Design of an Arabidopsis thaliana reporter line to detect heat-sensing and signaling mutants

Background Global warming is a major challenge for plant survival and growth. Understanding the molecular mechanisms by which higher plants sense and adapt to upsurges in the ambient temperature, is essential for developing strategies to enhance plant tolerance to heat stress. Here, we designed a special heat-responsive Arabidopsis thaliana reporter line that allowed an in-depth investigation of the mechanisms underlying the accumulation of protective heat-shock proteins (HSPs) in response to high temperature. Methods A transgenic Arabidopsis thaliana reporter line named “Heat-Inducible Bioluminescence And Toxicity” (HIBAT) was designed to express from a conditional heat-inducible promoter, a fusion gene encoding for nanoluciferase and D-amino acid oxidase, whose expression was found to be toxic only in the presence of D-valine. HIBAT seedlings were exposed to different heat treatments in presence or absence of D-valine and analyzed for survival rate, bioluminescence and HSP gene expression. Results Whereas at 22°C, HIBAT seedlings grew unaffected by D-valine, and all survived following iterative heat treatments without D-valine, 98% died following heat treatments on D-valine. The HSP17.3B promoter was highly specific to heat, as it remained unresponsive to various plant hormones, Flagellin, H2O2, osmotic stress and high salt. Confirming that HIBAT does not significantly differ from its Col-0 parent, RNAseq analysis of heat-treated seedlings showed a strong correlation between the two lines. Using HIBAT, a forward genetic screen revealed candidate loss-of-function mutants defective either at accumulating HSPs at high temperature or at repressing HSP accumulation at low, non-heat-shock temperatures. Conclusion This study adds insights into the molecular mechanisms by which higher plants sense and adapt to rapid elevations of ambient temperatures. HIBAT was a valuable tool to identify Arabidopsis mutants defective in the response to high temperature stress. Our findings open new avenues for future research on the regulation of HSP expression and understanding their role in the onset of plant acquired thermotolerance.

[1]  J. Napier,et al.  A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activation of defense responses in Arabidopsis. , 2023, Journal of Experimental Botany.

[2]  P. De Los Rios,et al.  A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70 , 2022, Nature Chemical Biology.

[3]  P. Goloubinoff,et al.  How do plants feel the heat and survive? , 2022, Trends in biochemical sciences.

[4]  Yanli Lu,et al.  PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants , 2022, Plant Biotechnology Journal.

[5]  R. Mittler,et al.  Plant responses to multifactorial stress combination. , 2022, The New phytologist.

[6]  P. Goloubinoff,et al.  How do humans and plants feel the heat? , 2022, Trends in plant science.

[7]  Fanglu Ma,et al.  Research advances in function and regulation mechanisms of plant small heat shock proteins (sHSPs) under environmental stresses. , 2022, The Science of the total environment.

[8]  P. De Los Rios,et al.  Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control , 2021, Frontiers in Molecular Biosciences.

[9]  T. Amen,et al.  Resveratrol and related stilbene derivatives induce stress granules with distinct clearance kinetics , 2021, Molecular biology of the cell.

[10]  A. Guihur,et al.  Heat Shock Signaling in Land Plants: From Plasma Membrane Sensing to the Transcription of Small Heat Shock Proteins , 2021, Frontiers in Plant Science.

[11]  B. Bukau,et al.  The diverse functions of small heat shock proteins in the proteostasis network. , 2021, Journal of molecular biology.

[12]  Hyun Ju Lee,et al.  The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress , 2021, bioRxiv.

[13]  J. Davies,et al.  The Complex Story of Plant Cyclic Nucleotide-Gated Channels , 2021, International journal of molecular sciences.

[14]  A. Glatz,et al.  Lipids and Trehalose Actively Cooperate in Heat Stress Management of Schizosaccharomyces pombe , 2021 .

[15]  Qianru Jia,et al.  HSP70-3 Interacts with Phospholipase Dδ and Participates in Heat Stress Defense. , 2020, Plant physiology.

[16]  Jianguo Zhao,et al.  Plant Responses to Heat Stress: Physiology, Transcription, Noncoding RNAs, and Epigenetics , 2020, International journal of molecular sciences.

[17]  M. Quadroni,et al.  Quantitative proteomic analysis to capture the role of heat‐accumulated proteins in moss plant acquired thermotolerance , 2020, Plant, cell & environment.

[18]  F. Fritschi,et al.  Meta-analysis of drought and heat stress combination impact on crop yield and yield components. , 2020, Physiologia plantarum.

[19]  Jinlong Li,et al.  A DMP-triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis , 2020, Nature Plants.

[20]  T. Taji,et al.  Arabidopsis Raf‐like kinases act as positive regulators of subclass III SnRK2 in osmostress signaling , 2020, The Plant journal : for cell and molecular biology.

