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Recent Submissions

  • Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens

    Chaudhary, Shahid; Ali, Zahir; Tehseen, Muhammad; Haney, Evan F.; Pantoja Angles, Aarón; Alshehri, Salwa; Wang, Tiannyu; Clancy, Gerard Jude; Ayach, Maya; Hauser, Charlotte; Hong, Pei-Ying; Hamdan, Samir; Hancock, Robert E. W.; Mahfouz, Magdy M. (Nature Communications, Springer Science and Business Media LLC, 2023-03-16) [Article]
    Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
  • Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia

    Cui, Guoxin; Konciute, Migle; Ling, Lorraine; Esau, Luke; Raina, Jean-Baptiste; Han, Baoda; Salazar Moya, Octavio Ruben; Presnell, Jason S.; Rädecker, Nils; Zhong, Huawen; Menzies, Jessica; Cleves, Phillip A.; Liew, Yi Jin; Krediet, Cory J.; Sawiccy, Val; Cziesielski, Maha Joana; Guagliardo, Paul; Bougoure, Jeremy; Pernice, Mathieu; Hirt, Heribert; Voolstra, Christian R.; Weis, Virginia M.; Pringle, John R.; Aranda, Manuel (Science Advances, American Association for the Advancement of Science (AAAS), 2023-03-15) [Article]
    Symbiotic cnidarians such as corals and anemones form highly productive and biodiverse coral reef ecosystems in nutrient-poor ocean environments, a phenomenon known as Darwin’s paradox. Resolving this paradox requires elucidating the molecular bases of efficient nutrient distribution and recycling in the cnidarian-dinoflagellate symbiosis. Using the sea anemone Aiptasia, we show that during symbiosis, the increased availability of glucose and the presence of the algae jointly induce the coordinated up-regulation and relocalization of glucose and ammonium transporters. These molecular responses are critical to support symbiont functioning and organism-wide nitrogen assimilation through glutamine synthetase/glutamate synthase–mediated amino acid biosynthesis. Our results reveal crucial aspects of the molecular mechanisms underlying nitrogen conservation and recycling in these organisms that allow them to thrive in the nitrogen-poor ocean environments.
  • Perpetual Motion Electric Truck, Transporting Cargo with Zero Fuel Costs

    Hunt, Julian David; Tong, Wenxuan; Zakeri, Behnam; Jurasz, Jakub; Patro, Epari Ritesh; Durin, Bojan; Pacheco, Diego Augusto de Jesus; Leal Filho, Walter; Wada, Yoshihide (Elsevier BV, 2023-03-06) [Preprint]
    The transportation sector is going through a rapid transition to electric vehicles to minimize our reliance on fossil fuels and reduce CO2 emissions. This is also happening in the cargo transport sector, with a rapid deployment of electric trucks. This paper proposes that the replacement of diesel trucks with electric trucks should first happen on routes where cargo is delivered from a location with a higher altitude to a location with a lower altitude. This way, the regenerative braking system of the truck can completely recharge the truck’s battery. This paper investigates scenarios where electric trucks could operate indefinitely without grid electricity to charge their batteries. This concept was named perpetual motion electric truck (PMET). Results show that with an average road slope of 5%, 60 km/h speed, the weight of the cargo should be at least 1.32 times the weight of the truck, PMET can be achieved. PMET is an interesting alternative to reduce electricity demand and increase the sustainability of the transport sector.
  • Genome-wide association analysis uncovers novel rice blast resistance alleles

    Greenwood, Julian; Lacorte-Apostol, Vanica; Kroj, Thomas; Padilla, Jonas; Telebano-Yanoria, Mary; Glaus, Anna; Roulin, Anne; Padilla, Andre; Zhou, Bo; Keller, Beat; Krattinger, Simon G. (Research Square Platform LLC, 2023-03-02) [Preprint]
    One of the most critical steps following genome-wide association studies (GWAS) is the identification and validation of candidate genes underlying genetic associations. Gene presence-absence and copy number variations can significantly hamper candidate gene discovery if high-quality genomic resources from specific crop cultivars are unavailable. This is particularly true for disease resistance genes, which are often located in highly dynamic genomic regions. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produced de-novo genome assemblies of ten rice accessions that showed rice blast resistance associations. These assemblies facilitated the identification and validation of novel alleles of the rice blast resistance genes Ptr and Pia. Our work shows that GWAS in combination with whole-genome sequencing are powerful tools for gene cloning and uncovers an allelic series for the unusual Ptr rice blast resistance gene.
  • Contesting with the Ganges Water Machine in South Asia: Theory versus Reality

