switching? Development 2023; 150:dev202084. [PMID: 37831057 PMCID: PMC10617622 DOI: 10.1242/dev.202084] [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] [Indexed: 10/13/2023]
Abstract
The distribution of mRNA in tissue is determined by the balance between transcription and decay. Understanding the control of RNA decay during development has been somewhat neglected compared with transcriptional control. Here, we explore the potential for mRNA decay to trigger rapid cell state transitions during development, comparing a bistable switch model of cell state conversion with experimental evidence from different developmental systems. We also consider another potential role for large-scale RNA decay that has emerged from studies of stress-induced cell state transitions, in which removal of mRNA unblocks the translation machinery to prioritise the synthesis of proteins that establish the new cell state.
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Affiliation(s)
- Elizabeth R. Westbrook
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Hugh Z. Ford
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Vlatka Antolović
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jonathan R. Chubb
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
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11
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Elías-Llumbet A, Tian Y, Reyes-San-Martin C, Reina-Mahecha A, Damle V, Morita A, van der Veen HC, Sharma PK, Sandovici M, Mzyk A, Schirhagl R. Quantum Sensing for Real-Time Monitoring of Drug Efficacy in Synovial Fluid from Arthritis Patients. NANO LETTERS 2023; 23:8406-8410. [PMID: 37676737 PMCID: PMC10540259 DOI: 10.1021/acs.nanolett.3c01506] [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: 04/21/2023] [Revised: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Diamond-based T1 relaxometry is a new technique that allows nanoscale magnetic resonance measurements. Here we present its first application in patient samples. More specifically, we demonstrate that relaxometry can determine the free radical load in samples from arthritis patients. We found that we can clearly differentiate between osteoarthritis and rheumatoid arthritis patients in both the synovial fluid itself and cells derived from it. Furthermore, we tested how synovial fluid and its cells respond to piroxicam, a common nonsteroidal anti-inflammatory drug (NSAID). It is known that this drug leads to a reduction in reactive oxygen species production in fibroblast-like synoviocytes (FLS). Here, we investigated the formation of free radicals specifically. While FLS from osteoarthritis patients showed a drastic decrease in the free radical load, cells from rheumatoid arthritis retained a similar radical load after treatment. This offers a possible explanation for why piroxicam is more beneficial for patients with osteoarthritis than those with rheumatoid arthritis.
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Affiliation(s)
- Arturo Elías-Llumbet
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
- Laboratory
of Genomic of Germ Cells, Biomedical Sciences Institute, Faculty of
Medicine, University of Chile, 1027 Independencia, Santiago, Chile
| | - Yuchen Tian
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Claudia Reyes-San-Martin
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Alejandro Reina-Mahecha
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Viraj Damle
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Aryan Morita
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Hugo C. van der Veen
- Department
of Orthopaedic Surgery, University of Groningen,
University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Prashant K. Sharma
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Maria Sandovici
- Department
of Rheumatology and Clinical Immunology, University Medical Center Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
| | - Aldona Mzyk
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
- Institute
of Metallurgy and Materials Science, Polish
Academy of Sciences, Reymonta 25, 30-059 Cracow, Poland
| | - Romana Schirhagl
- Department
of Biomedical Engineering, University of
Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW Groningen, The Netherlands
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12
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Decoupling of mRNA and Protein Expression in Aging Brains Reveals the Age-Dependent Adaptation of Specific Gene Subsets. Cells 2023; 12:cells12040615. [PMID: 36831282 PMCID: PMC9954025 DOI: 10.3390/cells12040615] [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: 01/26/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
During aging, changes in gene expression are associated with a decline in physical and cognitive abilities. Here, we investigate the connection between changes in mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that an increase in mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex, where we also observed an increase in cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post- transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, and also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.
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13
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [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: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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14
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Integrative analysis of differentially expressed mRNAs and proteins induced by PGC-1β in breast cancer cells. Biochem Biophys Res Commun 2022; 637:73-82. [DOI: 10.1016/j.bbrc.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
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15
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Heat-Induced Proteotoxic Stress Response in Placenta-Derived Stem Cells (PDSCs) Is Mediated through HSPA1A and HSPA1B with a Potential Higher Role for HSPA1B. Curr Issues Mol Biol 2022; 44:4748-4768. [PMID: 36286039 PMCID: PMC9600182 DOI: 10.3390/cimb44100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Placenta-derived stem cells (PDSCs), due to unique traits such as mesenchymal and embryonic characteristics and the absence of ethical constraints, are in a clinically and therapeutically advantageous position. To aid in stemness maintenance, counter pathophysiological stresses, and withstand post-differentiation challenges, stem cells require elevated protein synthesis and consequently augmented proteostasis. Stem cells exhibit source-specific proteostasis traits, making it imperative to study them individually from different sources. These studies have implications for understanding stem cell biology and exploitation in the augmentation of therapeutic applications. Here, we aim to identify the primary determinants of proteotoxic stress response in PDSCs. We generated heat-induced dose-responsive proteotoxic stress models of three stem cell types: placental origin cells, the placenta-derived mesenchymal stem cells (pMSCs), maternal origin cells, the decidua parietalis mesenchymal stem cells (DPMSCs), and the maternal–fetal interface cells, decidua basalis mesenchymal stem cells (DBMSCs), and measured stress induction through biochemical and cell proliferation assays. RT-PCR array analysis of 84 genes involved in protein folding and protein quality control led to the identification of Hsp70 members HSPA1A and HSPA1B as the prominent ones among 17 significantly expressed genes and with further analysis at the protein level through Western blotting. A kinetic analysis of HSPA1A and HSPA1B gene and protein expression allowed a time series evaluation of stress response. As identified by protein expression, an active stress response is in play even at 24 h. More prominent differences in expression between the two homologs are detected at the translational level, alluding to a potential higher requirement for HSPA1B during proteotoxic stress response in PDSCs.
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16
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Hernández-Elvira M, Sunnerhagen P. Post-transcriptional regulation during stress. FEMS Yeast Res 2022; 22:6585650. [PMID: 35561747 PMCID: PMC9246287 DOI: 10.1093/femsyr/foac025] [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: 12/22/2021] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
To remain competitive, cells exposed to stress of varying duration, rapidity of onset, and intensity, have to balance their expenditure on growth and proliferation versus stress protection. To a large degree dependent on the time scale of stress exposure, the different levels of gene expression control: transcriptional, post-transcriptional and post-translational, will be engaged in stress responses. The post-transcriptional level is appropriate for minute-scale responses to transient stress, and for recovery upon return to normal conditions. The turnover rate, translational activity, covalent modifications, and subcellular localisation of RNA species are regulated under stress by multiple cellular pathways. The interplay between these pathways is required to achieve the appropriate signalling intensity and prevent undue triggering of stress-activated pathways at low stress levels, avoid overshoot, and down-regulate the response in a timely fashion. As much of our understanding of post-transcriptional regulation has been gained in yeast, this review is written with a yeast bias, but attempts to generalise to other eukaryotes. It summarises aspects of how post-transcriptional events in eukaryotes mitigate short-term environmental stresses, and how different pathways interact to optimise the stress response under shifting external conditions.
