Now showing items 21-40 of 566

    • 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.
    • Manipulation of carotenoid metabolism stimulates biomass and stress tolerance in tomato

      Vallarino, José G; Mi, Jianing; Petřík, Ivan; Novak, Ondrej; Correa, Sandra Marcela; Kosmacz, Monika; Havaux, Michel; Rodriguez-Concepcion, Manuel; Al-Babili, Salim; Fernie, Alisdair R.; Skirycz, Aleksandra; Moreno, Juan C (Cold Spring Harbor Laboratory, 2021-05-07) [Preprint]
      Improving yield, nutritional value and tolerance to abiotic stress are major targets of current breeding and biotechnological approaches that aim at increasing crop production and ensuring food security. Metabolic engineering of carotenoids, the precursor of Vitamin-A and plant hormones that regulate plant growth and response to adverse growth conditions, has been mainly focusing on provitamin A biofortification or the production of high-value carotenoids. Here, we show that the introduction of a single gene of the carotenoid biosynthetic pathway in different tomato cultivars simultaneously improved photosynthetic capacity and tolerance to various abiotic stresses (e.g., high light, salt, and drought), caused an up to 77% fruit yield increase and enhanced fruit's provitamin A content and shelf life. Our findings pave the way for developing a new generation of crops that combine high productivity and increased nutritional value with the capability to cope with climate change-related environmental challenges.
    • Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation

      Butt, Haroon; Bazin, Jeremie; Alshareef, Sahar; Eid, Ayman; Benhamed, Moussa; Reddy, Anireddy S. N.; Crespi, Martin; Mahfouz, Magdy M. (Communications Biology, Springer Science and Business Media LLC, 2021-05-05) [Article]
      AbstractThe SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants.
    • Haplotype variations of major flowering time genes in quinoa unveil their role in the adaptation to different environmental conditions

      Patiranage, Dilan S.R.; Asare, Edward; Maldonado-Taipe, Nathaly; Rey, Elodie; Emrani, Nazgol; Tester, Mark A.; Jung, Christian (Plant, Cell & Environment, Wiley, 2021-05-05) [Article]
      Response to photoperiod is of major importance in crop production. It defines the adaptation of plants to local environments. Quinoa is a short day plant which had been domesticated in the Andeans regions. We wanted to understand the adaptation to long-day conditions by studying orthologs of two major flowering time regulators of Arabidopsis, FLOWERING LOCUS T (FT) and CONSTANS (CO) in quinoa accessions with contrasting photoperiod response. By searching the quinoa reference genome sequence, we identified 24 FT and six CO homologs. CqFT genes displayed remarkably different expression patterns between long-day and short-day conditions, whereas the influence of the photoperiod on CqCOL expressions was moderate. Cultivation of 276 quinoa accessions under short-day and long-day conditions revealed great differences in photoperiod sensitivity. After sequencing their genomes, we identified large sequence variations in 12 flowering time genes. We found non-random distribution of haplotypes across accessions from different geographical origins, highlighting the role of CqFT and CqCOL genes in the adaptation to different day-length conditions. We identified five haplotypes causing early flowering under long days. This study provides assets for quinoa breeding because superior haplotypes can be assembled in a predictive breeding approach to produce well-adapted early flowering lines under long-day photoperiods. This article is protected by copyright. All rights reserved.
    • Iso-anchorene is an endogenous metabolite that inhibits primary root growth in Arabidopsis.