    Mukherjee, Abhijit; Bhanja, Soumendra N.; Rodell, Matthew; Wada, Yoshihide; Malakar, Prangaditya; Saha, Dipankar; MacDonald, Alan M. (ACS ES&T Water, American Chemical Society (ACS), 2023-03-01) [Article]
  • Salt-Tolerant Crops: Time to Deliver

    Melino, Vanessa Jane; Tester, Mark A. (Annual Review of Plant Biology, Annual Reviews, 2023-02-28) [Article]
    Despite the numerous advances made in our understanding of the physiology and molecular genetics of salinity tolerance, there have been relatively few applications of these to improve the salt tolerance of crops. The most significant advances have historically utilized intraspecific variation, introgression of traits from close crop wild relatives, or, less frequently, introgression from more distant relatives. Advanced lines often fail due to difficulties in the introgression or tracking of traits or due to yield penalties associated with the alleles in nonsaline environments. However, the greatest limitation is that salinity is not a primary trait for breeders. We must close the gap between research and delivery, especially for farmers who have precious few alternatives. These efforts should include a reassessment of old techniques such as grafting current crops with salt-tolerant hybrid rootstocks. Alternatively, future crops can be produced via domestication of salt-tolerant wild species—an approach that is now feasible in our lifetime.
  • Does zaxinone counteract strigolactones in shaping rice architecture?

    Wang, Jian You; Braguy, Justine; Al-Babili, Salim (Plant signaling & behavior, 2023-02-28) [Article]
    The cleavage of plant carotenoids leads to apocarotenoids, a group of metabolites including precursors of the hormones strigolactones (SLs) and abscisic acid, regulatory and signaling molecules. Zaxinone is a recently discovered apocarotenoid growth regulator that improves growth and suppress SL biosynthesis in rice (Oryza sativa). To test if zaxinone also counteracts the growth regulatory effects of SLs in rice, we co-supplied zaxinone and the synthetic SL analog rac-GR24 to the rice SL-deficient DWARF17 (d17) mutant. Results showed that co-application of GR24 and zaxinone still rescued d17 phenotype, indicating that zaxinone and GR24 act independently in regulating root and shoot growth and development in rice.
  • Integration of Apocarotenoid Profile and Expression Pattern of Carotenoid Cleavage Dioxygenases during Mycorrhization in Rice

    Votta, Cristina; Wang, Jian You; Cavallini, Nicola; Savorani, Francesco; Liew, Kit Xi; Lanfranco, Luisa; Al-Babili, Salim; Fiorilli, Valentina (Cold Spring Harbor Laboratory, 2023-02-26) [Preprint]
    Carotenoids are susceptible to degrading processes initiated by oxidative cleavage reactions mediated by Carotenoid Cleavage Dioxygenases that break their backbone, leading to products called apocarotenoids. These carotenoid-derived metabolites include the phytohormones abscisic acid and strigolactones, and different signaling molecules and growth regulators, which are utilized by plants to coordinate many aspects of their life. Several apocarotenoids have been recruited for the communication between plants and arbuscular mycorrhizal (AM) fungi and as regulators of the establishment of AM symbiosis. However, our knowledge on their biosynthetic pathways and the regulation of their pattern during AM symbiosis is still limited. In this study, we generated a qualitative and quantitative profile of apocarotenoids in roots and shoots of rice plants exposed to high/low phosphate concentrations, and upon AM symbiosis in a time course experiment covering different stages of growth and AM development. To get deeper insights in the biology of apocarotenoids during this plant-fungal symbiosis, we complemented the metabolic profiles by determining the expression pattern of CCD genes, taking advantage of chemometric tools. This analysis revealed the specific profiles of CCD genes and apocarotenoids across different stages of AM symbiosis and phosphate supply conditions, identifying novel markers at both local and systemic levels.
  • Linker histone H1 modulates defense priming and immunity in plants