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Affiliation(s)
- Mariana Hernández-Elvira
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
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17
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Acidic and Alkaline Conditions Affect the Growth of Tree Peony Plants via Altering Photosynthetic Characteristics, Limiting Nutrient Assimilation, and Impairing ROS Balance. Int J Mol Sci 2022; 23:ijms23095094. [PMID: 35563483 PMCID: PMC9099645 DOI: 10.3390/ijms23095094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 12/04/2022] Open
Abstract
Exposure to acidic and alkaline conditions were found to cause the excess accumulation of reactive oxygen species in tree peony, thereby causing damage and inhibiting plant growth and development. The activities of antioxidant enzymes were also found to be significantly up-regulated, especially under alkaline conditions; this explained why tree peony is better adapted to alkaline than to acidic conditions. Through pairwise comparisons, 144 differentially expressed genes (DEGs) associated with plant growth, photosynthesis, and stress were identified. The DEGs related to stress were up-regulated, whereas the remaining DEGs were almost all down-regulated after acid and alkaline treatments. The nutrient assimilation was greatly inhibited. Chlorophyll synthesis genes were suppressed, and chlorophyll content was reduced. The development and structures of stomata and chloroplasts and the transcription of related genes were also influenced. Among photosynthesis-related DEGs, electron transport chains were the most sensitive. The suppressed expression of photosynthesis genes and the reduced light-harvesting capacity, together with the impairment of chloroplasts and stomata, finally led to a sharp decrease in the net photosynthetic rate. Carbohydrate accumulation and plant biomass were also reduced. The present study provides a theoretical basis for the response mechanisms of tree peony to adverse pH conditions and enriches knowledge of plant adaptation to alkaline conditions.
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18
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Choi EJ, Kim CH, Yoon JY, Kim JY, Kim HS, Yoon JU, Cho AR, Kim EJ. Propofol attenuates odontogenic/osteogenic differentiation of human dental pulp stem cells in vitro. J Dent Sci 2022; 17:1604-1611. [PMID: 36299329 PMCID: PMC9588817 DOI: 10.1016/j.jds.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/07/2022] [Indexed: 11/11/2022] Open
Abstract
Background/purpose Various studies have used stem cells in the field of bone tissue engineering to repair bone defects. Dental pulp stem cells (DPSCs) have multipotent properties and can be acquired in a noninvasive manner; therefore, they are frequently used in experiments in regenerative medicine. The objective of this study was to investigate the odontogenic/osteogenic differentiation of human DPSCs (hDPSCs) using propofol, a widely used intravenous anesthetic agent. Materials and methods Alkaline phosphatase (ALP) staining was used to investigate the effects of various concentrations of propofol (5, 20, 50 and 100 μM) on the osteogenic differentiation of hDPSCs. Real-time qPCR and Western blot analysis were used to detect the effect of propofol on the expression of odontogenic/osteogenic genes, such as DMP1, RUNX2, OCN, and BMP2. Odontogenic/osteogenic differentiation of hDPSCs was estimated at days 7 and 14. Results ALP staining of hDPSCs was significantly decreased by propofol treatment. The mRNA expression of DMP1, RUNX2, OCN, and BMP2 decreased after propofol treatment for 14 days. The protein expression of DMP1 and BMP2 was decreased by propofol at days 7 and 14, and that of RUNX2 was decreased by propofol at day 14 only. Conclusion Propofol attenuated odontogenic/osteogenic differentiation of hDPSCs in vitro. This result suggests that propofol, which is widely used for dental sedation, may inhibit the odontogenic/osteogenic differentiation of hDPSCs.
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19
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Tanner RL, Gleason LU, Dowd WW. Environment-driven shifts in inter-individual variation and phenotypic integration within subnetworks of the mussel transcriptome and proteome. Mol Ecol 2022; 31:3112-3127. [PMID: 35363903 PMCID: PMC9321163 DOI: 10.1111/mec.16452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene‐to‐protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter‐individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean and interindividual heterogeneity of body temperature. To target a diverse set of physiological functions, we assessed variation within 19 expression subnetworks, including canonical stress‐response pathways and empirically derived coexpression clusters that represent a diffuse set of cellular processes. Variation in expression was particularly pronounced in the treatments with high mean and heterogeneous body temperatures. However, with few exceptions, environment‐dependent shifts of variation in the transcriptome were not reflected in the proteome. A metric of phenotypic integration provided evidence for a greater degree of constraint on relative expression levels (i.e., stronger correlation) within expression subnetworks in benign, homogeneous environments. Our results suggest that environments that are more stressful on average – and which also tend to be more heterogeneous – can relax these expression constraints and reduce phenotypic integration within biochemical subnetworks. Context‐dependent “unmasking” of functional variation may contribute to interindividual differences in physiological phenotype and performance in stressful environments.
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Affiliation(s)
- Richelle L Tanner
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.,Environmental Science & Policy Program, Chapman University, Orange, CA, 92866, USA
| | - Lani U Gleason
- Department of Biological Sciences, California State University, Sacramento, Sacramento, CA, 95819, USA
| | - W Wesley Dowd
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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20
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Fan X, Bao T, Yi H, Zhang Z, Zhang K, Liu X, Lin X, Zhang Z, Feng Z. Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103. Front Microbiol 2021; 12:781454. [PMID: 34899662 PMCID: PMC8656396 DOI: 10.3389/fmicb.2021.781454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.
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Affiliation(s)
- Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Tianyu Bao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Huaxi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zongcai Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Kenan Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xin Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Lin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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21
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Harnik Y, Buchauer L, Ben-Moshe S, Averbukh I, Levin Y, Savidor A, Eilam R, Moor AE, Itzkovitz S. Spatial discordances between mRNAs and proteins in the intestinal epithelium. Nat Metab 2021; 3:1680-1693. [PMID: 34931081 DOI: 10.1038/s42255-021-00504-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
The use of transcriptomes as reliable proxies for cellular proteomes is controversial. In the small intestine, enterocytes operate for 4 days as they migrate along villi, which are highly graded microenvironments. Spatial transcriptomics have demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here we show that enterocyte proteins and messenger RNAs along the villus axis are zonated, yet often spatially discordant. Using spatial sorting with zonated surface markers, together with a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, we find that, while many genes exhibit proteins zonated toward the villus tip, mRNA is zonated toward the villus bottom. Finally, we demonstrate that space-independent protein synthesis delays can explain many of the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium, highlighting the importance of protein measurements for inferring cell states in tissues that operate outside of steady state.
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Affiliation(s)
- Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lisa Buchauer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Averbukh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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22
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Mocciaro E, Runfola V, Ghezzi P, Pannese M, Gabellini D. DUX4 Role in Normal Physiology and in FSHD Muscular Dystrophy. Cells 2021; 10:3322. [PMID: 34943834 PMCID: PMC8699294 DOI: 10.3390/cells10123322] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/10/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
In the last decade, the sequence-specific transcription factor double homeobox 4 (DUX4) has gone from being an obscure entity to being a key factor in important physiological and pathological processes. We now know that expression of DUX4 is highly regulated and restricted to the early steps of embryonic development, where DUX4 is involved in transcriptional activation of the zygotic genome. While DUX4 is epigenetically silenced in most somatic tissues of healthy humans, its aberrant reactivation is associated with several diseases, including cancer, viral infection and facioscapulohumeral muscular dystrophy (FSHD). DUX4 is also translocated, giving rise to chimeric oncogenic proteins at the basis of sarcoma and leukemia forms. Hence, understanding how DUX4 is regulated and performs its activity could provide relevant information, not only to further our knowledge of human embryonic development regulation, but also to develop therapeutic approaches for the diseases associated with DUX4. Here, we summarize current knowledge on the cellular and molecular processes regulated by DUX4 with a special emphasis on FSHD muscular dystrophy.
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Affiliation(s)
| | | | | | | | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milano, Italy; (E.M.); (V.R.); (P.G.); (M.P.)
