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Mechanisms Controlling the Selective Iron and Zinc Biofortification of Rice
Nom/Logotip de la Universitat on s’ha llegit la tesi Mechanisms controlling the selective iron and zinc biofortification of rice Raviraj Banakar http://hdl.handle.net/10803/384320 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora. -
Integration of Adaptive Changes to Iron Deficiency in Plants
G Model CPB-30; No. of Pages 12 ARTICLE IN PRESS Current Plant Biology xxx (2016) xxx–xxx Contents lists available at ScienceDirect Current Plant Biology jo urnal homepage: www.elsevier.com/locate/cpb From the proteomic point of view: Integration of adaptive changes to iron deficiency in plants a a,b,∗ Hans-Jörg Mai , Petra Bauer a Institute of Botany, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Building 26.13, 02.36, 40225 Düsseldorf, Germany b CEPLAS Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany a r t i c l e i n f o a b s t r a c t Article history: Knowledge about the proteomic adaptations to iron deficiency in plants may contribute to find possible Received 10 July 2015 new research targets in order to generate crop plants that are more tolerant to iron deficiency, to increase Received in revised form 22 January 2016 the iron content or to enhance the bioavailability of iron in food plants. We provide this update on adap- Accepted 1 February 2016 tations to iron deficiency from the proteomic standpoint. We have mined the data and compared ten studies on iron deficiency-related proteomic changes in six different Strategy I plant species. We sum- Keywords: marize these results and point out common iron deficiency-induced alterations of important biochemical Arabidopsis pathways based on the data provided by these publications, deliver explanations on the possible benefits Iron Proteome that arise from these adaptations in iron-deficient plants and present a concluding model of these adap- tations. -
A Bacterial Aromatic Aldehyde Dehydrogenase Critical for The
www.nature.com/scientificreports OPEN A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of Received: 21 October 2016 Accepted: 07 February 2017 syringaldehyde Published: 15 March 2017 Naofumi Kamimura1, Takayuki Goto1, Kenji Takahashi1, Daisuke Kasai1, Yuichiro Otsuka2, Masaya Nakamura2, Yoshihiro Katayama3, Masao Fukuda1 & Eiji Masai1 Vanillin and syringaldehyde obtained from lignin are essential intermediates for the production of basic chemicals using microbial cell factories. However, in contrast to vanillin, the microbial conversion of syringaldehyde is poorly understood. Here, we identified an aromatic aldehyde dehydrogenase (ALDH) gene responsible for syringaldehyde catabolism from 20 putative ALDH genes of Sphingobium sp. strain SYK-6. All these genes were expressed in Escherichia coli, and nine gene products, including previously characterized BzaA, BzaB, and vanillin dehydrogenase (LigV), exhibited oxidation activities for syringaldehyde to produce syringate. Among these genes, SLG_28320 (desV) and ligV were most highly and constitutively transcribed in the SYK-6 cells. Disruption of desV in SYK-6 resulted in a significant reduction in growth on syringaldehyde and in syringaldehyde oxidation activity. Furthermore, a desV ligV double mutant almost completely lost its ability to grow on syringaldehyde. Purified DesV showed −1 −1 −1 −1 similar kcat/Km values for syringaldehyde (2100 s ·mM ) and vanillin (1700 s ·mM ), whereas LigV substantially preferred vanillin (8800 s−1·mM−1) over syringaldehyde (1.4 s−1·mM−1). These results clearly demonstrate that desV plays a major role in syringaldehyde catabolism. Phylogenetic analyses showed that DesV-like ALDHs formed a distinct phylogenetic cluster separated from the vanillin dehydrogenase cluster. Lignin is the second most abundant bio-resource on earth after cellulose, and its decomposition is essential for the carbon cycle. -
Supplementary Materials
1 Supplementary Materials: Supplemental Figure 1. Gene expression profiles of kidneys in the Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice. (A) A heat map of microarray data show the genes that significantly changed up to 2 fold compared between Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice (N=4 mice per group; p<0.05). Data show in log2 (sample/wild-type). 2 Supplemental Figure 2. Sting signaling is essential for immuno-phenotypes of the Fcgr2b-/-lupus mice. (A-C) Flow cytometry analysis of splenocytes isolated from wild-type, Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice at the age of 6-7 months (N= 13-14 per group). Data shown in the percentage of (A) CD4+ ICOS+ cells, (B) B220+ I-Ab+ cells and (C) CD138+ cells. Data show as mean ± SEM (*p < 0.05, **p<0.01 and ***p<0.001). 3 Supplemental Figure 3. Phenotypes of Sting activated dendritic cells. (A) Representative of western blot analysis from immunoprecipitation with Sting of Fcgr2b-/- mice (N= 4). The band was shown in STING protein of activated BMDC with DMXAA at 0, 3 and 6 hr. and phosphorylation of STING at Ser357. (B) Mass spectra of phosphorylation of STING at Ser357 of activated BMDC from Fcgr2b-/- mice after stimulated with DMXAA for 3 hour and followed by immunoprecipitation with STING. (C) Sting-activated BMDC were co-cultured with LYN inhibitor PP2 and analyzed by flow cytometry, which showed the mean fluorescence intensity (MFI) of IAb expressing DC (N = 3 mice per group). 4 Supplemental Table 1. Lists of up and down of regulated proteins Accession No. -