    Sheikh, Arsheed Hussain; Nawaz, Kashif; Tabassum, Naheed; Trapp, Marilia Almeida; Mariappan, Kiruthiga; Alhoraibi, Hanna; Rayapuram, Naganand; Aranda, Manuel; Groth, Martin; Hirt, Heribert (Nucleic Acids Research, Oxford University Press (OUP), 2023-02-25) [Article]
    Linker H1 histones play an important role in animal and human pathogenesis, but their function in plant immunity is poorly understood. Here, we analyzed mutants of the three canonical variants of Arabidopsis H1 histones, namely H1.1, H1.2 and H1.3. We observed that double h1.1h1.2 and triple h1.1h1.2h1.3 (3h1) mutants were resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis of 3h1 mutant plants showed H1s play a key role in regulating the expression of early and late defense genes upon pathogen challenge. Moreover, 3h1 mutant plants showed enhanced production of reactive oxygen species and activation of mitogen activated protein kinases upon pathogen-associated molecular pattern (PAMP) treatment. However, 3h1 mutant plants were insensitive to priming with flg22, a well-known bacterial PAMP which induces enhanced resistance in WT plants. The defective defense response in 3h1 upon priming was correlated with altered DNA methylation and reduced global H3K56ac levels. Our data place H1 as a molecular gatekeeper in governing dynamic changes in the chromatin landscape of defense genes during plant pathogen interaction.
  • Quantifying lifetime water scarcity

    Vanderkelen, Inne; Davin, Édouard; Keune, Jessica; Miralles, Diego G.; Wada, Yoshihide; Müller-Schmied, Hannes; Gosling, Simon; Pokhrel, Yadu; Satoh, Yusuke; Hanasaki, Naota; Burek, Peter; Ostberg, Sebastian; Grant, Luke; Taranu, Sabin; Mengel, Matthias; Volkholz, Jan; Thiery, Wim (Copernicus GmbH, 2023-02-25) [Presentation]
    Water scarcity is a growing concern in many regions worldwide, as demand for clean water increases and supply becomes increasingly uncertain under climate change. Already today, more than 4 billion people experience water scarcity at least one month per year (Mekonnen and Hoekstra, 2016). Developing socio-economic conditions and growing population increase water demands, while climate change leads to changes in freshwater availability. Most studies quantify water scarcity in discrete time windows, with fixed population and climate change signals (e.g., 30 years or long-term averages). Recently, however, Thiery et al. (2021) proposed a novel approach, in which climate change impacts are integrated over a person's lifetime. In this cohort perspective, lifetime impact values are comparable across generations and regions. Evaluating this perspective for natural hazards, they showed, for example, that a newborn will experience a sixfold increase in drought exposure compared to a 60-year-old (Thiery et al., 2021). In this study, we use this cohort perspective to study how much water scarcity a person experiences during their lifetime. Based on monthly fluctuations in water demand and availability, we estimate the total amount of water demand not met and refer to it as 'lifetime water deficit'. To this end, we use an ensemble of four global hydrological models (MATSIRO, CWatM, LPJmL and H08), each forced by four GCMs and two RCP scenarios from the InterSectoral Impact Model Intercomparison Project (ISIMIP2b). The simulations account for varying population and socio-economic conditions in the historical and future period, following the SSP2 scenario. Combined with country-based population, cohort distribution and life expectancies, lifetime water deficits are quantified for different generations on a country level. Our findings reveal high water lifetime deficit values for regions that are already water scarce today, such as the Mediterranean, North Africa and the Middle East. In these regions, more than 70% of the lifetime water demand is not met when needed. Further comparison reveals differences in spatial, intergenerational and climate change scenarios, and provides information on different scenarios. Overall, this study provides a new perspective on quantifying water scarcity and the climate and population impacts.
  • Harnessing the strigolactone biosynthesis mutant lgs1 to combat food insecurity in Africa