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23
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Zhang Q, Yu S, Wang Q, Yang M, Ge F. Quantitative Proteomics Reveals the Protein Regulatory Network of Anabaena sp. PCC 7120 under Nitrogen Deficiency. J Proteome Res 2021; 20:3963-3976. [PMID: 34270261 DOI: 10.1021/acs.jproteome.1c00302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anabaena sp. PCC 7120 (Anabaena 7120) is a photoautotrophic filamentous cyanobacterium capable of fixing atmospheric nitrogen. It is a model organism used for studying cell differentiation and nitrogen fixation. Under nitrogen deficiency, Anabaena 7120 forms specialized heterocysts capable of nitrogen fixation. However, the molecular mechanisms involved in the cyanobacterial adaptation to nitrogen deficiency are not well understood. Here, we employed a label-free quantitative proteomic strategy to systematically investigate the nitrogen deficiency response of Anabaena 7120 at different time points. In total, 363, 603, and 669 proteins showed significant changes in protein abundance under nitrogen deficiency for 3, 12, and 24 h, respectively. With mapping onto metabolic pathways, we revealed proteomic perturbation and regulation of carbon and nitrogen metabolism in response to nitrogen deficiency. Functional analysis confirmed the involvement of nitrogen stress-responsive proteins in biological processes, including nitrogen fixation, photosynthesis, energy and carbon metabolism, and heterocyst development. The expression of 10 proteins at different time points was further validated by using multiple reaction monitoring assays. In particular, many dysregulated proteins were found to be time-specific and involved in heterocyst development, providing new candidates for future functional studies in this model cyanobacterium. These results provide novel insights into the molecular mechanisms of nitrogen stress responses and heterocyst development in Anabaena 7120.
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Affiliation(s)
- Qi Zhang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116000, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Shengchao Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
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24
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Wu B, Qiao J, Wang X, Liu M, Xu S, Sun D. Factors affecting the rapid changes of protein under short-term heat stress. BMC Genomics 2021; 22:263. [PMID: 33849452 PMCID: PMC8042900 DOI: 10.1186/s12864-021-07560-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Protein content determines the state of cells. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. RESULTS We quantified 47,535 mRNAs and 3742 proteins in the filling grains of wheat in two different thermal environments. The impact of mRNA abundance and sequence features involved in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency were the main drivers of changes in protein expression under heat stress, and their combined contribution explains 58.2 and 66.4% of the protein variation at 30 and 40 °C (20 °C as control), respectively. Transcription contributes more to alterations in protein content at 40 °C (31%) than at 30 °C (6%). Furthermore, the usage of codon AAG may be closely related to the rapid alteration of proteins under heat stress. The contributions of AAG were 24 and 13% at 30 and 40 °C, respectively. CONCLUSION In this study, we analyzed the factors affecting the changes in protein expression in the early stage of heat stress and evaluated their influence.
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Affiliation(s)
- Bingjin Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jianwen Qiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Manshuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Daojie Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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25
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Rubio A, Ghosh S, Mülleder M, Ralser M, Mata J. Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast. Nucleic Acids Res 2021; 49:383-399. [PMID: 33313903 PMCID: PMC7797079 DOI: 10.1093/nar/gkaa1180] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Translational control is essential in response to stress. We investigated the translational programmes launched by the fission yeast Schizosaccharomyces pombe upon five environmental stresses. We also explored the contribution of defence pathways to these programmes: The Integrated Stress Response (ISR), which regulates translation initiation, and the stress-response MAPK pathway. We performed ribosome profiling of cells subjected to each stress, in wild type cells and in cells with the defence pathways inactivated. The transcription factor Fil1, a functional homologue of the yeast Gcn4 and the mammalian Atf4 proteins, was translationally upregulated and required for the response to most stresses. Moreover, many mRNAs encoding proteins required for ribosome biogenesis were translationally downregulated. Thus, several stresses trigger a universal translational response, including reduced ribosome production and a Fil1-mediated transcriptional programme. Surprisingly, ribosomes stalled on tryptophan codons upon oxidative stress, likely due to a decrease in charged tRNA-Tryptophan. Stalling caused ribosome accumulation upstream of tryptophan codons (ribosome queuing/collisions), demonstrating that stalled ribosomes affect translation elongation by other ribosomes. Consistently, tryptophan codon stalling led to reduced translation elongation and contributed to the ISR-mediated inhibition of initiation. We show that different stresses elicit common and specific translational responses, revealing a novel role in Tryptophan-tRNA availability.
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Affiliation(s)
- Angela Rubio
- Department of Biochemistry, University of Cambridge, UK
| | - Sanjay Ghosh
- Department of Biochemistry, University of Cambridge, UK
| | - Michael Mülleder
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, UK
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26
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Poopedi E, Marimani M, AlOmar SY, Aldahmash B, Ahmad A. Modulation of antioxidant defence system in response to berberine in Candida albicans. Yeast 2020; 38:157-169. [PMID: 33141949 DOI: 10.1002/yea.3531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
Emergence of multidrug resistant species of Candida is evolving, which advocates an urgent need for the development of new therapeutic strategies and antifungal drugs. Activation of antioxidant defence system in Candida albicans is known as forefront mechanism to escape drug toxicity. This study evaluated the role of antioxidant defence genes in the susceptibility to fluconazole in C. albicans and also determined the effect of berberine on growth, antioxidant enzymes and the expression of their genes in C. albicans isolates. Expression of major antioxidant genes was significantly increased in fluconazole-resistant isolates in comparison with the susceptible group. Antifungal susceptibility against berberine showed MIC values ranging from 125 to 500 μg/ml. Berberine treatment caused upregulation of mRNA expression and enzymatic activities of the targeted major antioxidants. Interestingly, C. albicans exhibited efficient antioxidant response at lower concentrations but could not sufficiently alleviate berberine-induced oxidative stress occurring at concentrations greater than 250 μg/ml. Therefore, berberine could serve as a potent Reactive Oxygen Species (ROS)-inducing agent, disrupting the antioxidant system especially in fluconazole-resistant C. albicans to overcome antifungal drug resistance. TAKE AWAYS: Evaluated the role of antioxidant enzymes in FLC resistance in C. albicans Studied the effect of berberine on growth of different C. albicans isolates Investigated the modulation of antioxidant enzymes by berberine in C. albicans Studied the effect of berberine on antioxidant gene expression in C. albicans.
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Affiliation(s)
- Evida Poopedi
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Musa Marimani
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Suliman Yousef AlOmar
- Doping Research, Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Badr Aldahmash
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa.,Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193, South Africa
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27
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Gbotsyo YA, Rowarth NM, Weir LK, MacRae TH. Short-term cold stress and heat shock proteins in the crustacean Artemia franciscana. Cell Stress Chaperones 2020; 25:1083-1097. [PMID: 32794096 PMCID: PMC7591681 DOI: 10.1007/s12192-020-01147-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/02/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023] Open
Abstract
In their role as molecular chaperones, heat shock proteins (Hsps) mediate protein folding thereby mitigating cellular damage caused by physiological and environmental stress. Nauplii of the crustacean Artemia franciscana respond to heat shock by producing Hsps; however, the effects of cold shock on Hsp levels in A. franciscana have not been investigated previously. The effect of cold shock at 1 °C followed by recovery at 27 °C on the amounts of ArHsp90, Hsp70, ArHsp40, and ArHsp40-2 mRNA and their respective proteins in A. franciscana nauplii was examined by quantitative PCR (qPCR) and immunoprobing of western blots. The same Hsp mRNAs and proteins were also quantified during incubation of nauplii at their optimal growth temperature of 27 °C. qPCR analyses indicated that the abundance of ArHsp90, Hsp70, and ArHsp40 mRNA remained relatively constant during both cold shock and recovery and was not significantly different compared with levels at optimal temperature. Western blotting revealed that ArHsp90, ArHsp40, and ArHsp40-2 were generally below baseline, but at detectable levels during the 6 h of cold shock, and persisted in early recovery stages before declining. Hsp70 was the only protein that remained constant in quantity throughout cold shock and recovery. By contrast, all Hsps declined rapidly during 6 h when nauplii were incubated continuously at 27 °C optimal temperature. Generally, the amounts of ArHsp90, ArHsp40, and ArHsp40-2 were higher during cold shock/recovery than those during continuous incubation at 27 °C. Our data support the conclusion that low temperature preserves Hsp levels, making them available to assist in protein repair and recovery after cold shock.
