Formerly the "Center for Desert Agriculture"

Recent Submissions

  • Expression of a carotenogenic gene allows faster biomass production by redesigning plant architecture and improving photosynthetic efficiency in tobacco.

    Moreno, Juan C; Mi, Jianing; Agrawal, Shreya; Kössler, Stella; Turečková, Veronika; Tarkowská, Danuše; Thiele, Wolfram; Al-Babili, Salim; Bock, Ralph; Schöttler, Mark Aurel (The Plant journal : for cell and molecular biology, Wiley, 2020-07-06) [Article]
    Because carotenoids act as accessory pigments in photosynthesis, play a key photoprotective role, and are of major nutritional importance, carotenogenesis has been a target for crop improvement. Although carotenoids are important precursors of phytohormones, previous genetic manipulations reported little if any effects on biomass production and plant development, but resulted in specific modifications in carotenoid content. Unexpectedly, the expression of the carrot lycopene b-cyclase (DcLCYB1) in Nicotiana tabacum cv. Xanthi not only resulted in increased carotenoid accumulation, but also in altered plant architecture characterized by longer internodes, faster plant growth, early flowering and increased biomass. Here, we have challenged these transformants with a range of growth conditions to determine the robustness of their phenotype and analyze the underlying mechanisms. Transgenic DcLCYB1 lines showed increased transcript levels of key genes involved in carotenoid, chlorophyll, gibberellin (GA) and abscisic acid (ABA) biosynthesis, but also in photosynthesis-related genes. Accordingly, their carotenoid, chlorophyll, ABA and GA contents were increased. Hormone application and inhibitor experiments confirmed the key role of altered GA/ABA contents in the growth phenotype. Because the longer internodes reduce shading of mature leaves, induction of leaf senescence was delayed, and mature leaves maintained a high photosynthetic capacity. This increased total plant assimilation, as reflected in higher plant yields under both fully-controlled constant and fluctuating light, and in non-controlled conditions. Furthermore, our data is a warning that engineering of isoprenoid metabolism can cause complex changes in phytohormone homeostasis and therefore plant development, which have not been sufficiently considered in previous studies.
  • iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

    Ali, Zahir; Aman, Rashid; Mahas, Ahmed; gundra, sivakrishna; Tehseen, Muhammad; Marsic, Tin; Salunke, Rahule; Subudhi, Amit; Hala, Sharif; Hamdan, Samir; Pain, Arnab; Hassan, Norhan; Mahfouz, Magdy M. (Cold Spring Harbor Laboratory, 2020-06-05) [Preprint]
    <jats:p>The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.</jats:p>
  • The Apocarotenoid Zaxinone Is a Positive Regulator of Strigolactone and Abscisic Acid Biosynthesis in Arabidopsis Roots.

    Ablazov, Abdugaffor; Mi, Jianing; Jamil, Muhammad; Jia, Kunpeng; Wang, Jian You; Feng, Qitong; Al-Babili, Salim (Frontiers in plant science, Frontiers Media SA, 2020-05-31) [Article]
    Carotenoids are ubiquitous precursors of important metabolites including hormones, such as strigolactones (SLs) and abscisic acid (ABA), and signaling and regulatory molecules, such as the recently discovered zaxinone. Strigolactones and ABA are key regulators of plant growth and development, adaptation to environmental changes and response to biotic and abiotic stress. Previously, we have shown that zaxinone, an apocarotenoid produced in rice by the enzyme zaxinone synthase (ZAS) that is common in mycorrhizal plants, is required for normal rice growth and development, and a negative regulator of SL biosynthesis. Zaxinone is also formed in Arabidopsis, which lacks ZAS, via an unknown route. In the present study, we investigated the biological activity of zaxinone in Arabidopsis, focusing on its effect on SL and ABA biosynthesis. For this purpose, we quantified the content of both hormones and determined the levels of related transcripts in Arabidopsis (Arabidopsis thaliana), roots upon zaxinone treatment. For SL quantification, we also employed Striga seed germination bioassay. Results obtained show that zaxinone application to hydroponically grown Arabidopsis seedlings enhanced transcript levels of key biosynthetic genes of both hormones, led to higher root ABA and SL (methyl carlactonoate, MeCLA) content, and increased SL release, even under sufficient phosphate supply. Using the SL insensitive (max2-1) and the ABA deficient (aba1-6, aba2-1, and nced3) mutants, we also show that zaxinone application reduced hypocotyl growth and that this effect is caused by increasing ABA content. Our results suggest that zaxinone is a regulatory metabolite also in Arabidopsis, which triggers the biosynthesis of both carotenoid-derived hormones, SLs and ABA, in roots. In the non-mycotrophic plant Arabidopsis, zaxinone does not increase growth and may be perceived as a stress signal, while it acts as a growth-promoting metabolite and suppressor of SL biosynthesis in rice.
  • Engineering herbicide resistance via prime editing in rice

