Now showing items 1-20 of 563

    • Cell-to-Cell Communication During Plant-Pathogen Interaction

      Tabassum, Naheed; Blilou, Ikram (Molecular Plant-Microbe Interactions®, Scientific Societies, 2021-10-19) [Article]
      Recognition of pathogen activates cellular signaling such as ROS, MAPK, Ca2+ signaling which ultimately fine-tunes the cell to cell communication. These further coordinates with the hormone signaling to execute the defense response at local and systemic level. Interestingly, phytopathogens have also evolved to manipulate the cellular and hormonal signaling and/or exploit hosts cell to cell connection in multiple ways at multiple levels. Overall, the triumph over the pathogen depends on prime decisions and actions-how the plant maintain, regulate and eventually break the intercellular communication through apoplastic and symplastic routes. Here, we review how intercellular communication in plants is mediated, manipulated and maneuvered during plant-pathogen interaction. Key words: Cell to cell communication, plant defense, plasmodesmata, phytohormones
    • A thermophilic Cas13 enzyme for sensitive and specific one-pot detection of SARS-CoV-2

      Mahas, Ahmed; Marsic, Tin; Masson, Mauricio Lopez Portillo; Wang, Qiaochu; Aman, Rashid; Zheng, Cheng; Ali, Zahir; Ghanem, Bernard; Mahfouz, Magdy M. (Research Square Platform LLC, 2021-09-22) [Preprint]
      Robust, sensitive, and specific diagnostic platforms for early pathogen detection are essential for the identification of infected patients and management of current and future pandemics. CRISPR-Cas systems have been repurposed for SARS-CoV-2 detection in two-pot assays. Two-pot assays require extra steps and are prone to cross-contamination; however, the temperature range of current Cas enzymes limits the development of one-pot assays Here, we characterized TccCas13a, a thermophilic Cas13a enzyme with cis and trans activities from 37–70°C, and HheCas13a, which had a limited range and lower activity. We harnessed TccCas13a in a one-pot SARS-CoV-2 assay with two layers of amplification and TccCas13a-mediated collateral degradation of a single-stranded RNA reporter. This assay showed 95% sensitivity and 100% specificity compared with RT-qPCR on clinical samples. We also developed a mobile phone application to facilitate data reading, collection, and sharing. Our OPTIMA-dx detection module exhibits key features for point-of-care SARS-CoV-2 screening and pathogen detection in general.
    • Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen

      Melino, Vanessa J.; Tester, Mark A.; Okamoto, Mamoru (Current Opinion in Biotechnology, Elsevier BV, 2021-09-22) [Article]
      Global use of nitrogen (N) fertilizers has increased sevenfold from 1960 to 1995 but much of the N applied is lost to the environment. Modifying the temporal and spatial distribution of organic N within the plant can lead to improved grain yield and/or grain protein content for the same or reduced N fertilizer inputs. Biotechnological approaches to modify whole plant distribution of amino acids and ureides has proven successful in several crop species. Manipulating selective autophagy pathways in crops has also improved N remobilization efficiency to sink tissues whilst the contribution of ribophagy, RNA and purine catabolism to N recycling in crops is still too early to foretell. Improved recycling and remobilization of N must exploit N-stress responsive transcriptional regulators, N-sensing or phloem-localized promotors and genetic variation for N-responsive traits.
    • A Novel Miniature CRISPR-Cas13 System for SARS-CoV-2 Diagnostics