Kramers' Theory and the Dependence of Enzyme Dynamics on Trehalose
catalysts Review Kramers’ Theory and the Dependence of Enzyme Dynamics on Trehalose-Mediated Viscosity José G. Sampedro 1,* , Miguel A. Rivera-Moran 1 and Salvador Uribe-Carvajal 2 1 Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí C.P. 78290, Mexico; [email protected] 2 Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico; [email protected] * Correspondence: [email protected]fisica.uaslp.mx; Tel.: +52-(444)-8262-3200 (ext. 5715) Received: 29 April 2020; Accepted: 29 May 2020; Published: 11 June 2020 Abstract: The disaccharide trehalose is accumulated in the cytoplasm of some organisms in response to harsh environmental conditions. Trehalose biosynthesis and accumulation are important for the survival of such organisms by protecting the structure and function of proteins and membranes. Trehalose affects the dynamics of proteins and water molecules in the bulk and the protein hydration shell. Enzyme catalysis and other processes dependent on protein dynamics are affected by the viscosity generated by trehalose, as described by the Kramers’ theory of rate reactions. Enzyme/protein stabilization by trehalose against thermal inactivation/unfolding is also explained by the viscosity mediated hindering of the thermally generated structural dynamics, as described by Kramers’ theory. The analysis of the relationship of viscosity–protein dynamics, and its effects on enzyme/protein function and other processes (thermal inactivation and unfolding/folding), is the focus of the present work regarding the disaccharide trehalose as the viscosity generating solute. Finally, trehalose is widely used (alone or in combination with other compounds) in the stabilization of enzymes in the laboratory and in biotechnological applications; hence, considering the effect of viscosity on catalysis and stability of enzymes may help to improve the results of trehalose in its diverse uses/applications. -
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
bioRxiv preprint doi: https://doi.org/10.1101/205583; this version posted November 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Oxidative pathways of deoxyribose and deoxyribonate catabolism 1* 1 2 1 Morgan N. Price, Jayashree Ray, Anthony T. Iavarone, Hans K. Carlson, Elizabeth M. 3 3 1,4,* 1,5,* Ryan, Rex R. Malmstrom, Adam P. Arkin, and Adam M. Deutschbauer 1 Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA 2 QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley CA, USA 3 DOE Joint Genome Institute, Walnut Creek CA, USA 4 Department of Bioengineering, University of California, Berkeley CA, USA 5 Department of Plant and Microbial Biology, University of California, Berkeley CA, USA * [email protected], [email protected], [email protected] Abstract Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-D-ribose and 2-deoxy-D-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl-CoA and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. -
Targeting Glioblastoma Stem Cells Through Disruption of the Circadian Clock
Published OnlineFirst August 27, 2019; DOI: 10.1158/2159-8290.CD-19-0215 RESEARCH ARTICLE Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock Zhen Dong1, Guoxin Zhang1, Meng Qu2, Ryan C. Gimple1,3, Qiulian Wu1, Zhixin Qiu1, Briana C. Prager1,3, Xiuxing Wang1, Leo J.Y. Kim1,3, Andrew R. Morton3, Deobrat Dixit1, Wenchao Zhou4, Haidong Huang4, Bin Li5, Zhe Zhu1, Shideng Bao4, Stephen C. Mack6, Lukas Chavez7, Steve A. Kay2, and Jeremy N. Rich1 Downloaded from cancerdiscovery.aacrjournals.org on September 24, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst August 27, 2019; DOI: 10.1158/2159-8290.CD-19-0215 ABSTRACT Glioblastomas are highly lethal cancers, containing self-renewing glioblastoma stem cells (GSC). Here, we show that GSCs, differentiated glioblastoma cells (DGC), and nonmalignant brain cultures all displayed robust circadian rhythms, yet GSCs alone displayed exquisite dependence on core clock transcription factors, BMAL1 and CLOCK, for optimal cell growth. Downregulation of BMAL1 or CLOCK in GSCs induced cell-cycle arrest and apoptosis. Chromatin immu- noprecipitation revealed that BMAL1 preferentially bound metabolic genes and was associated with active chromatin regions in GSCs compared with neural stem cells. Targeting BMAL1 or CLOCK attenu- ated mitochondrial metabolic function and reduced expression of tricarboxylic acid cycle enzymes. Small-molecule agonists of two independent BMAL1–CLOCK negative regulators, the cryptochromes and REV-ERBs, downregulated stem cell factors and reduced GSC growth. Combination of cryp- tochrome and REV-ERB agonists induced synergistic antitumor effi cacy. Collectively, these fi ndings show that GSCs co-opt circadian regulators beyond canonical circadian circuitry to promote stemness maintenance and metabolism, offering novel therapeutic paradigms. -