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Affiliation(s)
- Yayra A Gbotsyo
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Nathan M Rowarth
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Laura K Weir
- Biology Department, Saint Mary's University Halifax, Halifax, N. S., B3H 3C3, Canada.
| | - Thomas H MacRae
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
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28
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Usher J, Chaudhari Y, Attah V, Ho HL, Haynes K. Functional Characterization of a Novel Oxidative Stress Protection Protein in the Pathogenic Yeast Candida glabrata. Front Genet 2020; 11:530915. [PMID: 33101372 PMCID: PMC7545072 DOI: 10.3389/fgene.2020.530915] [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: 01/30/2020] [Accepted: 08/27/2020] [Indexed: 11/25/2022] Open
Abstract
Candida species are important pathogens of humans and the fourth most commonly isolated pathogen from nosocomial blood stream infections. Although Candida albicans is the principle causative agent of invasive candidosis, the incidence of Candida glabrata infections has rapidly grown. The reason for this increase is not fully understood, but it is clear that the species has a higher innate tolerance to commonly administered azole antifungals, in addition to being highly tolerant to stresses especially oxidative stress. Taking the approach that using the model organism, Saccharomyces cerevisiae, with its intrinsic sensitivity to oxidative stress, we hypothesized that by expressing mediators of stress resistance from C. glabrata in S. cerevisiae, it would result in induced resistance. To test this we transformed, en-masse, the C. glabrata ORFeome library into S. cerevisiae. This resulted in 1,500 stress resistant colonies and the recovered plasmids of 118 ORFs. Sequencing of these plasmids revealed a total of 16 different C. glabrata ORFs. The recovery of genes encoding known stress protectant proteins such as GPD1, GPD2 and TRX3 was predicted and validated the integrity of the screen. Through this screen we identified a C. glabrata unique ORF that confers oxidative stress resistance. We set to characterise this gene herein, examining expression in oxidative stress sensitive strains, comet assays to measure DNA damage and synthetic genetic array analysis to identify genetic interaction maps in the presence and absence of oxidative stress.
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Affiliation(s)
- Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Yogesh Chaudhari
- School of Biosciences, University of Exeter, Exeter, United Kingdom
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Victoria Attah
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Hsueh-lui Ho
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Ken Haynes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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29
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Hapala I, Griac P, Holic R. Metabolism of Storage Lipids and the Role of Lipid Droplets in the Yeast Schizosaccharomyces pombe. Lipids 2020; 55:513-535. [PMID: 32930427 DOI: 10.1002/lipd.12275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Storage lipids, triacylglycerols (TAG), and steryl esters (SE), are predominant constituents of lipid droplets (LD) in fungi. In several yeast species, metabolism of TAG and SE is linked to various cellular processes, including cell division, sporulation, apoptosis, response to stress, and lipotoxicity. In addition, TAG are an important source for the generation of value-added lipids for industrial and biomedical applications. The fission yeast Schizosaccharomyces pombe is a widely used unicellular eukaryotic model organism. It is a powerful tractable system used to study various aspects of eukaryotic cellular and molecular biology. However, the knowledge of S. pombe neutral lipids metabolism is quite limited. In this review, we summarize and discuss the current knowledge of the homeostasis of storage lipids and of the role of LD in the fission yeast S. pombe with the aim to stimulate research of lipid metabolism and its connection with other essential cellular processes. We also discuss the advantages and disadvantages of fission yeast in lipid biotechnology and recent achievements in the use of S. pombe in the biotechnological production of valuable lipid compounds.
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Affiliation(s)
- Ivan Hapala
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Peter Griac
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Roman Holic
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
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30
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Deciphering carbohydrate metabolism during wheat grain development via integrated transcriptome and proteome dynamics. Mol Biol Rep 2020; 47:5439-5449. [PMID: 32627139 DOI: 10.1007/s11033-020-05634-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
Abstract
Grain development of Triticum aestivum is being studied extensively using individual OMICS tools. However, integrated transcriptome and proteome studies are limited mainly due to complexity of genome. Current study focused to unravel the transcriptome-proteome coordination of key mechanisms underlying carbohydrate metabolism during whole wheat grain development. Wheat grains were manually dissected to obtain grain tissues for proteomics and transcriptomics analyses. Differentially expressed proteins and transcripts at the 11 stages of grain development were compared. Computational workflow for integration of two datasets related to carbohydrate metabolism was designed. For CM proteins, output peptide sequences of proteomic analyses (via LC-MS/MS) were used as source to search corresponding transcripts. The transcript that turned out with higher number of peptides was selected as bona fide ribonucleotide sequence for respective protein synthesis. More than 90% of hits resulted in successful identification of respective transcripts. Comparative analysis of protein and transcript expression profiles resulted in overall 32% concordance between these two series of data. However, during grain development correlation of two datasets gradually increased up to ~ tenfold from 152 to 655 °Cd and then dropped down. Proteins involved in carbohydrate metabolism were divided in five categories in accordance with their functions. Enzymes involved in starch and sucrose biosynthesis showed the highest correlations between proteome-transcriptome profiles. High percentage of identification and validation of protein-transcript hits highlighted the power of omics data integration approach over existing gene functional annotation tools. We found that correlation of two datasets is highly influenced by stage of grain development. Further, gene regulatory networks would be helpful in unraveling the mechanisms underlying the complex and significant traits such as grain weight and yield.
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31
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Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. J Proteome Res 2020; 19:1183-1195. [PMID: 32027144 DOI: 10.1021/acs.jproteome.9b00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance but also post-translational modifications (PTMs) that regulate protein activity. We implemented and validated using the well-characterized heat shock response of budding yeast, a tandem mass tagging (TMT), triple-stage mass spectrometry (MS3) strategy to measure global changes in the proteome during the yeast heat shock response over nine time points. We report that basic-pH, ultra-high performance liquid chromatography (UPLC) fractionation of tryptic peptides yields superfractions of minimal redundancy, a crucial requirement for deep coverage and quantification by subsequent LC-MS3. We quantified 2275 proteins across three biological replicates and found that differential expression peaked near 90 min following heat shock (with 868 differentially expressed proteins at 5% false discovery rate). The sensitivity of the approach also allowed us to detect changes in the relative abundance of ubiquitination and phosphorylation PTMs over time. Remarkably, relative quantification of post-translationally modified peptides revealed striking evidence of regulation of the heat shock response by protein PTMs. These data demonstrate that the high precision of TMT-MS3 enables peptide-level quantification of samples, which can reveal important regulation of protein abundance and regulatory PTMs under various experimental conditions.