      Mahas, Ahmed; Wang, Qiaochu; Marsic, Tin; Mahfouz, Magdy M. (ACS Synthetic Biology, American Chemical Society (ACS), 2021-09-21) [Article]
      Rapid, point-of-care (POC) diagnostics are essential to mitigate the impacts of current (and future) epidemics; however, current methods for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) require complicated laboratory tests that are generally conducted off-site and require substantial time. CRISPR-Cas systems have been harnessed to develop sensitive and specific platforms for nucleic acid detection. These detection platforms take advantage of CRISPR enzymes' RNA-guided specificity for RNA and DNA targets and collateral trans activities on single-stranded RNA and DNA reporters. Microbial genomes possess an extensive range of CRISPR enzymes with different specificities and levels of collateral activity; identifying new enzymes may improve CRISPR-based diagnostics. Here, we identified a new Cas13 variant, which we named as miniature Cas13 (mCas13), and characterized its catalytic activity. We then employed this system to design, build, and test a SARS-CoV-2 detection module coupling reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the mCas13 system to detect SARS-CoV-2 in synthetic and clinical samples. Our system exhibits sensitivity and specificity comparable to other CRISPR systems. This work expands the repertoire and application of Cas13 enzymes in diagnostics and for potential <i>in vivo</i> applications, including RNA knockdown and editing. Importantly, our system can be potentially adapted and used in large-scale testing for diverse pathogens, including RNA and DNA viruses, and bacteria.
    • An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants

      Jia, Kunpeng; Mi, Jianing; Ali, Shawkat; Ohyanagi, Hajime; Moreno, Juan C.; Ablazov, Abdugaffor; Balakrishna, Aparna; Berqdar, Lamis; Fiore, Alessia; Diretto, Gianfranco; Martínez, Claudio; de Lera, Angel R.; Gojobori, Takashi; Al-Babili, Salim (Molecular Plant, Elsevier BV, 2021-09-20) [Article]
      Abscisic acid (ABA) is an important carotenoid-derived phytohormone that plays essential roles in plant response to biotic and abiotic stresses as well as in various physiological and developmental processes. In Arabidopsis, ABA biosynthesis starts with the epoxidation of zeaxanthin by the ABA DEFICIENT 1 (ABA1) enzyme, leading to epoxycarotenoids, e.g., violaxanthin. The oxidative cleavage of 9-cis-epoxycarotenoids, a key regulatory step catalyzed by 9-CIS-EPOXYCAROTENOID DIOXYGENASE, forms xanthoxin that is converted in further reactions mediated by ABA DEFICIENT 2 (ABA2), ABA DEFICIENT 3 (ABA3), and ABSCISIC ALDEHYDE OXIDASE 3 (AAO3) into ABA. By combining genetic and biochemical approaches, we unravel here an ABA1-independent ABA biosynthetic pathway starting upstream of zeaxanthin. We identified the carotenoid cleavage products, i.e., apocarotenoids, β-apo-11-carotenal, 9-cis-β-apo-11-carotenal, 3-OH-β-apo-11-carotenal, and 9-cis-3-OH-β-apo-11-carotenal as intermediates of this ABA1-independent ABA biosynthetic pathway. Using labeled compounds, we showed that β-apo-11-carotenal, 9-cis-β-apo-11-carotenal, and 3-OH-β-apo-11-carotenal are successively converted into 9-cis-3-OH-β-apo-11-carotenal, xanthoxin, and finally into ABA in both Arabidopsis and rice. When applied to Arabidopsis, these β-apo-11-carotenoids exert ABA biological functions, such as maintaining seed dormancy and inducing the expression of ABA-responsive genes. Indeed, the transcriptomic analysis revealed a high overlap of differentially expressed genes regulated by β-apo-11-carotenoids and ABA, but also suggested that these compounds exert ABA-independent regulatory activities. Taken together, our study identifies a biological function for the common plant metabolites β-apo-11-carotenoids, extends our knowledge about ABA biosynthesis and provides new insights into plant apocarotenoid metabolic networks.
    • The DNA–carbon nanotube binding mode determines the efficiency of carbon nanotube-mediated DNA delivery to intact plants