    Butt, Haroon; Rao, Gundra Sivakrishna; Sedeek, Khalid Elwy Mohamed; Aman, Rashid; Kamel, Radwa; Mahfouz, Magdy M. (Plant Biotechnology Journal, Wiley, 2020-05-16) [Article]
    Although CRISPR-Cas9 has revolutionized our ability to generate site-specific double-strand breaks, precise editing of the genome remains challenging in most eukaryotes, including plants (Shan et al., 2013). In plants homology-directed repair is inefficient, limiting our ability to make precise edits of the DNA sequence (Ali et al., 2020; Butt et al., 2017). Moreover, cytosine and adenine base editors have serious drawbacks including lower efficiency, unclean edited sequence, and the possibility of off-target mutations at other loci (Rees and Liu, 2018). Chimeric single guide RNAs (sgRNAs) can provide editing information, in RNA form, but this modality suffers from several limitations including lower efficiency, less versatility, and the need for long homology arms (Butt et al., 2017).
  • Wheat chromatin architecture is organized in genome territories and transcription factories

    Concia, Lorenzo; Veluchamy, Alaguraj; Ramirez-Prado, Juan S.; Martin-Ramirez, Azahara; Huang, Ying; Perez, Magali; Domenichini, Severine; Rodriguez Granados, Natalia Y.; Kim, SoonKap; Blein, Thomas; Duncan, Susan; Pichot, Clement; Manza-Mianza, Deborah; Juery, Caroline; Paux, Etienne; Moore, Graham; Hirt, Heribert; Bergounioux, Catherine; Crespi, Martin; Mahfouz, Magdy M.; Bendahmane, Abdelhafid; Liu, Chang; Hall, Anthony; Raynaud, Cécile; Latrasse, David; Benhamed, Moussa (Genome Biology, Springer Science and Business Media LLC, 2020-04-29) [Article]
    Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures.
  • Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

    Bazin, Jeremie; Mariappan, Kiruthiga; Jiang, Yunhe; Blein, Thomas; Volz, Ronny; Crespi, Martin; Hirt, Heribert (PLOS Pathogens, Public Library of Science (PLoS), 2020-04-17) [Article]
    Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1950 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants in the absence of PAMP treatment showed no major splicing changes. However, in contrast to MPK3 and MPK6, MPK4 was found to be a key regulator of PAMP-induced DAS events as the AS of a number of splicing factors and immunity-related protein kinases is affected, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, supporting the notion that PAMP-triggered MPK4 activation mediates regulation of alternative splicing.
  • A New Series of Carlactonoic Acid Based Strigolactone Analogs for Fundamental and Applied Research

    Jamil, Muhammad; Kountche, Boubacar Amadou; Wang, Jian You; Haider, Imran; Jia, Kunpeng; Takahashi, Ikuo; Ota, Tsuyoshi; Asami, Tadao; Al-Babili, Salim (Frontiers in Plant Science, Frontiers Media SA, 2020-04-15) [Article]
    Strigolactones (SLs) are a group of carotenoid derived plant hormones that play a key role in establishing plant architecture and adapting it to environmental changes, and are involved in plants response to biotic and abiotic stress. SLs are also released into the soil to serve as a chemical signal attracting beneficial mycorrhizal fungi. However, this signal also induces seed germination in root parasitic weeds that represent a major global threat for agriculture. This wide spectrum of biological functions has made SL research one of the most important current topics in fundamental and applied plant science. The availability of SLs is crucial for investigating SL biology as well as for agricultural application. However, natural SLs are produced in very low amounts, and their organic synthesis is quite difficult, which creates a need for efficient and easy-to-synthesize analogs and mimics. Recently, we have generated a set of SL analogs, Methyl Phenlactonoates (MPs), which resemble the non-canonical SL carlactonoic acid. In this paper, we describe the development and characterization of a new series of easy-to-synthesize MPs. The new analogs were assessed with respect to regulation of shoot branching, impact on leaf senescence, and induction of seed germination in different root parasitic plants species. Some of the new analogs showed higher efficiency in inhibiting shoot branching as well as in triggering parasitic seed germination, compared to the commonly used GR24. MP16 was the most outstanding analog showing high activity in different SL biological functions. In summary, our new analogs series contains very promising candidates for different applications, which include the usage in studies for understanding different aspects of SL biology as well as large scale field application for combating root parasitic weeds, such as Striga hermonthica that devastates cereal yields in sub-Saharan Africa.
  • Wounding and Insect Feeding Trigger two Independent MAPK Pathways with Distinct Regulation and Kinetics.

