A Multifaceted Analysis Reveals Two Distinct Phases of Chloroplast
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Comparing the Reaction Mechanism of Dark-Operative Protochlorophyllide
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase Pedro J. Silva REQUIMTE, Faculdade de Cienciasˆ da Saude,´ Universidade Fernando Pessoa, Rua Carlos da Maia, Porto, Portugal ABSTRACT The addition of two electrons and two protons to the C17DC18 bond in protochloro- phyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a .Cys/3Asp-ligated [4Fe–4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17DC18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311CG(d,p)//B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the .Cys/3Asp-ligated [4Fe–4S], yielding a negatively-charged intermediate. Depending on the rate of Fe–S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe–S cluster re-reduction should be Submitted 24 March 2014 the rate-limiting stage of the process. Poisson–Boltzmann computations on the Accepted 9 August 2014 full enzyme–substrate complex, followed by Monte Carlo simulations of redox Published 2 September 2014 and protonation titrations revealed a hitherto unsuspected pH-dependence of the Corresponding author reaction potential of the Fe–S cluster. -
Short De-Etiolation Increases the Rooting of VC801 Avocado Rootstock
plants Article Short De-Etiolation Increases the Rooting of VC801 Avocado Rootstock Zvi Duman 1,2, Gal Hadas-Brandwein 1,2, Avi Eliyahu 1,2, Eduard Belausov 1, Mohamad Abu-Abied 1, Yelena Yeselson 1, Adi Faigenboim 1, Amnon Lichter 3, Vered Irihimovitch 1 and Einat Sadot 1,* 1 The Institute of Plant Sciences, The Volcani Center, ARO, 68 HaMaccabim Road, Rishon LeZion 7528809, Israel; [email protected] (Z.D.); [email protected] (G.H.-B.); [email protected] (A.E.); [email protected] (E.B.); [email protected] (M.A.-A.); [email protected] (Y.Y.); [email protected] (A.F.); [email protected] (V.I.) 2 The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel 3 The Institute of Post Harvest and Food Sciences, The Volcani Center, ARO, 68 HaMaccabim Road, Rishon LeZion 7528809, Israel; [email protected] * Correspondence: [email protected] Received: 5 August 2020; Accepted: 2 November 2020; Published: 3 November 2020 Abstract: Dark-grown (etiolated) branches of many recalcitrant plant species root better than their green counterparts. Here it was hypothesized that changes in cell-wall properties and hormones occurring during etiolation contribute to rooting efficiency. Measurements of chlorophyll, carbohydrate and auxin contents, as well as tissue compression, histological analysis and gene-expression profiles were determined in etiolated and de-etiolated branches of the avocado rootstock VC801. Differences in chlorophyll content and tissue rigidity, and changes in xyloglucan and pectin in cambium and parenchyma cells were found. -
Surprising Roles for Bilins in a Green Alga Jean-David Rochaix1 Departments of Molecular Biology and Plant Biology, University of Geneva,1211 Geneva, Switzerland
COMMENTARY COMMENTARY Surprising roles for bilins in a green alga Jean-David Rochaix1 Departments of Molecular Biology and Plant Biology, University of Geneva,1211 Geneva, Switzerland It is well established that the origin of plastids which serves as chromophore of phyto- can be traced to an endosymbiotic event in chromes (Fig. 1). An intriguing feature of which a free-living photosynthetic prokaryote all sequenced chlorophyte genomes is that, invaded a eukaryotic cell more than 1 billion although they lack phytochromes, their years ago. Most genes from the intruder genomes encode two HMOXs, HMOX1 were gradually transferred to the host nu- andHMOX2,andPCYA.InPNAS,Duanmu cleus whereas a small number of these genes et al. (6) investigate the role of these genes in were maintained in the plastid and gave the green alga Chlamydomonas reinhardtii rise to the plastid genome with its associated and made unexpected findings. protein synthesizing system. The products of Duanmu et al. first show that HMOX1, many of the genes transferred to the nucleus HMOX2, and PCYA are catalytically active were then retargeted to the plastid to keep it and produce bilins in vitro (6). They also functional. Altogether, approximately 3,000 demonstrate in a very elegant way that these nuclear genes in plants and algae encode proteins are functional in vivo by expressing plastid proteins, whereas chloroplast ge- a cyanobacteriochrome in the chloroplast Fig. 1. Tetrapyrrole biosynthetic pathways. The heme nomes contain between 100 and 120 genes of C. reinhardtii, where, remarkably, the and chlorophyll biosynthetic pathways diverge at pro- (1). A major challenge for eukaryotic pho- photoreceptor is assembled with bound toporphyrin IX (ProtoIX). -
Chromophores in Photomorphogenesis W