      Ali, Zahir; Serag, Maged F.; Demirer, Gozde; Torre, Bruno; Di Fabrizio, Enzo M.; Landry, Markita; Habuchi, Satoshi; Mahfouz, Magdy M. (Cambridge University Press (CUP), 2021-09-20) [Preprint]
      Efficient delivery of DNA, RNA, and genome engineering machinery to plant cells will enable efforts to genetically modify plants for global food security, sustainable energy production, synthetic biology applications, and climate change resilience. For the delivery of functional genetic units into plant cells, charged nanoparticles, particularly carbon nanotubes (CNT), have attracted considerable interest. Although some success has been achieved using CNT-based approaches, the efficiency, batch reproducibility, and the limits of their applicability remain to be assessed. Here, we provide a mechanistic understanding of plasmid DNA-loaded CNTs based transfection of plant cells, and factors affecting the expression of the transformed plasmid. We show that transfection is inherently limited by the presence of the cell wall, Coulomb interactions between DNA and polymer coated CNT, and DNA size, whereas expression of the transformed plasmid is limited by relative gene-to-plasmid size and the intracellular accessibility of DNA. We further show that the formation of partially condensed DNA on the CNT surface is a prerequisite for successful transfection and expression. Furthermore, DNA does not detach completely from the CNT, so the accessibility of the transcription machinery to DNA is the key for transformation efficiency. This irreversible DNA plasmid binding and partial condensation limit the length of DNA that can be expressed, thus negatively affecting efficiency and reproducibility. Understanding the underlying mechanisms and limitations of CNT-mediated delivery of DNA through the plant cell wall is of considerable importance in guiding efforts to design nanomaterials for efficient transformation, trait engineering, and synthetic biology applications.
    • Synthetic Directed Evolution in Plants: Unlocking Trait Engineering and Improvement

      Gundra, Sivakrishna Rao; Jiang, Wenjun; Mahfouz, Magdy M. (Synthetic Biology, Oxford University Press (OUP), 2021-09-08) [Article]
      ABSTRACT Genetic variation accelerates adaptation and resilience and enables the survival of species to their changing environment. Increasing the genetic diversity of crop species is essential to improve their yield and enhance food security. Synthetic directed evolution (SDE) employs localized sequence diversification (LSD) of gene sequence and selection pressure to evolve gene variants with better fitness, improved properties, and desired phenotypes. Recently, CRISPR-Cas dependent and independent technologies have been applied for LSD to mediate synthetic evolution in diverse species, including plants. SDE holds excellent promise to discover, accelerate, and expand the range of traits of value in crop species. Here, we highlight the efficient SDE approaches for the LSD of plant genes, selection strategies, and critical traits for targeted improvement. We discuss the potential of emerging technologies, including CRISPR-Cas base editing, retron editing, EvolvR, and prime editing, to establish efficient SDE in plants. Moreover, we cover CRISPR-Cas independent technologies, including T7 polymerase editor for continuous evolution. We highlight the key challenges and potential solutions of applying SDE technologies to improve plant traits of value.
    • Multiple strategies of plant colonization by beneficial endophytic Enterobacter sp. SA187

      Synek, Lukas; Rawat, Anamika; L'Haridon, Floriane; Weisskopf, Laure; Saad, Maged; Hirt, Heribert (Environmental Microbiology, Wiley, 2021-09-01) [Article]
      Although many endophytic plant growth-promoting rhizobacteria have been identified, relatively little is still known about the mechanisms by which they enter plants and promote plant growth. The beneficial endophyte Enterobacter sp. SA187 was shown to maintain productivity of crops in extreme agricultural conditions. Here we present that roots of its natural host (Indigofera argentea), alfalfa, tomato, wheat, barley and Arabidopsis are all efficiently colonized by SA187. Detailed analysis of the colonization process in Arabidopsis showed that colonization already starts during seed germination, where seed-coat mucilage supports SA187 proliferation. The meristematic zone of growing roots attracts SA187, allowing epiphytic colonization in the elongation zone. Unlike primary roots, lateral roots are significantly less epiphytically colonized by SA187. Root endophytic colonization was found to occur by passive entry of SA187 at lateral-root bases. However, SA187 also actively penetrates the root epidermis by enzymatic disruption of plant cell wall material. In contrast to roots, endophytic colonization of shoots occurs via stomata, whereby SA187 can actively re-open stomata similarly to pathogenic bacteria. In summary, several entry strategies were identified that allow SA187 to establish itself as a beneficial endophyte in several plant species, supporting it's use as a plant growth-promoting bacterium in agriculture systems. This article is protected by copyright. All rights reserved.
    • Plant genome engineering from lab to field—a Keystone Symposia report