      Jia, Kunpeng; Mi, Jianing; Ablazov, Abdugaffor; Ali, Shawkat; Yang, Yu; Balakrishna, Aparna; Berqdar, Lamis; Feng, Qitong; Blilou, Ikram; Al-Babili, Salim (The Plant journal : for cell and molecular biology, Wiley, 2021-04-27) [Article]
      Carotenoid-derived regulatory metabolites and hormones are generally known to arise through the oxidative cleavage of a single double bond in the carotenoid backbone, which yields mono-carbonyl products called apocarotenoids. However, the extended conjugated double bond system of these pigments predestines them also to repeated cleavage forming di-aldehyde products, diapocarotenoids, which have been less investigated due to their instability and low abundance. Recently, we reported on the short diapocarotenoid anchorene as an endogenous Arabidopsis metabolite and specific signaling molecule that promotes anchor root formation. In this work, we investigated the biological activity of a synthetic isomer of anchorene, iso-anchorene, which can derive from repeated carotenoid cleavage. We show that iso-anchorene is a growth inhibitor that specifically inhibits primary root growth by reducing cell division rates in the root apical meristem. Using auxin efflux transporter marker lines, we also show that the effect of iso-anchorene on primary root growth involves the modulation of auxin homeostasis. Moreover, by using liquid chromatography mass spectrometry (LC-MS) analysis, we demonstrate that iso-anchorene is a natural Arabidopsis metabolite. Chemical inhibition of carotenoid biosynthesis led to a significant decrease in the iso-anchorene level, indicating that it originates from this metabolic pathway. Taken together, our results reveal a further carotenoid-derived regulatory metabolite with a specific biological function that affects root growth, manifesting the biological importance of diapocarotenoids.
    • SeedQuant: A deep learning-based tool for assessing stimulant and inhibitor activity on root parasitic seeds.

      Braguy, Justine; Ramazanova, Merey; Giancola, Silvio; Jamil, Muhammad; Kountche, Boubacar Amadou; Zarban, Randa Alhassan Yahya; Felemban, Abrar; Wang, Jian You; Lin, Pei-Yu; Haider, Imran; Zurbriggen, Matias; Ghanem, Bernard; Al-Babili, Salim (Plant physiology, Oxford University Press (OUP), 2021-04-15) [Article]
      Witchweeds (Striga spp.) and broomrapes (Orobanchaceae and Phelipanche spp.) are root parasitic plants that infest many crops in warm and temperate zones, causing enormous yield losses and endangering global food security. Seeds of these obligate parasites require rhizospheric, host-released stimulants to germinate, which opens up possibilities for controlling them by applying specific germination inhibitors or synthetic stimulants that induce lethal germination in host's absence. To determine their effect on germination, root exudates or synthetic stimulants/inhibitors are usually applied to parasitic seeds in in vitro bioassays, followed by assessment of germination ratios. Although these protocols are very sensitive, the germination recording process is laborious, representing a challenge for researchers and impeding high-throughput screens. Here, we developed an automatic seed census tool to count and discriminate germinated from non-germinated seeds. We combined deep learning, a powerful data-driven framework that can accelerate the procedure and increase its accuracy, for object detection with computer vision latest development based on the Faster R-CNN algorithm. Our method showed an accuracy of 94% in counting seeds of Striga hermonthica and reduced the required time from ˜5 minutes to 5 seconds per image. Our proposed software, SeedQuant, will be of great help for seed germination bioassays and enable high-throughput screening for germination stimulants/inhibitors. ​SeedQuant is an open-source software that can be further trained to count different types of seeds for research purposes.
    • Vigilant: An Engineered VirD2-Cas9 Complex for Lateral Flow Assay-Based Detection of SARS-CoV2