    Mutinda, Sylvia; Jamil, Muhammad; Wang, Jian You; Berqdar, Lamis; Ateka, Elijah; Bellis, Emily S.; Al-Babili, Salim; Runo, Steven (Authorea, Inc., 2023-02-21) [Preprint]
    Sorghum is a food staple for millions of people in sub-Saharan Africa, but parasitic weeds of the Striga genus greatly diminish its production. An efficient and cost-effective way of managing Striga in smallholder farms in Africa is to deploy resistant varieties. Here, we leverage genomics and the vast genetic diversity of sorghum – evolutionarily adapted to cope with Striga parasitism in Africa – to identify new Striga-resistant sorghum genotypes. We exploit a Striga resistance mechanism that hinges on essential communication molecules – strigolactones exuded by hosts to trigger parasite seed germination. We used the Sorghum Association Panel (SAP) to search for sorghum genotypes with a mutation on the LOW GERMINATION STIMULANT 1 ( LGS1) locus that makes them ineffective in inducing Striga germination. Our analysis led us to identify new lgs1 sorghum genotypes which we named SAP lgs1. SAP lgs1 had the SL exudation profile of known lgs1 sorghum whose hallmark is the production of the low inducer of germination, orobanchol. Laboratory and field resistance screens showed that the SAP lgs1 genotypes also exhibited remarkable resistance against Striga. Our findings have far-reaching implications for improving food security in Africa by potentially reducing crop losses due to Striga parasitism.
  • FrangiPANe, a tool for creating a panreference using left behind reads

    Christine, Tranchant-Dubreuil; Clothilde, Chenal; Mathieu, Blaison; Laurence, Albar; Valentin, Klein; Cédric, Mariac; Wing Rod, A.; Yves, Vigouroux; Francois, Sabot (NAR Genomics and Bioinformatics, Oxford University Press (OUP), 2023-02-20) [Article]
    We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.
  • A comprehensive characterization of agronomic and end-use quality phenotypes across a quinoa world core collection

    Craine, Evan B.; Davies, Alathea; Packer, Daniel; Miller, Nathan D.; Schmöckel, Sandra M.; Spalding, Edgar P.; Tester, Mark A.; Murphy, Kevin M. (Frontiers in plant science, Frontiers Media SA, 2023-02-16) [Article]
    Quinoa (Chenopodium quinoa Willd.), a pseudocereal with high protein quality originating from the Andean region of South America, has broad genetic variation and adaptability to diverse agroecological conditions, contributing to the potential to serve as a global keystone protein crop in a changing climate. However, the germplasm resources currently available to facilitate quinoa expansion worldwide are restricted to a small portion of quinoa’s total genetic diversity, in part because of day-length sensitivity and issues related to seed sovereignty. This study aimed to characterize phenotypic relationships and variation within a quinoa world core collection. The 360 accessions were planted in a randomized complete block design with four replicates in each of two greenhouses in Pullman, WA during the summer of 2018. Phenological stages, plant height, and inflorescence characteristics were recorded. Seed yield, composition, thousand seed weight, nutritional composition, shape, size, and color were measured using a high-throughput phenotyping pipeline. Considerable variation existed among the germplasm. Crude protein content ranged from 11.24% to 17.81% (fixed at 14% moisture). We found that protein content was negatively correlated with yield and positively correlated with total amino acid content and days to harvest. Mean essential amino acids values met adult daily requirements but not leucine and lysine infant requirements. Yield was positively correlated with thousand seed weight and seed area, and negatively correlated with ash content and days to harvest. The accessions clustered into four groups, with one-group representing useful accessions for long-day breeding programs. The results of this study establish a practical resource for plant breeders to leverage as they strategically develop germplasm in support of the global expansion of quinoa.
  • A wheat kinase and immune receptor form host-specificity barriers against the blast fungus.