[21]  Mario J. Avellaneda,et al.  Processive extrusion of polypeptide loops by a Hsp100 disaggregase , 2020, Nature.

[22]  D. Macherel,et al.  Arabidopsis seedlings display a remarkable resilience under severe mineral starvation using their metabolic plasticity to remain self-sufficient for weeks. , 2019, The Plant journal : for cell and molecular biology.

[23]  Colleen J. Doherty,et al.  Novel transcriptional responses to heat revealed by turning up the heat at night , 2019, Plant Molecular Biology.

[24]  Dawn H. Nagel,et al.  Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis , 2019, Scientific Reports.

[25]  N. Smirnoff,et al.  Hydrogen peroxide metabolism and functions in plants. , 2018, The New phytologist.

[26]  N. R. R. Neelapu,et al.  Role and Regulation of Osmolytes as Signaling Molecules to Abiotic Stress Tolerance , 2019, Plant Signaling Molecules.

[27]  M. Černý,et al.  Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks , 2018, International journal of molecular sciences.

[28]  K. Chong,et al.  Cold signaling in plants: Insights into mechanisms and regulation. , 2018, Journal of integrative plant biology.

[29]  S. Wingett,et al.  FastQ Screen: A tool for multi-genome mapping and quality control. , 2018, F1000Research.

[30]  Frank Van Breusegem,et al.  Reactive oxygen species in plant development , 2018, Development.

[31]  G. Chiosis,et al.  Adapting to stress — chaperome networks in cancer , 2018, Nature Reviews Cancer.

[32]  A. Barducci,et al.  Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins , 2018, Nature Chemical Biology.

[33]  S. Wingett,et al.  FastQ Screen: A tool for multi-genome mapping and quality control , 2018, F1000Research.

[34]  Katja E. Jaeger,et al.  Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. , 2017, Molecular plant.

[35]  P. Benfey,et al.  A SIMPLE pipeline for mapping point mutations , 2016, bioRxiv.

[36]  P. Rios,et al.  Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling , 2016, Nature Structural &Molecular Biology.

[37]  Ya-Chen Huang,et al.  The Heat Stress Factor HSFA6b Connects ABA Signaling and ABA-Mediated Heat Responses1[OPEN] , 2016, Plant Physiology.

[38]  Andrija Finka,et al.  Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes. , 2016, Annual review of biochemistry.

[39]  Zhigang Li,et al.  AsHSP17, a creeping bentgrass small heat shock protein modulates plant photosynthesis and ABA-dependent and independent signalling to attenuate plant response to abiotic stress. , 2016, Plant, cell & environment.

[40]  Weibo Cai,et al.  NanoLuc: A Small Luciferase Is Brightening Up the Field of Bioluminescence. , 2016, Bioconjugate chemistry.

[41]  M. Tesar,et al.  NanoLuc Luciferase – A Multifunctional Tool for High Throughput Antibody Screening , 2016, Front. Pharmacol..

[42]  Nobuhiro Suzuki,et al.  ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress , 2016, PloS one.

[43]  M. Mayer,et al.  Molecular mechanism of thermosensory function of human heat shock transcription factor Hsf1 , 2016, eLife.

[44]  Zhulong Chan,et al.  Physiological and Metabolic Changes of Purslane (Portulaca oleracea L.) in Response to Drought, Heat, and Combined Stresses , 2016, Front. Plant Sci..

[45]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[46]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[47]  T. Serio,et al.  Defining the limits: Protein aggregation and toxicity in vivo , 2014, Critical reviews in biochemistry and molecular biology.

[48]  Jaroslav Bendl,et al.  PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations , 2014, PLoS Comput. Biol..

[49]  Anton J. Enright,et al.  Kraken: A set of tools for quality control and analysis of high-throughput sequence data , 2013, Methods.

[50]  T. Gerats,et al.  Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops , 2013, Front. Plant Sci..

[51]  Sean M. Hartig,et al.  Basic Image Analysis and Manipulation in ImageJ , 2013, Current protocols in molecular biology.

[52]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[53]  A. Day,et al.  Growth of Transplastomic Cells Expressing d-Amino Acid Oxidase in Chloroplasts Is Tolerant to d-Alanine and Inhibited by d-Valine1[W][OA] , 2012, Plant Physiology.

[54]  Wei Li,et al.  RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..

[55]  F. Maathuis,et al.  Plasma Membrane Cyclic Nucleotide Gated Calcium Channels Control Land Plant Thermal Sensing and Acquired Thermotolerance[C][W] , 2012, Plant Cell.

[56]  A. Glatz,et al.  Heat shock response in photosynthetic organisms: membrane and lipid connections. , 2012, Progress in lipid research.

[57]  M. Tamoi,et al.  H2O2-triggered Retrograde Signaling from Chloroplasts to Nucleus Plays Specific Role in Response to Stress* , 2012, The Journal of Biological Chemistry.