    Sözen, Cécile; Schenk, Sebastian Timo; Boudsocq, Marie; Chardin, Camille; Almeida-Trapp, Marilia; Krapp, Anne; Hirt, Heribert; Mithöfer, Axel; Colcombet, Jean (The Plant cell, American Society of Plant Biologists (ASPB), 2020-04-09) [Article]
    Abiotic and biotic factors cause plant wounding and trigger complex short- and long-term responses at the local and systemic levels. These responses are under the control of complex signaling pathways, which are still poorly understood. Here, we show that the rapid activation of clade-A Mitogen Activated Protein Kinases (MAPKs) MPK3 and MPK6 by wounding depends on the upstream MAPK Kinases (MAP2Ks) MKK4 and MKK5 but is independent of jasmonic acid (JA) signaling. In addition, this fast module does not control wound-triggered JA accumulation in Arabidopsis, unlike its orthologues in tobacco. We also demonstrate that a second MAPK module, composed of MKK3 and the clade-C MAPKs MPK½/7, is activated by wounding in a MKK4/5-independent manner. We provide evidence that the activation of this MKK3-MPK½/7 module occurs mainly through wound-induced JA production via the transcriptional regulation of upstream clade-III MAP3Ks, particularly MAP3K14. We show that mkk3 mutant plants are more susceptible to herbivory from larvae of the generalist lepidopteran herbivore Spodoptera littoralis, indicating that the MKK3-MPK½/7 module is involved in counteracting insect feeding.
  • Nanofabrication of Isoporous Membranes for Cell Fractionation

    Sabirova, Ainur; Pisig, Florencio Jr; Rayapuram, Naganand; Hirt, Heribert; Nunes, Suzana Pereira (Scientific Reports, Springer Science and Business Media LLC, 2020-04-09) [Article]
    Cell fractionations and other biological separations frequently require several steps. They could be much more effectively done by filtration, if isoporous membranes would be available with high pore density, and sharp pore size distribution in the micro- and nanoscale. We propose a combination of two scalable methods, photolithography and dry reactive ion etching, to fabricate a series of polyester membranes with isopores of size 0.7 to 50 μm and high pore density with a demonstrated total area of 38.5 cm2. The membranes have pore sizes in the micro- and submicro-range, and pore density 10-fold higher than track-etched analogues, which are the only commercially available isoporous polymeric films. Permeances of 220,000 L m-2 h-1bar-1 were measured with pore size 787 nm. The method does not require organic solvents and can be applied to many homopolymeric materials. The pore reduction from 2 to 0.7 μm was obtained by adding a step of chemical vapor deposition. The isoporous system was successfully demonstrated for the organelle fractionation of Arabidopsis homogenates and could be potentially extended to other biological fractionations.
  • Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

    Arrigoni, Roberto; Berumen, Michael L.; Mariappan, Kiruthiga; Beck, Pieter S.A.; Hulver, Ann Marie; Montano, Simone; Pichon, Michel; Strona, Giovanni; Terraneo, Tullia Isotta; Benzoni, Francesca (Coral Reefs, Springer Science and Business Media LLC, 2020-04-08) [Article]
    Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals.
  • Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans.

    Eida, Abdul Aziz; Bougouffa, Salim; L’Haridon, Floriane; Alam, Intikhab; Weisskopf, Laure; Bajic, Vladimir B.; Saad, Maged M.; Hirt, Heribert (Frontiers in Microbiology, Frontiers Media SA, 2020-03-28) [Article]
    Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography–mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes’ involvement in JZ38’s functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.
  • Complete genome sequence of the endophytic bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of the perennial desert tussock grass Panicum turgidum.