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Affiliation(s)
- Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rebecca E Hardman
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas 72701, United States.,Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rick D Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Jeffrey A Lewis
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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32
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Irvine SQ. Embryonic canalization and its limits-A view from temperature. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:128-144. [PMID: 32011096 DOI: 10.1002/jez.b.22930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 02/06/2023]
Abstract
Many animals are able to produce similar offspring over a range of environmental conditions. This property of the developmental process has been termed canalization-the channeling of developmental pathways to generate a stable outcome despite varying conditions. Temperature is one environmental parameter that has fundamental effects on cell physiology and biochemistry, yet developmental programs generally result in a stable phenotype under a range of temperatures. On the other hand, there are typically upper and lower temperature limits beyond which the developmental program is unable to produce normal offspring. This review summarizes data on how development is affected by temperature, particularly high temperature, in various animal species. It also brings together information on potential cell biological and developmental genetic factors that may be responsible for developmental stability in varying temperatures, and likely critical mechanisms that break down at high temperature. Also reviewed are possible means for studying temperature effects on embryogenesis and how to determine which factors are most critical at the high-temperature limits for normal development. Increased knowledge of these critical factors will point to the targets of selection under climate change, and more generally, how developmental robustness in varying environments is maintained.
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Affiliation(s)
- Steven Q Irvine
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island
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33
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Modified expression of antioxidant genes in lobster cockroach, Nauphoeta cinerea exposed to methylmercury and monosodium glutamate. Chem Biol Interact 2020; 318:108969. [DOI: 10.1016/j.cbi.2020.108969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/19/2020] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
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34
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Jiang B, Xing Y, Li G, Zhang N, Lian L, Sun G, Zhang D. iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources. Front Microbiol 2020; 10:2906. [PMID: 31993023 PMCID: PMC6971185 DOI: 10.3389/fmicb.2019.02906] [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: 06/20/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022] Open
Abstract
DNA damage response allows microorganisms to repair or bypass DNA damage and maintain the genome integrity. It has attracted increasing attention but the underlying influential factors affecting DNA damage response are still unclear. In this work, isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis was used to investigate the influence of carbon sources on the translational response of Acinetobacter baylyi ADP1 to DNA damage. After cultivating in a nutrient-rich medium (LB) and defined media supplemented with four different carbon sources (acetate, citrate, pyruvate, and succinate), a total of 2807 proteins were identified. Among them, 84 proteins involved in stress response were significantly altered, indicating the strong influence of carbon source on the response of A. baylyi ADP1 to DNA damage and other stresses. As the first study on the comparative global proteomic changes in A. baylyi ADP1 under DNA damage across nutritional environments, our findings revealed that DNA damage response in A. baylyi ADP1 at the translational level is significantly altered by carbon source, providing an insight into the complex protein interactions across carbon sources and offering theoretical clues for further study to elucidate their general regulatory mechanism to adapt to different nutrient environments.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Nana Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Luning Lian
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.,Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, China
| | - Guangdong Sun
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, China.,State Key Joint Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, China
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35
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Cardarelli S, Giorgi M, Poiana G, Biagioni S, Saliola M. Metabolic role of cGMP in S. cerevisiae: the murine phosphodiesterase-5 activity affects yeast cell proliferation by altering the cAMP/cGMP equilibrium. FEMS Yeast Res 2019; 19:5322165. [PMID: 30772891 DOI: 10.1093/femsyr/foz016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 12/22/2022] Open
Abstract
In higher eukaryotes, cAMP and cGMP are signal molecules of major transduction pathways while phosphodiesterases (PDE) are a superfamily of cAMP/cGMP hydrolysing enzymes, modulatory components of these routes. Saccharomyces cerevisiae harbours two genes for PDE: Pde2 is a high affinity cAMP-hydrolysing enzyme, while Pde1 can hydrolyse both cAMP and cGMP. To gain insight into the metabolic role of cGMP in the physiology of yeast, the murine Pde5a1 gene encoding a specific cGMP-hydrolysing enzyme, was expressed in S. cerevisiae pdeΔ strains. pde1Δ and pde2Δ PDE5A1-transformed strain displayed opposite growth-curve profiles; while PDE5A1 recovered the growth delay of pde1Δ, PDE5A1 reversed the growth profile of pde2Δ to that of the untransformed pde1Δ. Growth test analysis and the use of Adh2 and Adh1 as respiro-fermentative glycolytic flux markers confirmed that PDE5A1 altered the metabolism by acting on Pde1-Pde2/cyclic nucleotides content and also on the TORC1 nutrient-sensing cascade. cGMP is required during the log-phase of cell proliferation to adjust/modulate cAMP levels inside well-defined ranges. A model is presented proposing the role of cGMP in the cAMP/PKA pathway. The expression of the PDE5A1 cassette in other mutant strains might constitute the starting tool to define cGMP metabolic role in yeast nutrient signaling.
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Affiliation(s)
- Silvia Cardarelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, Rome 5, 00185, Italy
| | - Mauro Giorgi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, Rome 5, 00185, Italy
| | - Giancarlo Poiana
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, Rome 5, 00185, Italy
| | - Stefano Biagioni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, Rome 5, 00185, Italy
| | - Michele Saliola
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Piazzale A. Moro, Rome 5, 00185, Italy
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Cellular models of Batten disease. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165559. [PMID: 31655107 PMCID: PMC7338907 DOI: 10.1016/j.bbadis.2019.165559] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
The Neuronal Ceroid Lipofuscinoses (NCL), otherwise known as Batten disease, are a group of neurodegenerative diseases caused by mutations in 13 known genes. All except one NCL is autosomal recessive in inheritance, with similar aetiology and characterised by the accumulation of autofluorescent storage material in the lysosomes of cells. Age of onset and the rate of progression vary between the NCLs. They are collectively one of the most common lysosomal storage diseases, but the enigma remains of how genetically distinct diseases result in such remarkably similar pathogenesis. Much has been learnt from cellular studies about the function of the proteins encoded by the affected genes. Such research has utilised primitive unicellular models such as yeast and amoeba containing gene orthologues, cells derived from naturally occurring (sheep) and genetically engineered (mouse) animal models or patient-derived cells. Most recently, patient-derived induced pluripotent stem cell (iPSC) lines have been differentiated into neural cell-types to study molecular pathogenesis in the cells most profoundly affected by disease. Here, we review how cell models have informed much of the biochemical understanding of the NCLs and how more complex models are being used to further this understanding and potentially act as platforms for therapeutic efficacy studies in the future. Developments made in cellular models for neuronal ceroid lipofuscinosis (NCL) in basic biology and use as therapeutic platforms. Cellular models elucidating function of NCL proteins. NCL proteins implicated in the mTor signalling pathway. Patient-derived induced pluripotent stem cell (iPSC) lines have been differentiated into neural cell-types providing insights into the molecular pathogenesis of NCL.
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Sanchez M, Lin Y, Yang CC, McQuary P, Rosa Campos A, Aza Blanc P, Wolf DA. Cross Talk between eIF2α and eEF2 Phosphorylation Pathways Optimizes Translational Arrest in Response to Oxidative Stress. iScience 2019; 20:466-480. [PMID: 31627132 PMCID: PMC6823656 DOI: 10.1016/j.isci.2019.09.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/14/2019] [Accepted: 09/23/2019] [Indexed: 01/26/2023] Open
Abstract
The cellular stress response triggers a cascade of events leading to transcriptional reprogramming and a transient inhibition of global protein synthesis, which is thought to be mediated by phosphorylation of eukaryotic initiation factor-2α (eIF2α). Using mouse embryonic fibroblasts (MEFs) and the fission yeast S. pombe, we report that rapid translational arrest and cell survival in response to hydrogen peroxide-induced oxidative stress do not rely on eIF2α kinases and eIF2α phosphorylation. Rather, H2O2 induces a block in elongation through phosphorylation of eukaryotic elongation factor 2 (eEF2). Kinetic and dose-response analyses uncovered cross talk between the eIF2α and eEF2 phosphorylation pathways, indicating that, in MEFs, eEF2 phosphorylation initiates the acute shutdown in translation, which is maintained by eIF2α phosphorylation. Our results challenge the common conception that eIF2α phosphorylation is the primary trigger of translational arrest in response to oxidative stress and point to integrated control that may facilitate the survival of cancer cells. Oxidative stress-induced translation arrest is independent of eIF2α phosphorylation Oxidative stress blocks translation elongation Oxidative stress triggers eEF2 kinase activation eEF2K KO cells are hypersensitive to oxidative stress
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Affiliation(s)
- Marisa Sanchez
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Yingying Lin
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research and Center for Stress Signaling Networks, Xiamen University, Xiamen 361102, China
| | - Chih-Cheng Yang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Philip McQuary
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Pedro Aza Blanc
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Dieter A Wolf
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research and Center for Stress Signaling Networks, Xiamen University, Xiamen 361102, China.