Polyamines Under Abiotic Stress: Metabolic Crossroads and Hormonal Crosstalks in Plants
Metabolites 2012, 2, 516-528; doi:10.3390/metabo2030516 OPEN ACCESS metabolites ISSN 2218-1989 www.mdpi.com/journal/metabolites/ Review Polyamines under Abiotic Stress: Metabolic Crossroads and Hormonal Crosstalks in Plants Marta Bitrián, Xavier Zarza, Teresa Altabella, Antonio F. Tiburcio and Rubén Alcázar * Unit of Plant Physiology, Department of Natural Products and Plant Biology, Faculty of Pharmacy, University of Barcelona, Diagonal, 643, 08028 Barcelona, Spain * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel: +34 934024492; Fax: +34 934029043. Received: 22 June 2012; in revised form: 6 August 2012 / Accepted: 10 August 2012 / Published: 20 August 2012 Abstract: Polyamines are essential compounds for cell survival and have key roles in plant stress protection. Current evidence points to the occurrence of intricate cross-talks between polyamines, stress hormones and other metabolic pathways required for their function. In this review we integrate the polyamine metabolic pathway in the context of its immediate metabolic network which is required to understand the multiple ways by which polyamines can maintain their homeostasis and participate in plant stress responses. Keywords: polyamines; stress; metabolism; SAM; GABA; proline; ABA 1. Introduction Abiotic stresses such as cold/freezing, salinity, heat and drought represent serious threats to agriculture. Climatic change is predicted to increase global temperature, alter precipitation patterns and intensify drought, increasing the need to grow crops in saline soil [1,2]. Plants, which are sessile organisms, have evolved metabolic and hormonal pathways to cope with environmental challenges. The study of this natural evolution on stress responsiveness is providing new leads to crop protection. -
Cutinase Structure, Function and Biocatalytic Applications
EJB Electronic Journal of Biotechnology ISSN: 0717-345 Vol.1 No.3, Issue of August 15, 1998. © 1998 by Universidad Católica de Valparaíso –- Chile Invited review paper/ Received 20 October, 1998. REVIEW ARTICLE Cutinase structure, function and biocatalytic applications Cristina M. L. Carvalho Centro de Engenharia Biológica e Química Instituto Superior Técnico 1000 Lisboa – Portugal Maria Raquel Aires-Barros Centro de Engenharia Biológica e Química Instituto Superior Técnico 1000 Lisboa – Portugal 1 Joaquim M. S. Cabral Centro de Engenharia Biológica e Química Instituto Superior Técnico 1000 Lisboa – Portugal Tel: + 351.1.8419065 Fax: + 351.1.8419062 E-mail: [email protected] http://www.ist.utl.pt/ This review analyses the role of cutinases in nature and Some microorganisms, including plant pathogens, have their potential biotechnological applications. The been shown to live on cutin as their sole carbon source cloning and expression of a fungal cutinase from (Purdy and Kolattukudy, 1975) and the production of Fusarium solani f. pisi, in Escherichia coli and extracellular cutinolytic enzymes has been presented (Purdy Saccharomyces cerevisiae hosts are described. The three and Kolattukudy, 1975; Lin and Kolattukudy, 1980). dimensional structure of this cutinase is also analysed Cutinases have been purified and characterized from and its function as a lipase discussed and compared with several different sources, mainly fungi (Purdy and other lipases. The biocatalytic applications of cutinase Kolattukudy, 1975 ; Lin and Kolattukudy, 1980; Petersen et are described taking into account the preparation of al., 1997; Dantzig et al., 1986; Murphy et al., 1996) and different cutinase forms and the media where the pollen (Petersen et al., 1997; Sebastian et al., 1987). -
Characterization of Cd36 03230P, a Putative Vanillin Dehydrogenase from Candida Dubliniensis† Cite This: RSC Adv.,2016,6, 99774 Suprama Datta,Ab Uday S