      Marsic, Tin; Ali, Zahir; Tehseen, Muhammad; Mahas, Ahmed; Hamdan, Samir; Mahfouz, Magdy M. (Nano Letters, American Chemical Society (ACS), 2021-04-12) [Article]
      Rapid, sensitive, and specific point-of-care testing for pathogens is crucial for disease control. Lateral flow assays (LFAs) have been employed for nucleic acid detection, but they have limited sensitivity and specificity. Here, we used a fusion of catalytically inactive SpCas9 endonuclease and VirD2 relaxase for sensitive, specific nucleic acid detection by LFA. In this assay, the target nucleic acid is amplified with biotinylated oligos. VirD2-dCas9 specifically binds the target sequence via dCas9 and covalently binds to a FAM-tagged oligonucleotide via VirD2. The biotin label and FAM tag are detected by a commercially available LFA. We coupled this system, named Vigilant (<u>Vi</u>rD2-dCas9 <u>g</u>u<u>i</u>ded and <u>L</u>FA-coupled <u>n</u>ucleic acid <u>t</u>est), to reverse transcription-recombinase polymerase amplification to detect SARS-CoV2 in clinical samples. Vigilant exhibited a limit of detection of 2.5 copies/μL, comparable to CRISPR-based systems, and showed no cross-reactivity with SARS-CoV1 or MERS. Vigilant offers an easy-to-use, rapid, cost-effective, and robust detection platform for SARS-CoV2.
    • Early growth stage characterization and the biochemical responses for salinity stress in tomato

      Alam, Md Sarowar; Tester, Mark A.; Fiene, Gabriele; Mousa, Magdi Ali Ahmed (Plants, MDPI AG, 2021-04-07) [Article]
      Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological character-istics; however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.
    • Digital insights: bridging the phenotype-to-genotype divide

      McCabe, Matthew; Tester, Mark A. (Journal of Experimental Botany, Oxford University Press (OUP), 2021-04-02) [Article]
      The convergence of autonomous platforms for field-based phenotyping with advances in machine learning for big data analytics and rapid sequencing for genome description herald the promise of new insights and discoveries in the plant sciences. Han et al. (2021) leverage these emerging tools to navigate the challenging path from field-based mapping of phenotypic features to identifying specific genetic loci in the laboratory: in this case, loci responsible for regulating daily flowering time in lettuce. While their contribution neatly illustrates these exciting technological developments, it also highlights the work that remains to bridge these multidisciplinary fields to more fully deliver upon the promise of digital agriculture.
    • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

      Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (NCBI, 2021-03-22) [Bioproject, Dataset]
      We report the transcriptome composition of ahl13-1 compared to WT (col-0) plant without treatment and after Pst hrcC-application Overall design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of col0 and ahl13-1 under treated and untreated conditions. col0 samples are in GEO Series GSE118854.
    • Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

      Abrouk, Michael; Athiyannan, Naveenkumar; Müller, Thomas; Pailles, Yveline; Stritt, Christoph; Roulin, Anne C.; Chu, Chenggen; Liu, Shuyu; Morita, Takumi; Handa, Hirokazu; Poland, Jesse; Keller, Beat; Krattinger, Simon G. (Communications Biology, Springer Nature, 2021-03-19) [Article]
      The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.
    • Microbial communities of wheat plants inoculated with endophytic bacterium Enterobacter sp. SA187

      Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (NCBI, 2021-03-16) [Bioproject, Dataset]
      Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces thermotolerance of crops in a sustainable manner. Microbiome diversity of wheat plants is positively influenced by SA187 in open field agriculture, indicating that beneficial microbes can be a powerful tool to enhance agriculture in open field agriculture. Overall design: We examined the effect the SA187 inoculation on the root endosphere microbiome of wheat plant growing under desert farming condition.
    • Molecular mechanisms of Enterobacter sp. SA187 induced thermotolerance in Arabidopsis thaliana

      Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (NCBI, 2021-03-16) [Bioproject, Dataset]
      Global warming and heat stress belong to the most critical environmental challenges to agriculture worldwide, causing severe losses of major crop yields. In present study we report that the endophytic bacterium Enterobacter sp. SA187 protects Arabidopsis thaliana to heat stress. To understand the mechanisms at molecular level we performed RNA-seq Overall design: mRNA seq to elucidate the SA187 mediated thermotolerance in Arabidopsis thaliana inoculated with entrobacter sp SA187
    • LAMP-Coupled CRISPR–Cas12a Module for Rapid and Sensitive Detection of Plant DNA Viruses