      Cable, Jennifer; Ronald, Pamela C.; Voytas, Daniel; Zhang, Feng; Levy, Avraham A.; Takatsuka, Ayumu; Arimura, Shin-ichi; Jacobsen, Steven E.; Toki, Seiichi; Toda, Erika; Gao, Caixia; Zhu, Jian-Kang; Boch, Jens; Van Eck, Joyce; Mahfouz, Magdy M.; Andersson, Mariette; Fridman, Eyal; Weiss, Trevor; Wang, Kan; Qi, Yiping; Jores, Tobias; Adams, Tom; Bagchi, Rammyani (Annals of the New York Academy of Sciences, Wiley, 2021-08-25) [Article]
      Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
    • Quinoa Phenotyping Methodologies: An International Consensus

      Stanschewski, Clara; Rey, Elodie; Fiene, Gabriele; Craine, Evan; Wellman, Gordon; Melino, Vanessa J.; Patiranage, Dilan; Johansen, Kasper; Schmöckel, Sandra; Bertero, Daniel; Oakey, Helena; Colque-Little, Carla; Afzal, Irfan; Raubach, Sebastian; Miller, Nathan; Streich, Jared; Amby, Daniel; Emrani, Nazgol; Warmington, Mark; Mousa, Magdi; Wu, David; Jacobson, Daniel; Andreasen, Christian; Jung, Christian; Murphy, Kevin; Bazile, Didier; Tester, Mark A.; on behalf of the Quinoa Phenotyping Consortium (Plants, MDPI AG, 2021-08-24) [Article]
      Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.
    • CRISPR-Based Crop Improvements: A Way Forward to Achieve Zero Hunger

      Ahmad, Shakeel; Tang, Liqun; Shahzad, Rahil; Mawia, Amos Musyoki; Rao, Gundra Sivakrishna; Jamil, Shakra; Wei, Chen; Sheng, Zhonghua; Shao, Gaoneng; Wei, Xiangjin; Hu, Peisong; Mahfouz, Magdy M.; Hu, Shikai; Tang, Shaoqing (Journal of Agricultural and Food Chemistry, American Chemical Society (ACS), 2021-07-21) [Article]
      Zero hunger is one of the sustainable development goals set by the United Nations in 2015 to achieve global food security by 2030. The current harvest of crops is insufficient; feeding the world's population and meeting the goal of zero hunger by 2030 will require larger and more consistent crop production. Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) technology is widely used for the plant genome editing. In this review, we consider this technology as a potential tool for achieving zero hunger. We provide a comprehensive overview of CRISPR-Cas technology and its most important applications for food crops' improvement. We also conferred current and potential technological breakthroughs that will help in breeding future crops to end global hunger. The regulatory aspects of deploying this technology in commercial sectors, bioethics, and the production of transgene-free plants are also discussed. We hope that the CRISPR-Cas system will accelerate the breeding of improved crop cultivars compared with conventional breeding and pave the way toward the zero hunger goal.
    • Pre-mRNA alternative splicing as a modulator for heat stress response in plants

      Ling, Yu; Mahfouz, Magdy M.; Zhou, Shuangxi (Trends in Plant Science, Elsevier BV, 2021-07) [Article]
      The molecular responses of plants to the important abiotic stress, heat stress (HS), have been extensively studied at the transcriptional level. Alternative splicing (AS) is a post-transcriptional regulatory process in which an intron-containing gene can generate more than one mRNA variant. The impact of HS on the premRNA splicing process has been reported in various eukaryotes but seldom discussed in-depth, especially in plants. Here, we review AS regulation in response to HS in different plant species. We discuss potential molecular mechanisms controlling heat-inducible AS regulation in plants and hypothesize that AS regulation participates in heat-priming establishment and HS memory maintenance. We propose that the pre-mRNA splicing variation is an important regulator of plant HS responses (HSRs).
    • Robust, Long-Term, and Exceptionally Sensitive Microneedle-Based Bioimpedance Sensor for Precision Farming