RSC Advances View Article Online COMMUNICATION View Journal | View Issue Characterization of Cd36_03230p, a putative vanillin dehydrogenase from Candida dubliniensis† Cite this: RSC Adv.,2016,6, 99774 Suprama Datta,ab Uday S. Annapureb and David J. Timson*ac Received 5th September 2016 Accepted 10th October 2016 DOI: 10.1039/c6ra22209a www.rsc.org/advances A coding sequence (CD36-03230) from the yeast Candida dubliniensis derived phenylpropanoids (such as vanillin, vanillate, caffeate, p- had been previously annotated as a vanillin dehydrogenase (VDH). The coumarate, cinnamate and benzaldehyde). These aromatic alde- corresponding protein (CD36-03230p) was recombinantly expressed hydes, especially vanillin, are abundant as avour and aromas in in Escherichia coli and analysed. The protein is most likely a tetramer in food and cosmetic industries. It is important to elucidate the Creative Commons Attribution 3.0 Unported Licence. solution as judged by crosslinking and gel filtration experiments. structural and functional characteristics of these enzymes given CD36-03230p is an active aldehyde dehydrogenase favouring cyclic their potential role in food chemistry and biotechnology. This and aromatic substrates. Positive cooperativity and substrate inhibition group of enzymes has been characterized in a number of eubac- were observed with some substrates. The redox cofactor NADP+ and terial species, including Pseudomonas uorescens,6 Pseudomonas substrates affected the thermal stability of the protein. Interestingly, putida KT2440,13 Corynebacterium -
Activation of a Gene Network in Durum Wheat Roots Exposed to Cadmium
Aprile et al. BMC Plant Biology (2018) 18:238 https://doi.org/10.1186/s12870-018-1473-4 RESEARCH ARTICLE Open Access Activation of a gene network in durum wheat roots exposed to cadmium Alessio Aprile, Erika Sabella*, Marzia Vergine, Alessandra Genga, Maria Siciliano, Eliana Nutricati, Patrizia Rampino, Mariarosaria De Pascali, Andrea Luvisi, Antonio Miceli, Carmine Negro and Luigi De Bellis Abstract Background: Among cereals, durum wheat (Triticum turgidum L. subsp. durum) accumulates cadmium (Cd) at higher concentration if grown in Cd-polluted soils. Since cadmium accumulation is a risk for human health, the international trade organizations have limited the acceptable concentration of Cd in edible crops. Therefore, durum wheat cultivars accumulating low cadmium in grains should be preferred by farmers and consumers. To identify the response of durum wheat to the presence of Cd, the transcriptomes of roots and shoots of Creso and Svevo cultivars were sequenced after a 50-day exposure to 0.5 μM Cd in hydroponic solution. Results: No phytotoxic effects or biomass reduction was observed in Creso and Svevo plants at this Cd concentration. Despite this null effect, cadmium was accumulated in root tissues, in shoots and in grains suggesting a good cadmium translocation rate among tissues. The mRNA sequencing revealed a general transcriptome rearrangement after Cd treatment and more than 7000 genes were found differentially expressed in root and shoot tissues. Among these, the up-regulated genes in roots showed a clear correlation with cadmium uptake and detoxification. In particular, about three hundred genes were commonly up-regulated in Creso and Svevo roots suggesting a well defined molecular strategy characterized by the transcriptomic activation of several transcription factors mainly belonging to bHLH and WRKY families. -
Cutinases from Mycobacterium Tuberculosis
Identification of Residues Involved in Substrate Specificity and Cytotoxicity of Two Closely Related Cutinases from Mycobacterium tuberculosis Luc Dedieu, Carole Serveau-Avesque, Ste´phane Canaan* CNRS - Aix-Marseille Universite´ - Enzymologie Interfaciale et Physiologie de la Lipolyse - UMR 7282, Marseille, France Abstract The enzymes belonging to the cutinase family are serine enzymes active on a large panel of substrates such as cutin, triacylglycerols, and phospholipids. In the M. tuberculosis H37Rv genome, seven genes coding for cutinase-like proteins have been identified with strong immunogenic properties suggesting a potential role as vaccine candidates. Two of these enzymes which are secreted and highly homologous, possess distinct substrates specificities. Cfp21 is a lipase and Cut4 is a phospholipase A2, which has cytotoxic effects on macrophages. Structural overlay of their three-dimensional models allowed us to identify three areas involved in the substrate binding process and to shed light on this substrate specificity. By site-directed mutagenesis, residues present in these Cfp21 areas were replaced by residues occurring in Cut4 at the same location. Three mutants acquired phospholipase A1 and A2 activities and the lipase activities of two mutants were 3 and 15 fold greater than the Cfp21 wild type enzyme. In addition, contrary to mutants with enhanced lipase activity, mutants that acquired phospholipase B activities induced macrophage lysis as efficiently as Cut4 which emphasizes the relationship between apparent phospholipase A2 activity and cytotoxicity. Modification of areas involved in substrate specificity, generate recombinant enzymes with higher activity, which may be more immunogenic than the wild type enzymes and could therefore constitute promising candidates for antituberculous vaccine production.