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Saad, Maged M; Hirt, Heribert (Archives of microbiology, Springer Science and Business Media LLC, 2020-03-16) [Article]
    Cellulosimicrobium sp. JZ28, a root endophytic bacterium from the desert plant Panicum turgidum, was previously identified as a plant growth-promoting bacterium. The genome of JZ28 consists of a 4378,193 bp circular chromosome and contains 3930 CDSs with an average GC content of 74.5%. Whole-genome sequencing analysis revealed that JZ28 was closely related to C. aquatile 3 bp. The genome harbors genes responsible for protection against oxidative, osmotic and salinity stresses, such as the production of osmoprotectants. It also contains genes with a role in the production of volatiles, such as hydrogen sulfide, which promote biotic and abiotic stress tolerance in plants. The presence of three copies of chitinase genes indicates a possible role of JZ28 as biocontrol agent against fungal pathogens, while a number of genes for the degradation of plant biopolymers indicates potential application in industrial processes. Genome sequencing and mining of culture-dependent collections of bacterial endophytes from desert plants provide new opportunities for biotechnological applications.
  • Tailoring Plant-Associated Microbial Inoculants in Agriculture - A Roadmap for Successful Application.

    Saad, Maged M; Eida, Abdul Aziz; Hirt, Heribert (Journal of experimental botany, Oxford University Press (OUP), 2020-03-12) [Article]
    Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim to establish sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we also suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the field of microbial inoculant application.
  • Nucleic Acid Detection Using CRISPR/Cas Biosensing Technologies

    Aman, Rashid; Mahas, Ahmed; Mahfouz, Magdy M. (ACS Synthetic Biology, American Chemical Society (ACS), 2020-03-11) [Article]
    For infectious diseases, rapid and accurate identification of the pathogen is critical for effective management and treatment, but diagnosis remains challenging, particularly in resource-limited areas. Methods that accurately detect pathogen nucleic acids can provide robust, accurate, rapid, and ultrasensitive technologies for point-of-care diagnosis of pathogens, and thus yield information that is invaluable for disease management and treatment. Several technologies, mostly PCR-based, have been employed for pathogen detection; however, these require expensive reagents and equipment, and skilled personnel. CRISPR/Cas systems have been used for genome editing, based on their ability to accurately recognize and cleave specific DNA and RNA sequences. Moreover, following recognition of the target sequence, certain CRISPR/Cas systems including orthologues of Cas13, Cas12a, and Cas14 exhibit collateral nonspecific catalytic activities that can be employed for nucleic acid detection, for example by degradation of a labeled nucleic acid to produce a fluorescent signal. CRISPR/Cas systems are amenable to multiplexing, thereby enabling a single diagnostic test to identify multiple targets down to attomolar (10–18 mol/L) concentrations of target molecules. Developing devices that couple CRISPR/Cas with lateral flow systems may allow inexpensive, accurate, highly sensitive, in-field deployable diagnostics. These sensors have myriad applications, from human health to agriculture. In this review, we discuss the recent advances in the field of CRISPR-based biosensing technologies and highlight insights of their potential use in a myriad of applications.
  • Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big.

    Clark, Natalie M; Van den Broeck, Lisa; Guichard, Marjorie; Stager, Adam; Tanner, Herbert G; Blilou, Ikram; Grossmann, Guido; Iyer-Pascuzzi, Anjali S; Maizel, Alexis; Sparks, Erin E; Sozzani, Rosangela (Annual review of plant biology, Annual Reviews, 2020-03-03) [Article]
    The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometric and physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale. Expected final online publication date for the Annual Review of Plant Biology, Volume 71 is April 29, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
  • Carotenoid biofortification in crop plants: citius, altius, fortius.

    Zheng, Xiongjie; Guliano, Giovanni; Al-Babili, Salim (Biochimica et biophysica acta. Molecular and cell biology of lipids, Elsevier BV, 2020-02-19) [Article]
    Carotenoids are indispensable for human health, required as precursors of vitamin A and efficient antioxidants. However, these plant pigments that play a vital role in photosynthesis are represented at insufficient levels in edible parts of several crops, which creates a need for increasing their content or optimizing their composition through biofortification. In particular, vitamin A deficiency, a severe health problem affecting the lives of millions in developing countries, has triggered the development of a series of high-provitamin A crops, including Golden Rice as the best-known example. Further carotenoid-biofortified crops have been generated by using genetic engineering approaches or through classical breeding. In this review, we depict carotenoid metabolism in plants and provide an update on the development of carotenoid-biofortified plants and their potential to meet needs and expectations. Furthermore, we discuss the possibility of using natural variation for carotenoid biofortification and the potential of gene editing tools. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
  • Complete Genome Sequence of Paenibacillus sp. JZ16, a Plant Growth Promoting Root Endophytic Bacterium of the Desert Halophyte Zygophyllum Simplex.