Encyclopedia of Plant Physiolo New Series Volume 16 A Editors A.Pirson, Göttingen M.H.Zimmermann, Harvard Photo- morphogenesis Edited by W. Shropshire, Jr. and H. Möhr Contributors K. Apel M. Black A.E. Canham J.A. De Greef M.J. Dring H. Egnéus B. Frankland H. Frédéricq L. Fukshansky M. Furuya V. Gaba A.W. Galston J. Gressel W. Haupt S.B. Hendricks M.G. Holmes M. Jabben H. Kasemir C. J.Lamb M.A. Lawton K. Lüning A.L. Mancinelli H. Möhr D.C.Morgan L.H.Pratt P.H.Quail R.H.Racusen W. Rau W. Rüdiger E. Schäfer H. Scheer J.A. Schiff P. Schopfer S. D. Schwartzbach W. Shropshire, Jr. H. Smith W.O. Smith R. Taylorson W.J. VanDerWoude D. Vince-Prue H.I. Virgin E. Wellmann With 173 Figures Springer-Verlag Berlin Heidelberg New York Tokyo 1983 Univers;:^.'::- Bibüw i-,L* München W. SHROPSHIRE, JR. Smithsonian Institution Radiation Biology Laboratory 12441 Parklawn Drive Rockville, MD 20852/USA H. MOHR Biologisches Institut II der Universität Lehrstuhl für Botanik Schänzlestr. 1 D-7800 Freiburg/FRG ISBN 3-540-12143-9 (in 2 Bänden) Springer-Verlag Berlin Heidelberg New York Tokyo ISBN 0-387-12143-9 (in 2 Volumes) Springer-Verlag New York Heidelberg Berlin Tokyo Library of Congress Cataloging in Publication Data. Main entry under title: Pholomorphogcncsis. (Encyclo• pedia of plant physiology; new ser., v. 16) Includes indexes. 1. Plants Photomorphogenesis Addresses, essays, lectures. I. Shropshire, Walter. II. Mohr, Hans, 1930. III. Apel, K. IV. Scries. QK711.2.E5 vol. 16 581.1s [581.L9153] 83-10615 [QK757] ISBN 0-387-12143-9 (U.S.). -
The DIMINUTO Gene of Arabidopsis Is Involved in Regulating Cell Elongation
Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press The DIMINUTO gene of Arabidopsis is involved in regulating cell elongation Taku Takahashi, Alexander Gasch, Naoko Nishizawa, 1 and Nam-Hai Chua 2 Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10021-6399 USA; 1Faculty of Agriculture, University of Tokyo, Bunkyo-ku, Tokyo 113, Japan We have isolated a recessive mutation named diminuto (dim) from T-DNA transformed lines of Arabidopsis thaliana. Under normal growth conditions, the dim mutant has very short hypocotyls, petioles, stems, and roots because of the reduced size of cells along the longitudinal axes of these organs. In addition, dim results in the development of open cotyledons and primary leaves in dark-grown seedlings. The gene for DIM was cloned by T-DNA tagging. DIM encodes a novel protein of 561 amino acids that possesses bipartite sequence domains characteristic of nuclear localization signals. Molecular and physiological studies indicate that the loss-of-function mutant allele does not abolish the response of seedlings to light or phytohormones, although the inhibitory effect of light on hypocotyl elongation is greater in the mutant than in wild type. Moreover, the dim mutation affects the expression of a ~-tubulin gene, TUB1, which is thought to be important for plant cell growth. Our results suggest that the DIM gene product plays a critical role in the general process of plant cell elongation. [Key Words: Arabidopsis mutant; T-DNA tagging; cell elongation; tubulin genes; nuclear localization signals] Received October 13, 1994; revised version accepted November 29, 1994. -
Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme
Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme David Robert Armstrong Department of Molecular Biology and Biotechnology A thesis submitted for the degree of Doctor of Philosophy September 2014 Abstract The light-dependent enzyme protochlorophyllide oxidoreductase (POR) is a key enzyme in the chlorophyll biosynthesis pathway, catalysing the reduction of the C17 - C18 bond in protochlorophyllide (Pchlide) to form chlorophyllide (Chlide). This reaction involves the light- induced transfer of a hydride from the nicotinamide adenine dinucleotide phosphate (NADPH) cofactor, followed by proton transfer from a catalytic tyrosine residue. Much work has been done to elucidate the catalytic mechanism of POR, however little is known about the protein structure. POR isoforms in plants are also notable as components of the prolamellar bodies (PLBs), large paracrystalline structures that are precursors to the thylakoid membranes in mature chloroplasts. Bioinformatics studies have identified a number of proteins, related to POR, which contain similar structural features, leading to the production of a structural model for POR. A unique loop region of POR was shown by EPR to be mobile, with point mutations within this region causing a reduction in enzymatic activity. Production of a 2H, 13C, 15N-labelled sample of POR for NMR studies has enabled significant advancement in the understanding of the protein structure. This includes the calculation of backbone torsion angles for the majority of the protein, in addition to the identification of multiple dynamic regions of the protein. The protocol for purification of Pchlide, the substrate for POR, has been significantly improved, providing high quality pigment for study of the POR ternary complex. -