    Arora, Sanu; Steed, Andrew; Goddard, Rachel; Gaurav, Kumar; O'Hara, Tom; Schoen, Adam; Rawat, Nidhi; Elkot, Ahmed F; Korolev, Andrey V; Chinoy, Catherine; Nicholson, Martha H; Asuke, Soichiro; Antoniou-Kourounioti, Rea; Steuernagel, Burkhard; Yu, Guotai; Awal, Rajani; Forner-Martínez, Macarena; Wingen, Luzie; Baggs, Erin; Clarke, Jonathan; Saunders, Diane G O; Krasileva, Ksenia V; Tosa, Yukio; Jones, Jonathan; Tiwari, Vijay K; Wulff, Brande B H; Nicholson, Paul (Nature plants, Springer Science and Business Media LLC, 2023-02-16) [Article]
    Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. Here we show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes will enable study of the molecular interaction between pathogen effector and host resistance genes.
  • Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice

    Yu, Zhichao; Chen, Yongming; Zhou, Yong; Zhang, Yulu; Li, Mengyuan; Ouyang, Yidan; Chebotarov, Dmytro; Mauleon, Ramil; Zhao, Hu; Xie, Weibo; McNally, Kenneth; Wing, Rod Anthony; Guo, Weilong; Zhang, Jianwei (Cold Spring Harbor Laboratory, 2023-02-15) [Preprint]
    To integrate the genomic information of the rice pan-genome, we performed comparative analyses and established a user-friendly Rice Gene Index (RGI, platform with 16 platinum standard reference genomes and supplementary transcriptome data. To logically organize and scientifically the index of 744,233 genes among rice accessions, we detected 112,658 Ortholog Gene Indices, and provide ‘GeneCard’ pages to query genomic, transcriptomic, and homology information for each gene. The RGI allows users to search for relationships and comprehensive information of genes in keyword-based, sequence-based, and relationship-based ways. Furthermore, users can visualize these relationships at local and global scales corresponding to ‘Microcollinearity’ and ‘Macrocollinearity’ modules.
  • Transcriptome analysis of the phosphate starvation response sheds light on strigolactone biosynthesis in rice

    Haider, Imran; Yunmeng, Zhang; White, Fred; Li, Changsheng; Incitti, Roberto; Alam, Intikhab; Gojobori, Takashi; Ruyter-Spira, Carolien; Al-Babili, Salim; Bouwmeester, Harro J. (The Plant Journal, Wiley, 2023-02-12) [Article]
    Phosphorus (P) is a major element required for plant growth and development. To cope with P shortage, plants activate local and long-distance signaling pathways, such as the increase in the production and exudation of strigolactones (SLs). The role of the latter in mitigating P deficiency is, however, still largely unknown. To shed light on this, we studied the transcriptional response to P starvation and replenishment in wild-type rice and a SL mutant, dwarf10 (d10), and upon exogenous application of the synthetic SL GR24. P starvation resulted in major transcriptional alterations, such as the upregulation of P TRANSPORTER, SYG1/PHO81/XPR1 (SPX) and VACUOLAR PHOSPHATE EFFLUX TRANSPORTER. Gene Ontology (GO) analysis of the genes induced by P starvation showed enrichment in phospholipid catabolic process and phosphatase activity. In d10, P deficiency induced upregulation of genes enriched for sesquiterpenoid production, secondary shoot formation, and metabolic processes, including lactone biosynthesis. Furthermore, several genes induced by GR24 treatment shared the same GO terms with P starvation-induced genes, such as oxidation reduction, heme binding and oxidoreductase activity, hinting at the role that SLs play in the transcriptional reprogramming upon P starvation. Gene co-expression network analysis uncovered a METHYL TRANSFERASE that displayed co-regulation with known rice SL biosynthetic genes. Functional characterization showed that this gene encodes an enzyme catalyzing the conversion of carlactonoic acid to methyl carlactonoate. Our work provides a valuable resource to further studies on the response of crops to P deficiency and reveals a tool for the discovery of new SL biosynthetic genes.
  • PlantACT! - how to tackle the climate crisis.