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Rollins JA, Shaffer D, Snow SS, Kapahi P, Rogers AN. Dietary restriction induces posttranscriptional regulation of longevity genes. Life Sci Alliance 2019; 2:2/4/e201800281. [PMID: 31253655 PMCID: PMC6600014 DOI: 10.26508/lsa.201800281] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
Dietary restriction (DR) increases life span through adaptive changes in gene expression. To understand more about these changes, we analyzed the transcriptome and translatome of Caenorhabditis elegans subjected to DR. Transcription of muscle regulatory and structural genes increased, whereas increased expression of amino acid metabolism and neuropeptide signaling genes was controlled at the level of translation. Evaluation of posttranscriptional regulation identified putative roles for RNA-binding proteins, RNA editing, miRNA, alternative splicing, and nonsense-mediated decay in response to nutrient limitation. Using RNA interference, we discovered several differentially expressed genes that regulate life span. We also found a compensatory role for translational regulation, which offsets dampened expression of a large subset of transcriptionally down-regulated genes. Furthermore, 3' UTR editing and intron retention increase under DR and correlate with diminished translation, whereas trans-spliced genes are refractory to reduced translation efficiency compared with messages with the native 5' UTR. Finally, we find that smg-6 and smg-7, which are genes governing selection and turnover of nonsense-mediated decay targets, are required for increased life span under DR.
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Affiliation(s)
- Jarod A Rollins
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Dan Shaffer
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Santina S Snow
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Aric N Rogers
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
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Yang Y, Wei F, Braynen J, Wei X, Tian B, Shi G, Cao G, Yuan J, Zhang X. Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa. Cell Biosci 2019; 9:49. [PMID: 31236208 PMCID: PMC6580506 DOI: 10.1186/s13578-019-0313-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background Polyploidy is considered as a basic event in plant speciation and evolution in nature, and the cytological and proteomic profilings of floral buds at meiosis (FAM) would definitely contribute to a better understanding of the polyploid-associated effects during plant reproduction cycle. Results Herein, the cytological investigations demonstrated that chromosome behaviors such as univalent and multivalent at prophase I, chaotic alignments at metaphase, aberrant segregation at telophase, were frequently observed during meiosis in autotetraploid Brassica rapa. The proteomic analysis showed a total of 562 differentially expressed proteins (DEPs) were identified in FAM between autotetraploid and diploid B. rapa. Notably, PARP2 and LIG1 related to base excision repair and BARD1 involved in recombination were significantly down-regulated in autotetraploid B. rapa, which indicated DNA repair pathway were more likely affected during meiosis in autotetraploid B. rapa. The functional analysis showed that DEPs assigned to “chromatin structure and dynamics”, “cell cycle control, cell division, chromosome partitioning” and “cytoskeleton” were preferentially up-regulated, which suggested a robust regulation of cell division in autotetraploid B. rapa. In combination with the floral RNA-seq data released, a number of DEPs were found positively correlated with their transcript abundance, but posttranslational modification of proteins might also play a role in regulating meiosis course after polyploidization. Conclusions In general, this study provides a detailed cytology and proteome landscape of FAM between diploid and autotetraploid B. rapa, which definitely affords us a better understanding of uniformity and discrepancy of meiosis at the plant reproductive stage before and after polyploidization. Electronic supplementary material The online version of this article (10.1186/s13578-019-0313-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Yang
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Fang Wei
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Janeen Braynen
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China.,3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Xiaochun Wei
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
| | - Baoming Tian
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gongyao Shi
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Gangqiang Cao
- 1School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Jiachen Yuan
- 2School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan People's Republic of China
| | - Xiaowei Zhang
- 3Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan People's Republic of China
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Milo-Cochavi S, Pareek M, Delulio G, Almog Y, Anand G, Ma LJ, Covo S. The response to the DNA damaging agent methyl methanesulfonate in a fungal plant pathogen. Fungal Biol 2019; 123:408-422. [PMID: 31053330 DOI: 10.1016/j.funbio.2019.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/27/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
DNA damage can cause mutations that in fungal plant pathogens lead to hypervirulence and resistance to pesticides. Almost nothing is known about the response of these fungi to DNA damage. We performed transcriptomic and phosphoproteomic analyses of Fusarium oxysporum exposed to methyl methanesulfonate (MMS). At the RNA level we observe massive induction of DNA repair pathways including the global genome nucleotide excision. Cul3, Cul4, several Ubiquitin-like ligases and components of the proteasome are significantly induced. In agreement, we observed drug synergism between a proteasome inhibitor and MMS. While our data suggest that Yap1 and Xbp1 networks are similarly activated in response to damage in yeast and F. oxysporum we were able to observe modules that were MMS-responsive in F. oxysporum and not in yeast. These include transcription/splicing modules that are upregulated and respiration that is down-regulated. In agreement, MMS treated cells are much more sensitive to a respiration inhibitor. At the phosphoproteomic level, Adenylate cyclase, which generates cAMP, is phosphorylated in response to MMS and forms a network of phosphorylated proteins that include cell cycle regulators and several MAPKs. Our analysis provides a starting point in understanding how genomic changes in response to DNA damage occur in Fusarium species.
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Affiliation(s)
- Shira Milo-Cochavi
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Manish Pareek
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Gregory Delulio
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Yael Almog
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Gautam Anand
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel.
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Li P, Fu X, Chen M, Zhang L, Li S. Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:49. [PMID: 30899329 PMCID: PMC6408782 DOI: 10.1186/s13068-019-1390-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/28/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND The thermotolerant yeast Kluyveromyces marxianus is a potential candidate for high-temperature fermentation. When K. marxianus was used for high-temperature ethanol fermentation, a fermentation arrest was observed during the late fermentation stage and the stress responses have been investigated based on the integration of RNA-Seq and metabolite data. In order to bring new insights into the cellular responses of K. marxianus after the fermentation arrest during high-temperature ethanol fermentation, quantitative proteomic profiling and integrated analysis with transcriptomic data were performed in this study. RESULTS Samples collected at 14, 16, 18, 20 and 22 h during high-temperature fermentation were subjected to isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic profiling and integrated analysis with transcriptomic data. The correlations between transcripts and proteins for the comparative group 16 h vs 14 h accounted for only 4.20% quantified proteins and 3.23% differentially expressed proteins (DEPs), respectively, much higher percentages of correlations (30.56%-59.11%) were found for other comparative groups (i.e., 18 h vs 14 h, 20 h vs 14 h, and 22 h vs 14 h). According to Spearman correlation tests between transcriptome and proteome (the absolute value of a correlation coefficient between 0.5 and 1 indicates a strong correlation), poor correlations were found for all quantified proteins (R = - 0.0355 to 0.0138), DEPs (R = - 0.0079 to 0.0233) and the DEPs with opposite expression trends to corresponding differentially expressed genes (DEGs) (R = - 0.0478 to 0.0636), whereas stronger correlations were observed in terms of the DEPs with the same expression trends as the correlated DEGs (R = 0.5593 to 0.7080). The results of multiple reaction monitoring (MRM) verification indicate that the iTRAQ results were reliable. After the fermentation arrest, a number of proteins involved in transcription, translation, oxidative phosphorylation and fatty acid metabolism were down-regulated, some molecular chaperones and proteasome proteins were up-regulated, the ATPase activity significantly decreased, and the total fatty acids gradually accumulated. In addition, the contents of palmitic acid, oleic acid, C16, C18, C22 and C24 fatty acids increased by 16.77%, 28.49%, 14.14%, 26.88%, 628.57% and 125.29%, respectively. CONCLUSIONS This study confirmed some biochemical and enzymatic alterations provoked by the stress conditions in the specific case of K. marxianus: such as decreases in transcription, translation and oxidative phosphorylation, alterations in cellular fatty acid composition, and increases in the abundance of molecular chaperones and proteasome proteins. These findings provide potential targets for further metabolic engineering towards improvement of the stress tolerance in K. marxianus.