      Bu Khamsin, Abdullah; Moussi, Khalil; Tao, Ran; Lubineau, Gilles; Blilou, Ikram; Salama, Khaled N.; Kosel, Jürgen (Advanced Science, Wiley, 2021-06-17) [Article]
      Precision farming has the potential to increase global food production capacity whilst minimizing traditional inputs. However, the adoption and impact of precision farming are contingent on the availability of sensors that can discern the state of crops, while not interfering with their growth. Electrical impedance spectroscopy offers an avenue for nondestructive monitoring of crops. To that end, it is reported on the deployment of impedimetric sensors utilizing microneedles (MNs) that can be used to pierce the waxy exterior of plants to obtain sensitive impedance spectra in open-air settings with an average relative noise value of 3.83%. The sensors are fabricated using a novel micromolding and release method that is compatible with UV photocurable and thermosetting polymers. Assessments of the quality of the MNs under scanning electron microscopy show that the replication process is high in fidelity to the original design of the master mold and that it can be used for upward of 20 replication cycles. The sensor's performance is validated against conventional planar sensors for obtaining the impedance values of Arabidopsis thaliana. As a change is detected in impedance due to lighting and hydration, this raises the possibility for their widespread use in precision farming.
    • G3BPs in Plant Stress

      Abulfaraj, Aala A.; Hirt, Heribert; Rayapuram, Naganand (Frontiers in Plant Science, Frontiers Media SA, 2021-06-10) [Article]
      The sessile nature of plants enforces highly adaptable strategies to adapt to different environmental stresses. Plants respond to these stresses by a massive reprogramming of mRNA metabolism. Balancing of mRNA fates, including translation, sequestration, and decay is essential for plants to not only coordinate growth and development but also to combat biotic and abiotic environmental stresses. RNA stress granules (SGs) and processing bodies (P bodies) synchronize mRNA metabolism for optimum functioning of an organism. SGs are evolutionarily conserved cytoplasmic localized RNA-protein storage sites that are formed in response to adverse conditions, harboring mostly but not always translationally inactive mRNAs. SGs disassemble and release mRNAs into a translationally active form upon stress relief. RasGAP SH3 domain binding proteins (G3BPs or Rasputins) are “scaffolds” for the assembly and stability of SGs, which coordinate receptor mediated signal transduction with RNA metabolism. The role of G3BPs in the formation of SGs is well established in mammals, but G3BPs in plants are poorly characterized. In this review, we discuss recent findings of the dynamics and functions of plant G3BPs in response to environmental stresses and speculate on possible mechanisms such as transcription and post-translational modifications that might regulate the function of this important family of proteins.
    • Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis

      Huang, Ying; Sircar, Sanchari; Ramirez-Prado, Juan Sebastian; Manza-Mianza, Deborah; Antunez-Sanchez, Javier; Brik-Chaouche, Rim; Rodriguez-Granados, Natalia; An, Jing; Bergounioux, Catherine; Mahfouz, Magdy M.; Hirt, Heribert; Crespi, Martin; Concia, Lorenzo; Barnech, Fredy; Amiard, Simon; Probst, Aline V; Gutierrez-Marcos, Jose; Ariel, Federico; Raynaud, Cecile; Latrasse, David; Benhamed, Moussa (Genome research, Cold Spring Harbor Laboratory, 2021-06-04) [Article]
      In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 act directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics and alternative 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac – a histone modification associated with active transcription, thus indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.
    • A protoplast-based bioassay to quantify strigolactone activity in arabidopsis using strigoquant

      Braguy, Justine; Samodelov, Sophia L.; Andres, Jennifer; Ochoa-Fernandez, Rocio; Al-Babili, Salim; Zurbriggen, Matias D. (Springer US, 2021-05-25) [Book Chapter, Protocol]
      Understanding the biological background of strigolactone (SL) structural diversity and the SL signaling pathway at molecular level requires quantitative and sensitive tools that precisely determine SL dynamics. Such biosensors may be also very helpful in screening for SL analogs and mimics with defined biological functions. Recently, the genetically encoded, ratiometric sensor StrigoQuant was developed and allowed the quantification of the activity of a wide concentration range of SLs. StrigoQuant can be used for studies on the biosynthesis, function and signal transduction of this hormone class. Here, we provide a comprehensive protocol for establishing the use of StrigoQuant in Arabidopsis protoplasts. We first describe the generation and transformation of the protoplasts with StrigoQuant and detail the application of the synthetic SL analogue GR24. We then show the recording of the luminescence signal and how the obtained data are processed and used to assess/determine SL perception.
    • NAC Transcription Factors ATAF1 and ANAC055 Negatively Regulate Thermomemory in Arabidopsis