      Mahas, Ahmed; Hassan, Norhan; Aman, Rashid; Maršić, Tin; Wang, Qiaochu; Ali, Zahir; Mahfouz, Magdy M. (Viruses, MDPI AG, 2021-03-12) [Article]
      One important factor for successful disease management is the ability to rapidly and accurately identify the causal agent. Plant viruses cause severe economic losses and pose a serious threat to sustainable agriculture. Therefore, optimization of the speed, sensitivity, feasibility, portability, and accuracy of virus detection is urgently needed. Here, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid diagnostic method utilizing the CRISPR–Cas12a system for detecting two geminiviruses, tomato yellow leaf curl virus (TYLCV) and tomato leaf curl New Delhi virus (ToLCNDV), which have single-stranded DNA genomes. Our assay detected TYLCV and ToLCNDV in infected plants with high sensitivity and specificity. Our newly developed assay can be performed in ~1 h and provides easy-to-interpret visual readouts using a simple, low-cost fluorescence visualizer, making it suitable for point-of-use applications.
    • Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa

      Maldonado-Taipe, Nathaly; Patirange, Dilan S. R.; Schmoeckel, Sandra Manuela; Jung, Christian; Emrani, Nazgol (PLOS ONE, Public Library of Science (PLoS), 2021-03-11) [Article]
      Quinoa depicts high nutritional quality and abiotic stress resistance, attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. Moreover, we validated our reference genes by normalizing two known diurnally regulated genes, BTC1 and BBX19. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.
    • Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum

      Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Hirt, Heribert; Saad, Maged (Current Microbiology, Springer Nature, 2021-03-08) [Article]
      Cellulomonas sp. JZ18 is a gram-positive, rod shaped bacterium that was previously isolated from the root endosphere of the perennial desert tussock-grass Panicum turgidum. Genome coverage of PacBio sequencing was approximately 199X. Genome assembly generated a single chromosome of 7,421,843 base pairs with a guanine-cytosine (GC) content of 75.60% with 3240 protein coding sequences, 361 pseudo genes, three ribosomal RNA operons, three non-coding RNAs and 45 transfer RNAs. Comparison of JZ18′s genome with type strains from the same genus, using digital DNA–DNA hybridization and average nucleotide identity calculations, revealed that JZ18 might potentially belong to a new species. Functional analysis revealed the presence of genes that may complement previously observed biochemical and plant phenotypes. Furthermore, the presence of a number of enzymes could be of potential use in industrial processes as biocatalysts. Genome sequencing and analysis, coupled with comparative genomics, of endophytic bacteria for their potential plant growth promoting activities under different soil conditions will accelerate the knowledge and applications of biostimulants in sustainable agriculture.
    • Chemical activation of Arabidopsis SnRK2.6 by pladienolide B

      Punkkinen, Matleena; Mahfouz, Magdy M.; Fujii, Hiroaki (Plant Signaling & Behavior, Informa UK Limited, 2021-03-08) [Article]
      Abscisic acid (ABA) is an important phytohormone mediating osmotic stress responses. SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASE 2.6 (SnRK2.6, also named OPEN STOMATA1 and SNF1-RELATED KINASE 2E) is central in the ABA signaling pathway; therefore, manipulating its activity may be useful to confer stress tolerance in plants. Pladienolide B (PB) is an mRNA splicing inhibitor and enhances ABA responses. Here, we analyzed the effect of PB on Arabidopsis SnRK2.6. PB enhanced the activity of recombinant SnRK2.6 in vitro through direct physical interaction as predicted by molecular docking simulations followed by mutation experiments and isothermal titration calorimetry. Structural modeling predicted probable interaction sites between PB and SnRK2.6, and experiments with mutated SnRK2.6 revealed that Leu-46 was the most essential amino acid residue for SnRK2.6 activation by PB. This study demonstrates the feasibility of SnRK2.6 chemical manipulation and paves the way for the modification of plant osmotic stress responses.