    Hirt, Heribert; Al-Babili, Salim; Almeida-Trapp, Marilia; Antoine, Martin; Aranda, Manuel; Bartels, Dorothea; Bennett, Malcolm; Blilou, Ikram; Boer, Damian; Boulouis, Alix; Bowler, Chris; Brunel-Muguet, Sophie; Chardon, Fabien; Colcombet, Jean; Colot, Vincent; Daszkowska-Golec, Agata; Dinneny, Jose R; Field, Ben; Froehlich, Katja; Gardener, Catherine H; Gojon, Alain; Gom�s, Eric; �lvarez, Eva Mar�a G�mez; Gutierrez, Crisanto; Havaux, Michel; Hayes, Scott; Heard, Edith; Hodges, Michael; Alghamdi, Amal Khalaf; Laplaze, Laurent; Lauersen, Kyle J; Leonhard, Nathalie; Johnson, Xenie; Jones, Jonathan; Kollist, Hannes; Kopriva, Stanislav; Krapp, Anne; Masson, Mauricio Lopez-Portillo; McCabe, Matthew F; Merendino, Livia; Molina, Antonio; Moreno Ramirez, Jose L; M�ller-R�ber, Bernd; Nicolas, Micha�l; Nir, Ido; Orduna, Izamar Olivas; Pardo-Tom�s, Jos�; Reichheld, Jean-Philippe; Egea, Pedro Luis Rodriguez; Rouached, Hatem; Saad, Maged M; Schl�gelhofer, Peter; Singh, Kirti A; De Smet, Ive; Stanschewski, Clara; Stra, Alice; Tester, Mark; Walshe, Catherine; Weber, Andreas P M; Weigel, Detlef; Wigge, Philip; Wrzaczek, Michael; Wulff, Brande; Young, Iain M (Trends in plant science, Elsevier BV, 2023-02-03) [Article]
    Greenhouse gas (GHG) emissions have created a global climate crisis which requires immediate interventions to mitigate the negative effects on all aspects of life on this planet. As current agriculture and land use contributes up to 25% of total GHG emissions, plant scientists take center stage in finding possible solutions for a transition to sustainable agriculture and land use. In this article, the PlantACT! (Plants for climate ACTion!) initiative of plant scientists lays out a road map of how and in which areas plant scientists can contribute to finding immediate, mid-term, and long-term solutions, and what changes are necessary to implement these solutions at the personal, institutional, and funding levels.
  • HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions.

    Huang, Ying; An, Jing; Sircar, Sanchari; Bergis, Clara; Lopes, Chloé Dias; He, Xiaoning; Da Costa, Barbara; Tan, Feng-Quan; Bazin, Jeremie; Antunez-Sanchez, Javier; Mammarella, Maria Florencia; Suresh Devani, Ravi; Brik-Chaouche, Rim; Bendahmane, Abdelhafid; Frugier, Florian; Xia, Chongjing; Rothan, Christophe; Probst, Aline V.; Mohamed, Zouine; Bergounioux, Catherine; Delarue, Marianne; Zhang, Yijing; Zheng, Shaojian; Crespi, Martin; Fragkostefanakis, Sotirios; Mahfouz, Magdy M.; Ariel, Federico; Gutierrez-Marcos, Jose; Raynaud, Cécile; Latrasse, David; Benhamed, Moussa (Nature communications, Springer Science and Business Media LLC, 2023-01-28) [Article]
    The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding the control of gene expression challenging, but also opens up possible ways to epigenetically modulate gene expression. Because plants are sessile, they evolved sophisticated ways to rapidly modulate gene expression in response to environmental stress, that are thought to be coordinated by changes in chromatin conformation to mediate specific cellular and physiological responses. However, to what extent and how stress induces dynamic changes in chromatin reorganization remains poorly understood. Here, we comprehensively investigated genome-wide chromatin changes associated with transcriptional reprogramming response to heat stress in tomato. Our data show that heat stress induces rapid changes in chromatin architecture, leading to the transient formation of promoter-enhancer contacts, likely driving the expression of heat-stress responsive genes. Furthermore, we demonstrate that chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato. In light of our findings, we propose that TFs play a key role in controlling dynamic transcriptional responses through 3D reconfiguration of promoter-enhancer contacts.
  • Physiological responses induced by phospholipase C isoform 5 upon heat stress in Arabidopsis thaliana