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Affiliation(s)
- Pengsong Li
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Ming Chen
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
- Agricultural Utilization Research Center, Nutrition and Health Research Institute, COFCO Corporation, No.4 Road, Future Science and Technology Park South, Beiqijia, Changping, Beijing, 102209 China
| | - Shizhong Li
- MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
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Bacterial diet and weak cadmium stress affect the survivability of Caenorhabditis elegans and its resistance to severe stress. Heliyon 2019; 5:e01126. [PMID: 30705981 PMCID: PMC6348244 DOI: 10.1016/j.heliyon.2019.e01126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/20/2018] [Accepted: 01/03/2019] [Indexed: 01/11/2023] Open
Abstract
Stress may have negative or positive effects in dependence of its intensity (hormesis). We studied this phenomenon in Caenorhabditis elegans by applying weak or severe abiotic (cadmium, CdCl2) and/or biotic stress (different bacterial diets) during cultivation/breeding of the worms and determining their developmental speed or survival and performing transcriptome profiling and RT-qPCR analyses to explore the genetic basis of the detected phenotypic differences. To specify weak or severe stress, developmental speed was measured at different cadmium concentrations, and survival assays were carried out on different bacterial species as feed for the worms. These studies showed that 0.1 μmol/L or 10 mmol/L of CdCl2 were weak or severe abiotic stressors, and that E. coli HT115 or Chitinophaga arvensicola feeding can be considered as weak or severe biotic stress. Extensive phenotypic studies on wild type (WT) and different signaling mutants (e.g., kgb-1Δ and pmk-1Δ) and genetic studies on WT revealed, inter alia, the following results. WT worms bred on E. coli OP50, which is a known cause of high lipid levels in the worms, showed high resistance to severe abiotic stress and elevated gene expression for protein biosynthesis. WT worms bred under weak biotic stress (E. coli HT115 feeding which causes lower lipid levels) showed an elevated resistance to severe biotic stress, elevated gene expression for the innate immune response and signaling but reduced gene expression for protein biosynthesis. WT worms bred under weak biotic and abiotic stress (E. coli HT115 feeding plus 0.1 μmol/L of CdCl2) showed high resistance to severe biotic stress, elevated expression of DAF-16 target genes (e.g., genes for small heat shock proteins) but further reduced gene expression for protein biosynthesis. WT worms bred under weak biotic but higher abiotic stress (E. coli HT115 feeding plus 10 μmol/L of CdCl2) showed re-intensified gene expression for the innate immune response, signaling, and protein biosynthesis, which, however, did not caused a higher resistance to severe biotic stress. E. coli OP50 feeding as well as weak abiotic and biotic stress during incubations also improved the age-specific survival probability of adult WT worms. Thus, this study showed that a bacterial diet resulting in higher levels of energy resources in the worms (E. coli OP50 feeding) or weak abiotic and biotic stress promote the resistance to severe abiotic or biotic stress and the age-specific survival probability of WT.
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Mi D, Manuel M, Huang YT, Mason JO, Price DJ. Pax6 Lengthens G1 Phase and Decreases Oscillating Cdk6 Levels in Murine Embryonic Cortical Progenitors. Front Cell Neurosci 2018; 12:419. [PMID: 30498434 PMCID: PMC6249377 DOI: 10.3389/fncel.2018.00419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/26/2018] [Indexed: 12/23/2022] Open
Abstract
Pax6 is a key regulator of the rates of progenitor cell division in cerebral corticogenesis. Previous work has suggested that this action is mediated at least in part by regulation of the cell cycle gene Cdk6, which acts largely on the transition from G1 to S phase. We began the present study by investigating whether, in addition to Cdk6, other Pax6-regulated cell cycle genes are likely to be primary mediators of Pax6’s actions on cortical progenitor cell cycles. Following acute cortex-specific deletion of Pax6, Cdk6 showed changes in expression a day earlier than any other Pax6-regulated cell cycle gene suggesting that it is the primary mediator of Pax6’s actions. We then used flow cytometry to show that progenitors lacking Pax6 have a shortened G1 phase and that their Cdk6 levels are increased in all phases. We found that Cdk6 levels oscillate during the cell cycle, increasing from G1 to M phase. We propose a model in which loss of Pax6 shortens G1 phase by raising overall Cdk6 levels, thereby shortening the time taken for Cdk6 levels to cross a threshold triggering transition to S phase.
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Affiliation(s)
- Da Mi
- Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Martine Manuel
- Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yu-Ting Huang
- Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - John O Mason
- Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - David J Price
- Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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Xu T, Lei L, Shi J, Wang X, Chen J, Xue M, Sun S, Zhan B, Xia Z, Jiang N, Zhou T, Lai J, Fan Z. Characterization of maize translational responses to sugarcane mosaic virus infection. Virus Res 2018; 259:97-107. [PMID: 30355529 DOI: 10.1016/j.virusres.2018.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/14/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Sugarcane mosaic virus (SCMV) frequently causes dramatic losses in maize production as the main pathogen of maize dwarf mosaic disease. It is important to understand the translational responses in maize to SCMV infection since viruses have to recruit host translation apparatus to express their proteins. However, due to technical limitations, research on virus translation lags far behind that on transcription. Here, we studied the relationship between systemic symptom expression and virus accumulation and found that both SCMV RNA and proteins accumulated rapidly during the systemic infection process in which varying degrees of chlorosis to mosaic symptoms developed on non-inoculated leaves. In addition, we applied ribosome profiling, which couples polysomal mRNA isolation with high-throughput sequencing, on the symptomatic leaves infected with SCMV to unravel the translational responses of maize to viral infection on a genome-wide scale. The results showed that only the genomic positive-stranded RNA of SCMV was involved in translation, and SCMV only occupied a small amount of translational resources of host plant at the early stage of infection. Further analyses on a global gene expression and gene ontology (GO) enrichment revealed that photosynthesis and metabolism were dramatically repressed at both transcriptional and translational levels. Altogether, our results laid a foundation for dissecting the molecular mechanism of plant translational responses to viral infection.
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Affiliation(s)
- Tengzhi Xu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China; Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Xin Wang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Mingshuo Xue
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Silong Sun
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Binhui Zhan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Zihao Xia
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Na Jiang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Tao Zhou
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Zaifeng Fan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China.
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Abstract
In this Opinion article, we aim to address how cells adapt to stress and the repercussions chronic stress has on cellular function. We consider acute and chronic stress-induced changes at the cellular level, with a focus on a regulator of cellular stress, the chaperome, which is a protein assembly that encompasses molecular chaperones, co-chaperones and other co-factors. We discuss how the chaperome takes on distinct functions under conditions of stress that are executed in ways that differ from the one-on-one cyclic, dynamic functions exhibited by distinct molecular chaperones. We argue that through the formation of multimeric stable chaperome complexes, a state of chaperome hyperconnectivity, or networking, is gained. The role of these chaperome networks is to act as multimolecular scaffolds, a particularly important function in cancer, where they increase the efficacy and functional diversity of several cellular processes. We predict that these concepts will change how we develop and implement drugs targeting the chaperome to treat cancer.