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Hirt, Heribert; Saad, Maged (Current microbiology, Springer Science and Business Media LLC, 2020-02-05) [Article]
    Paenibacillus sp. JZ16 is a gram-positive, rod-shaped, motile root endophytic bacterium of the pioneer desert halophytic plant Zygophyllum simplex. JZ16 was previously shown to promote salinity stress tolerance in Arabidopsis thaliana and possesses a highly motile phenotype on nutrient agar. JZ16 genome sequencing using PacBio generated 82,236 reads with a mean insert read length of 11,432 bp and an estimated genome coverage of 127X, resulting in a chromosome of 7,421,843 bp with a GC content of 49.25% encoding 6710 proteins, 8 rRNA operons, 117 ncRNAs and 73 tRNAs. Whole-genome sequencing analysis revealed a potentially new species for JZ16. Functional analysis revealed the presence of a number of enzymes involved in the breakdown of plant-based polymers. JZ16 could be of potential use in agricultural applications for promoting biotic and abiotic stress tolerance and for biotechnological processes (e.g., as biocatalysts for biofuel production). The culture-dependent collection of bacterial endophytes from desert plants combined with genome sequence mining provides new opportunities for industrial applications.
  • Visualizing Protein Associations in Living Arabidopsis Embryo

    Long, Yuchen; Stahl, Yvonne; Weidtkamp-Peters, Stefanie; Blilou, Ikram (Springer US, 2020-01-24) [Protocol]
    Protein–protein interactions (PPI) are essential for a plethora of biological processes. These interactions can be visualized and quantified with spatial resolution using Förster resonance energy transfer (FRET) measured by fluorescence lifetime imaging microscopy (FLIM) technology. Currently, FRET-FLIM is routinely used in cell biology, and it has become a powerful tool to map protein interactions in native environments. However, implementing this technology in living multicellular organism remains challenging, especially when dealing with developing plant embryos where tissues are confined in multiple cell layers preventing direct imaging. In this chapter, we describe a step-by-step protocol for studying PPI using FRET-FLIM of the two transcription factors SCARECROW and SHORTROOT in Arabidopsis embryos. We provide a detailed description from embryo isolation to data analysis and representation.
  • Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice

    Ali, Zahir; Shami, Ashwag; Sedeek, Khalid Elwy Mohamed; Kamel, Radwa; Alhabsi, Abdulrahman; Tehseen, Muhammad; Hassan, Norhan; Butt, Haroon; Kababji, Ahad; Hamdan, Samir; Mahfouz, Magdy M. (Communications Biology, Springer Science and Business Media LLC, 2020-01-23) [Article]
    Precise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.
  • Enterobacter sp. SA187 mediates plant thermotolerance by chromatin modification of heat stress genes

    Shekhawat, Kirti; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Jalal, Rewaa S.; Hirt, Heribert (Cold Spring Harbor Laboratory, 2020-01-17) [Preprint]
    Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Heat acclimation empowers plants to survive under extreme temperature conditions but the potential of beneficial microbes to make plants thermotolerant has not been considered so far. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces heat tolerance in Arabidopsis thaliana by reprogramming the plant transcriptome to a similar extent as acclimation. Acclimation induces priming of heat stress memory genes such as APX2 and HSP18.2 via the transcription factors HSFA1A, B, D, and E and the downstream master regulator HSFA2. hsfa1a,b,d,e and hsfa2 mutants compromised both acclimation and bacterial priming through the same pathway of HSF transcription factors. However, while acclimation transiently modifies H3K4me3 levels at heat stress memory gene loci, SA187 induces the constitutive priming of these loci. In summary, we demonstrate the molecular mechanism by which SA187 imparts thermotolerance in A. thaliana, suggesting that beneficial microbes might be a promising way to enhance crop production under global warming conditions.

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