Genetic and Molecular Analysis of Two New Loci Controlling Flowering in Garden Pea
Genetic and molecular analysis of two new loci controlling flowering in garden pea By A S M Mainul Hasan School of Natural Sciences Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy University of Tasmania, July 2018 Declaration of originality This thesis contains no material which has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledge in the thesis, and to the best of my knowledge and belief no material previously published or written by another person except where due acknowledgement is made in the text of the thesis, nor does the thesis contain any material that infringes copyright. Authority of access This thesis may be made available for loan. Copying and communication of any part of this thesis is prohibited for two years from the date this statement was signed; after that time limited copying and communication is permitted in accordance with the Copyright Act 1968. Date: 6-07-2018 A S M Mainul Hasan i Abstract Flowering is one of the key developmental process associated with the life cycle of plant and it is regulated by different environmental factors and endogenous cues. In the model species Arabidopsis thaliana a mobile protein, FLOWERING LOCUS T (FT) plays central role to mediate flowering time and expression of FT is regulated by photoperiod. While flowering mechanisms are well-understood in A. thaliana, knowledge about this process is limited in legume (family Fabaceae) which are the second major group of crops after cereals in satisfying the global demand for food and fodder. -
Stress and Signalling in Arabidopsis in Response to the Pollutant 2,4,6-Trinitrotoluene (TNT)
Stress and signalling in Arabidopsis in response to the pollutant 2,4,6-trinitrotoluene (TNT) Emily Jane Johnston Doctor of Philosophy University of York Biology September 2015 Abstract The explosive 2,4,6-trinitrotoluene (TNT) is a persistent and toxic pollutant. High levels of TNT and the water-mobile co-pollutant Royal Demolition Explosive (RDX) have accumulated at manufacturing waste sites and military training ranges. Due to the scale of these sites, phytoremediation could be the most cost-effective and environmentally-friendly means of cleaning up the pollution. Plant lines which are both tolerant to, and able to degrade explosives pollution, are therefore being developed. Prior to this PhD research, it was identified that Arabidopsis thaliana L. (Arabidopsis) plants deficient in MONODEHYDROASCORBATE REDUCTASE 6 (MDHAR6; At1g63940) have hugely enhanced TNT tolerance. In Chapter 3, the means behind this enhanced TNT tolerance is investigated. Enzymatic analysis identified that purified MDHAR6 reduces TNT by one electron, to a TNT nitro radical which autoxidises, generating superoxide. Reactive superoxide can oxidise and damage protein, DNA and lipids. This reaction could also be inhibitory to plant development, due to the futile use of NADH. In Chapter 4, the organelle-targeting of MDHAR6 is investigated; MDHAR6 is unusual in that dual targeting to mitochondria or plastids appears to be dependent on the transcription start site used. A further understanding of MDHAR6 location would provide useful insight as to the endogenous role of this enzyme. Preliminary experiments indicate that MDHAR6 is more highly expressed in roots than leaves, and that a previously undescribed third transcription start site is dominant, encoding plastid-targeted MDHAR6. -
Biosynthesis of Cobalamin (Vitamin B12) in Salmonella Typhimurium
Biosynthesis of cobalamin (vitamin B^^) in Salmonella typhimurium and Bacillus megaterium de Bary; Characterisation of the anaerobic pathway. By Evelyne Christine Raux A thesis submitted to the University of London for the degree of doctorate (PhD.) in Biochemistry. -k H « i d University College London Department of Molecular Genetics, Institute of Ophthalmology, London. Jan 1999 ProQuest Number: U121800 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U121800 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Abstract The transformation of uroporphyrinogen HI into cobalamin (vitamin B 1 2 ) requires about 25 enzymes and can be performed by either aerobic or anaerobic pathways. The aerobic route is dependent upon molecular oxygen, and cobalt is inserted after the ring contraction process. The anaerobic route occurs in the absence of oxygen and cobalt is inserted into precorrin- 2 , several steps prior to the ring contraction. A study of the biosynthesis in both S. typhimurium and B. megaterium reveals that two genes, cbiD and cbiG, are essential components of the pathway and constitute genetic hallmarks of the anaerobic pathway. -