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Affiliation(s)
- Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thaís L S Araujo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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46
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Liu M, Xiong LB, Tao X, Liu QH, Wang FQ, Wei DZ. Integrated Transcriptome and Proteome Studies Reveal the Underlying Mechanisms for Sterol Catabolism and Steroid Production in Mycobacterium neoaurum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9147-9157. [PMID: 30075077 DOI: 10.1021/acs.jafc.8b02714] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Integrated transcriptome and proteome studies were performed to investigate sterol biotransformation in wild-type Mycobacterium neoaurum ATCC 25795 ( Mn) and the mutant strains producing steroid intermediates. Transcriptome and proteome studies indicated that several metabolic activities were noticeably dynamic, including cholesterol degradation, central carbon metabolism, cell envelope biosynthesis, glycerol metabolism, and transport. Interestingly, a poor overall correlation between mRNA and translation profiles was found, which might contribute to the metabolic adaptation in cholesterol catabolism. A gene cluster covering 111 genes was discovered to encode for cholesterol catabolism in Mn. Generally, transcription and/or translation of the genes in KstR1 regulon was upregulated, and the induction of genes in KstR2 regulon was not as significant as that of KstR1 regulon. Several induced genes showing potential roles for cholesterol catabolism were found. Further identification of these genes and investigation of the correlation among key metabolic activities could help for the development of efficient steroid-producing strains.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Liang-Bin Xiong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Qing-Hai Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
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The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock. PLoS Genet 2018; 14:e1007563. [PMID: 30059503 PMCID: PMC6085073 DOI: 10.1371/journal.pgen.1007563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 08/09/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5’ end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered. When confronted with external physical or chemical stress, cells respond by increasing the mRNA output of a small number of genes required for stress survival, while shutting down the majority of other genes. Moreover, each mRNA is regulated under stress to either enhance or diminish its translation into proteins. The overall purpose is for the cell to optimize gene expression for survival and recovery during rapidly changing conditions. Much of this regulation is mediated by RNA-binding proteins. We have isolated proteins binding to specific mRNAs induced by stress, to investigate how they affect the stress response. We found members of one protein complex to be bound to stress-induced mRNAs. When mutants lacking these proteins were exposed to stress, ribosomes were more engaged with translating mRNAs than in the wild-type. In the mutants, it was also possible to trigger expression of stress proteins with only minimal stress levels. Tracing the passage of ribosomes over mRNAs, we saw that ribosomes accumulated around the start codon in the mutants. These findings indicate that the protein complex is required to moderate the stress response and prevent it from overreacting, which would be harmful for the cell.
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Shifts in the relationship between mRNA and protein abundance of gill ion-transporters during smolt development and seawater acclimation in Atlantic salmon (Salmo salar). Comp Biochem Physiol A Mol Integr Physiol 2018; 221:63-73. [DOI: 10.1016/j.cbpa.2018.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 11/24/2022]
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Becker D, Reydelet Y, Lopez JA, Jackson C, Colbourne JK, Hawat S, Hippler M, Zeis B, Paul RJ. The transcriptomic and proteomic responses of Daphnia pulex to changes in temperature and food supply comprise environment-specific and clone-specific elements. BMC Genomics 2018; 19:376. [PMID: 29783951 PMCID: PMC5963186 DOI: 10.1186/s12864-018-4742-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/30/2018] [Indexed: 02/07/2023] Open
Abstract
Background Regulatory adjustments to acute and chronic temperature changes are highly important for aquatic ectotherms because temperature affects their metabolic rate as well as the already low oxygen concentration in water, which can upset their energy balance. This also applies to severe changes in food supply. Thus, we studied on a molecular level (transcriptomics and/or proteomics) the immediate responses to heat stress and starvation and the acclimation to different temperatures in two clonal isolates of the model microcrustacean Daphnia pulex from more or less stressful environments, which showed a higher (clone M) or lower (clone G) tolerance to heat and starvation. Results The transcriptomic responses of clone G to acute heat stress (from 20 °C to 30 °C) and temperature acclimation (10 °C, 20 °C, and 24 °C) and the proteomic responses of both clones to acute heat, starvation, and heat-and-starvation stress comprised environment-specific and clone-specific elements. Acute stress (in particular heat stress) led to an early upregulation of stress genes and proteins (e.g., molecular chaperones) and a downregulation of metabolic genes and proteins (e.g., hydrolases). The transcriptomic responses to temperature acclimation differed clearly. They also varied depending on the temperature level. Acclimation to higher temperatures comprised an upregulation of metabolic genes and, in case of 24 °C acclimation, a downregulation of genes for translational processes and collagens. The proteomic responses of the clones M and G differed at any type of stress. Clone M showed markedly stronger and less stress-specific proteomic responses than clone G, which included the consistent expression of a specific heat shock protein (HSP60) and vitellogenin (VTG-SOD). Conclusions The expression changes under acute stress can be interpreted as a switch from standard products of gene expression to stress-specific products. The expression changes under temperature acclimation probably served for an increase in energy intake (via digestion) and, if necessary, a decrease in energy expenditures (e.g, for translational processes). The stronger and less stress-specific proteomic responses of clone M indicate a lower degree of cell damage and an active preservation of the energy balance, which allowed adequate proteomic responses under stress, including the initiation of resting egg production (VTG-SOD expression) as an emergency reaction. Electronic supplementary material The online version of this article (10.1186/s12864-018-4742-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dörthe Becker
- Institute of Zoophysiology, University of Münster, 48143, Münster, Germany.,Present address: Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Yann Reydelet
- Institute of Zoophysiology, University of Münster, 48143, Münster, Germany
| | - Jacqueline A Lopez
- Present address: Genomics Core Facility, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, USA
| | - Craig Jackson
- Present address: School of Public and Environmental Affairs, Indiana University, Bloomington, IN, USA
| | - John K Colbourne
- Present address: Environmental Genomics Group, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Susan Hawat
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Bettina Zeis
- Institute of Zoophysiology, University of Münster, 48143, Münster, Germany
| | - Rüdiger J Paul
- Institute of Zoophysiology, University of Münster, 48143, Münster, Germany.
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Miao Y, Xiong G, Li R, Wu Z, Zhang X, Weng P. Transcriptome profiling of Issatchenkia orientalis under ethanol stress. AMB Express 2018. [PMID: 29536208 PMCID: PMC5849708 DOI: 10.1186/s13568-018-0568-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Issatchenkia orientalis, a non-Saccharomyces yeast that can resist a wide variety of environmental stresses, has potential use in winemaking and bioethanol production. Little is known about gene expression or the physiology of I. orientalis under ethanol stress. In this study, high-throughput RNA sequencing was used to investigate the transcriptome profile of I. orientalis in response to ethanol. 502 gene transcripts were differentially expressed, of which 451 were more abundant, and 51 less abundant, in cells subjected to 4 h of ethanol stress (10% v/v). Annotation and statistical analyses suggest that multiple genes involved in ergosterol biosynthesis, trehalose metabolism, and stress response are differentially expressed under these conditions. The up-regulation of molecular chaperones HSP90 and HSP70, and also genes associated with the ubiquitin–proteasome proteolytic pathway suggests that ethanol stress may cause aggregation of misfolded proteins. Finally, ethanol stress in I. orientalis appears to have a nitrogen starvation effect, and many genes involved in nutrient uptake were up-regulated.
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