      Alshareef, Nouf Owdah Hameed; Woo, Yong; de Werk, Tobias; Kamranfar, Iman; Mueller-Roeber, Bernd; Tester, Mark A.; Balazadeh, Salma; Schmöckel, Sandra M.; Annapurna Devi Allu3 (Research Square Platform LLC, 2021-05-17) [Preprint]
      Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. ‘Thermomemory’ is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Arabidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like ataf1, anac055 mutants show improved thermomemory, revealing a potential co-control of both NAC TFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
    • The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis

      Jacob, Pierre; Brisou, Gwilherm; Dalmais, Marion; Thévenin, Johanne; van der Wal, Froukje; Latrasse, David; Suresh Devani, Ravi; Benhamed, Moussa; Dubreucq, Bertrand; Boualem, Adnane; Lepiniec, Loic; Immink, Richard G. H.; Hirt, Heribert; Bendahmane, Abdelhafid (Genes, MDPI AG, 2021-05-15) [Article]
      HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/myb5 loss of function mutants showed heat stress hypersensitivity. Transient expression assays confirmed that MYB5 and TT2 can regulate the HSFA2 promoter together with the other members of the MBW complex, TT8 and TRANSPARENT TESTA GLABRA 1 (TTG1) and that the SIIE was involved in this regulation. Transcriptomic analysis revealed that TT2/MYB5 target promoters were enriched in SIIE. Overall, we report a new function of TT2 and MYB5 in stress resistance and a role in SIIE-mediated HSFA2 regulation.
    • CRISPR/Cas systems versus plant viruses: engineering plant immunity and beyond

      Ali, Zahir; Mahfouz, Magdy M. (Plant Physiology, Oxford University Press (OUP), 2021-05-12) [Article]
      Abstract Molecular engineering of plant immunity to confer resistance against plant viruses holds great promise for mitigating crop losses and improving plant productivity and yields, thereby enhancing food security. Several approaches have been employed to boost immunity in plants by interfering with the transmission or lifecycles of viruses. In this review, we discuss the successful application of CRISPR/Cas (clustered regularly interspaced short palindromic repeats [CRISPR]/CRISPR-associated protein [Cas]) systems to engineer plant immunity, increase plant resistance to viruses, and develop viral diagnostic tools. Furthermore, we examine the use of plant viruses as delivery systems to engineer virus resistance in plants and provide insight into the limitations of current CRISPR/Cas approaches and the potential of newly discovered CRISPR/Cas systems to engineer better immunity and develop better diagnostics tools for plant viruses. Finally, we outline potential solutions to key challenges in the field to enable the practical use of these systems for crop protection and viral diagnostics.
    • Rooting in the Desert: A Developmental Overview on Desert Plants

      Kirschner, Gwendolyn Kristin; Xiao, Ting Ting; Blilou, Ikram (Genes, MDPI AG, 2021-05-10) [Article]
      Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how desert plants have evolved unique developmental programs like having determinate meristems in the case of cacti while forming a branched and compact root system that allows efficient water uptake during wet periods. The remote germination mechanism in date palms is another example of developmental adaptation to survive in the dry and hot desert surface. Date palms have also designed non-gravitropic secondary roots, termed pneumatophores, to maximize water and nutrient uptake. Next, we highlight the distinct anatomical features developed by desert species in response to drought like narrow vessels, high tissue suberization, and air spaces within the root cortex tissue. Finally, we discuss the beneficial impact of the microbiome in promoting root growth in desert conditions and how these characteristics can be exploited to engineer resilient crops with a greater ability to deal with salinity induced by irrigation and with the increasing drought caused by global warming.