And Formation
J Med Genet: first published as 10.1136/jmg.17.1.1 on 1 February 1980. Downloaded from Review article Journal of Medical Genetics, 1980, 17, 1-14 Haems and chlorophylls: comparison of function and formation G A F HENDRY AND 0 T G JONES From the Department ofBiochemistry, The Medical School, University ofBristol, Bristol BS8 ITD In 1844 Verdeill reported that acid treatment of at the same time by McMunn3 of cytochromes, chlorophyll or haem yielded apparently similar red another group of haem proteins. compounds; he even postulated that chlorophylls It was the demonstration by Nencki and co- would contain iron. Hoppe-Seyler2 confirmed the workers 45 that the degradation of both chlorophylls apparent similarity of acid derivatives of haems and and haems yielded monopyrroles that led them, in chlorophylls from their light absorption charac- true neo-Darwinian fashion, to postulate a common teristics, a point rather overshadowing the discovery origin for animals and plants. 0 0-'I CH2 II copyright. CH CH3 COOH CIH2 CH2 C-O CH2 http://jmg.bmj.com/ NH2 ( CH3' 'CH3 ® 5- Aminolaevulinic acid a CH2 2 1 12 2 CH2 )H COOH CD FIG 1 Structures ofprotohaem and Protoporphyrin IX chlorophyll a and two of their precursors, acid and 5-aminolaevulinic on September 30, 2021 by guest. Protected protoporphyrin IX (with substituent numbering positions). CH2 CH CH.--,j CH2 CH2 COOCH3 Protohoem (haem- b) CooC20H39 Chlorophyll a 1 J Med Genet: first published as 10.1136/jmg.17.1.1 on 1 February 1980. Downloaded from 2 G A F Hendry and 0 T G Jones Following the work ofWillstatter6 and Fischer and particularly those of avian egg shells, have no Stern,7 the structure of most natural and many central complexed metal. -
Integration of Light Signaling with Photoperiodic Flowering and Circadian Rhythm
REVIEW Min NI Integration of light signaling with photoperiodic flowering and circadian rhythm Min NI* Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA ABSTRACT Plants become photosynthetic through de-etiolation, a developmental process regulated by red/far-red light-absorbing phytochromes and blue/ultraviolet A light-absorbing cryptochromes. Genetic screens have identified in the last decade many far-red light signaling mutants and several red and blue light signaling mutants, suggesting the existence of distinct red, far-red, or blue light signaling pathways downstream of phytochromes and cryptochromes. However, genetic screens have also identified mutants with defective de-etiolation responses under multiple wavelengths. Thus, the opti- mal de-etiolation responses of a plant depend on coordination among the different light signaling pathways. This review intends to discuss several recently identified signaling components that have a potential role to integrate red, far-red, and blue light signalings. This review also highlights the recent discoveries on proteolytic degradation in the desensitization of light signal transmission, and the tight connection of light signaling with photoperiodic flowering and circadian rhythm. Studies on the controlling mechanisms of de-etiolation, photoperiodic flowering, and circadian rhythm have been the fascinating topics in Arabidopsis research. The knowledge obtained from Arabidopsis can be readily applied to food crops and ornamental species, and can be contributed to -
Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria Under Aerobic and Anaerobic Environments
Life 2015, 5, 1172-1203; doi:10.3390/life5021172 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Review Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments Yuichi Fujita *, Ryoma Tsujimoto and Rina Aoki Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan; E-Mails: [email protected] (R.T.); [email protected] (R.A.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +81-52-789-4105; Fax: +81-52-789-4107. Academic Editors: Robert Haselkorn and John C. Meeks Received: 10 November 2014 / Accepted: 24 March 2015 / Published: 30 March 2015 Abstract: Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, and the latter half, called the Mg-branch, is specific to Mg-containing Chl a. Bilin pigments, such as phycocyanobilin, are additionally produced from heme, so these light-harvesting pigments also share many common biosynthetic steps with Chl biosynthesis. Some of these common steps in the biosynthetic pathways of heme, Chl and bilins require molecular oxygen for catalysis, such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low-oxygen conditions, cyanobacteria have developed elaborate mechanisms to maintain Chl production, even under microoxic environments. The use of enzymes specialized for low-oxygen conditions, such as oxygen-independent coproporphyrinogen III oxidase, constitutes part of a mechanism adapted to low-oxygen conditions.