[58]  Paul Workman,et al.  Hsp90 Molecular Chaperone Inhibitors: Are We There Yet? , 2012, Clinical Cancer Research.

[59]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[60]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[61]  Y. Charng,et al.  The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis. , 2011, Plant, cell & environment.

[62]  Andrija Finka,et al.  Heat perception and signalling in plants: a tortuous path to thermotolerance. , 2011, The New phytologist.

[63]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[64]  I. Hara-Nishimura,et al.  A rapid and non-destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana. , 2010, The Plant journal : for cell and molecular biology.

[65]  P. Wigge,et al.  H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis , 2010, Cell.

[66]  Andrija Finka,et al.  Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells , 2010, Cell Stress and Chaperones.

[67]  I. Roy,et al.  Effect of trehalose on protein structure , 2008, Protein science : a publication of the Protein Society.

[68]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[69]  M. Hayashi,et al.  Cytosolic HSP90 Regulates the Heat Shock Response That Is Responsible for Heat Acclimation in Arabidopsis thaliana* , 2007, Journal of Biological Chemistry.

[70]  A. Wahid,et al.  Heat tolerance in plants: An overview , 2007 .

[71]  E. Vierling,et al.  Core Genome Responses Involved in Acclimation to High Temperature1[C][W][OA] , 2007, Plant Physiology.

[72]  P. Lansbury,et al.  A century-old debate on protein aggregation and neurodegeneration enters the clinic , 2006, Nature.

[73]  Rossana Henriques,et al.  Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method , 2006, Nature Protocols.

[74]  R. Volkov,et al.  Heat stress-induced H2O2 is required for effective expression of heat shock genes in Arabidopsis , 2006, Plant Molecular Biology.

[75]  Jian-Kang Zhu,et al.  EMS mutagenesis of Arabidopsis. , 2006, Methods in molecular biology.

[76]  D. Schaefer,et al.  Controlled Expression of Recombinant Proteins in Physcomitrella patens by a Conditional Heat-shock Promoter: a Tool for Plant Research and Biotechnology , 2005, Plant Molecular Biology.

[77]  Karen Schlauch,et al.  Cytosolic Ascorbate Peroxidase 1 Is a Central Component of the Reactive Oxygen Gene Network of Arabidopsisw⃞ , 2005, The Plant Cell Online.

[78]  R. Travis,et al.  Effect of NaCl and mannitol on plasma membrane proteins in corn roots , 1990, Protoplasma.

[79]  A. Altman,et al.  Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. , 2004, Trends in plant science.

[80]  M. Hertzberg,et al.  A conditional marker gene allowing both positive and negative selection in plants , 2004, Nature Biotechnology.

[81]  Joshua L. Heazlewood,et al.  Lipoic Acid-Dependent Oxidative Catabolism of α-Keto Acids in Mitochondria Provides Evidence for Branched-Chain Amino Acid Catabolism in Arabidopsis1 , 2004, Plant Physiology.

[82]  E. Vierling,et al.  Molecular chaperones and protein folding in plants , 1996, Plant Molecular Biology.

[83]  K. Scharf,et al.  Promoter specificity and deletion analysis of three heat stress transcription factors of tomato , 1993, Molecular and General Genetics MGG.

[84]  K. Shinozaki,et al.  Isolation and Functional Analysis of Arabidopsis Stress-Inducible NAC Transcription Factors That Bind to a Drought-Responsive cis-Element in the early responsive to dehydration stress 1 Promoter , 2004 .

[85]  Anushya Muruganujan,et al.  PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification , 2003, Nucleic Acids Res..

[86]  J. Saudubray,et al.  Branched-chain organic acidurias. , 2002, Seminars in neonatology : SN.

[87]  P. Goloubinoff,et al.  Chemical Chaperones Regulate Molecular Chaperones in Vitro and in Cells under Combined Salt and Heat Stresses* , 2001, The Journal of Biological Chemistry.

[88]  G. Balogh,et al.  Synechocystis HSP17 is an amphitropic protein that stabilizes heat-stressed membranes and binds denatured proteins for subsequent chaperone-mediated refolding , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[89]  R. Morimoto,et al.  Regulation of the Heat Shock Transcriptional Response: Cross Talk between a Family of Heat Shock Factors, Molecular Chaperones, and Negative Regulators the Heat Shock Factor Family: Redundancy and Specialization , 2022 .

[90]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[91]  J. Buchner,et al.  The Small Heat-shock Protein IbpB from Escherichia coli Stabilizes Stress-denatured Proteins for Subsequent Refolding by a Multichaperone Network* , 1998, The Journal of Biological Chemistry.

[92]  M. Havaux Carotenoids as membrane stabilizers in chloroplasts , 1998 .

[93]  D. Julius,et al.  The capsaicin receptor: a heat-activated ion channel in the pain pathway , 1997, Nature.

[94]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[95]  L. V. D. Eerden Toxicity of ammonia to plants , 1982 .