    Annum, Nazish; Ahmed, Moddassir; Tester, Mark A.; Mukhtar, Zahid; Saeed, Nasir Ahmad (Frontiers in plant science, Frontiers Media SA, 2023-01-25) [Article]
    Plant’s perception of heat stress involves several pathways and signaling molecules, such as phosphoinositide, which is derived from structural membrane lipids phosphatidylinositol. Phospholipase C (PLC) is a well-known signaling enzyme containing many isoforms in different organisms. In the present study, Phospholipase C Isoform 5 (PLC5) was investigated for its role in thermotolerance in Arabidopsis thaliana. Two over-expressing lines and one knock-down mutant of PLC5 were first treated at a moderate temperature (37 °C) and left for recovery. Then again exposed to a high temperature (45 °C) to check the seedling viability and chlorophyll contents. Root behavior and changes in 32Pi labeled phospholipids were investigated after their exposure to high temperatures. Over-expression of PLC5 (PLC5 OE) exhibited quick and better phenotypic recovery with bigger and greener leaves followed by chlorophyll contents as compared to wild-type (Col-0) and PLC5 knock-down mutant in which seedling recovery was compromised. PLC5 knock-down mutant illustrated well-developed root architecture under controlled conditions but stunted secondary roots under heat stress as compared to over-expressing PLC5 lines. Around 2.3-fold increase in phosphatidylinositol 4,5-bisphosphate level was observed in PLC5 OE lines upon heat stress compared to wild-type and PLC5 knock-down mutant lines. A significant increase in phosphatidylglycerol was also observed in PLC5 OE lines as compared to Col-0 and PLC5 knock-down mutant lines. The results of the present study demonstrated that PLC5 over-expression contributes to heat stress tolerance while maintaining its photosynthetic activity and is also observed to be associated with primary and secondary root growth in Arabidopsis thaliana.
  • Bio-SCAN V2: A CRISPR/dCas9-based lateral flow assay for rapid detection of theophylline

    Jiang, Wenjun; Aman, Rashid; Ali, Zahir; Mahfouz, Magdy M. (Frontiers in Bioengineering and Biotechnology, Frontiers Media SA, 2023-01-19) [Article]
    Rapid, specific, and robust diagnostic strategies are needed to develop sensitive biosensors for small molecule detection, which could aid in controlling contamination and disease transmission. Recently, the target-induced collateral activity of Cas nucleases [clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases] was exploited to develop high-throughput diagnostic modules for detecting nucleic acids and small molecules. Here, we have expanded the diagnostic ability of the CRISPR-Cas system by developing Bio-SCAN V2, a ligand-responsive CRISPR-Cas platform for detecting non-nucleic acid small molecule targets. The Bio-SCAN V2 consists of an engineered ligand-responsive sgRNA (ligRNA), biotinylated dead Cas9 (dCas9-biotin), 6-carboxyfluorescein (FAM)-labeled amplicons, and lateral flow assay (LFA) strips. LigRNA interacts with dCas9-biotin only in the presence of sgRNA-specific ligand molecules to make a ribonucleoprotein (RNP). Next, the ligand-induced ribonucleoprotein is exposed to FAM-labeled amplicons for binding, and the presence of the ligand (small molecule) is detected as a visual signal [(dCas9-biotin)-ligRNA-FAM labeled DNA-AuNP complex] at the test line of the lateral flow assay strip. With the Bio-SCAN V2 platform, we are able to detect the model molecule theophylline with a limit of detection (LOD) up to 2 μM in a short time, requiring only 15 min from sample application to visual readout. Taken together, Bio-SCAN V2 assay provides a rapid, specific, and ultrasensitive detection platform for theophylline.

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