Remembering Otto Kandler (1920–2017) and His Contributions
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Light-Induced Psba Translation in Plants Is Triggered by Photosystem II Damage Via an Assembly-Linked Autoregulatory Circuit
Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit Prakitchai Chotewutmontria and Alice Barkana,1 aInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403 Edited by Krishna K. Niyogi, University of California, Berkeley, CA, and approved July 22, 2020 (received for review April 26, 2020) The D1 reaction center protein of photosystem II (PSII) is subject to mRNA to provide D1 for PSII repair remain obscure (13, 14). light-induced damage. Degradation of damaged D1 and its re- The consensus view in recent years has been that psbA transla- placement by nascent D1 are at the heart of a PSII repair cycle, tion for PSII repair is regulated at the elongation step (7, 15–17), without which photosynthesis is inhibited. In mature plant chloro- a view that arises primarily from experiments with the green alga plasts, light stimulates the recruitment of ribosomes specifically to Chlamydomonas reinhardtii (Chlamydomonas) (18). However, we psbA mRNA to provide nascent D1 for PSII repair and also triggers showed recently that regulated translation initiation makes a a global increase in translation elongation rate. The light-induced large contribution in plants (19). These experiments used ribo- signals that initiate these responses are unclear. We present action some profiling (ribo-seq) to monitor ribosome occupancy on spectrum and genetic data indicating that the light-induced re- cruitment of ribosomes to psbA mRNA is triggered by D1 photo- chloroplast open reading frames (ORFs) in maize and Arabi- damage, whereas the global stimulation of translation elongation dopsis upon shifting seedlings harboring mature chloroplasts is triggered by photosynthetic electron transport. -
Photosynthetic Phosphorylation Above and Below 00C by David 0
VOL. 48, 1962 BIOCHEMISTRY: HALL AND ARNON 833 10 De Robertis, E., J. Biophy8. Biochem. Cytol., 2, 319 (1956). 11 Eakin, R. M., and J. A. Westfall, ibid., 8, 483 (1960). 12 Eakin, R. M., these PROCEEDINGS, 47, 1084 (1961). 13 Wolken, J. J., in The Structure of the Eye, ed. G. K. Smelser (New York: Academic Press, 1961). 14 Wald, G., ibid. 16 Eakin, R. M., and J. A. Westfall, Embryologia, 6, 84 (1961). 16 Sj6strand, F. S., in The Structure of the Eye, ed. G. K. Smelser (New York: Academic Press, 1961). 17 Miller, W. H., in The Cell, ed. J. Brachet and A. E. Mirsky (New York: Academic Press, 1960), part IV. 18 Miller, W. H., J. Biophys. Biochem. Cytol., 4, 227 (1958). 19 Hesse, R., Z. wiss. Zool., 61, 393 (1896). 20 Bradke, D. L., personal communication. 21 Wolken, J. J., Ann. N. Y. Acad. Sci., 74, 164 (1958). 22 Rohlich, P., and L. J. Torok, Z. wiss. Zool., 54, 362 (1961). 28 Eakin, R. M., and J. A. Westfall, J. Ultrastr. Res. (in press). 24 Franz, V., Jena. Z. Naturwiss., 59, 401 (1923). PHOTOSYNTHETIC PHOSPHORYLATION ABOVE AND BELOW 00C BY DAVID 0. HALL* AND DANIEL I. ARNONt DEPARTMENT OF CELL PHYSIOLOGY, UNIVERSITY OF CALIFORNIA, BERKELEY Read before the Academy, April 25, 1962 CO2 assimilation in photosynthesis consists of a series of dark enzymatic reactions that are driven solely by adenosine triphosphate and reduced pyridine nucleotide. 1-4 The same reactions are now known to operate in nonphotosynthetic cells.5-"3 It follows, therefore, that the distinction between carbon assimilation in photosyn- thetic and nonphotosynthetic cells lies in the manner in which ATP14 and PNH214 are formed. -
Direct Charging of Trnacua with Pyrrolysine in Vitro and in Vivo
letters to nature .............................................................. gene product (see Supplementary Fig. S1). The tRNA pool extracted from Methanosarcina acetivorans or tRNACUA transcribed in vitro Direct charging of tRNACUA with was used in charging experiments. Charged and uncharged tRNA species were separated by electrophoresis in a denaturing acid-urea pyrrolysine in vitro and in vivo 10,11 polyacrylamide gel and tRNACUA was specifically detected by northern blotting with an oligonucleotide probe. The oligonucleo- Sherry K. Blight1*, Ross C. Larue1*, Anirban Mahapatra1*, tide complementary to tRNA could hybridize to a tRNA in the David G. Longstaff1, Edward Chang1, Gang Zhao2†, Patrick T. Kang4, CUA Kari B. Green-Church5, Michael K. Chan2,3,4 & Joseph A. Krzycki1,4 pool of tRNAs isolated from wild-type M. acetivorans but not to the tRNA pool from a pylT deletion mutant of M. acetivorans (A.M., 1Department of Microbiology, 484 West 12th Avenue, 2Department of Chemistry, A. Patel, J. Soares, R.L. and J.A.K., unpublished observations). 3 100 West 18th Avenue, Department of Biochemistry, 484 West 12th Avenue, Both tRNACUA and aminoacyl-tRNACUA were detectable in the The Ohio State University, Columbus, Ohio 43210, USA isolated cellular tRNA pool (Fig. 1). Alkaline hydrolysis deacylated 4Ohio State University Biochemistry Program, 484 West 12th Avenue, The Ohio the cellular charged species, but subsequent incubation with pyrro- State University, Columbus, Ohio 43210, USA lysine, ATP and PylS-His6 resulted in maximal conversion of 50% of 5CCIC/Mass Spectrometry and Proteomics Facility, The Ohio State University, deacylated tRNACUA to a species that migrated with the same 116 W 19th Ave, Columbus, Ohio 43210, USA electrophoretic mobility as the aminoacyl-tRNACUA present in the * These authors contributed equally to this work. -
Hydrogenases of Methanogens
ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. -
Bacterial Photophosphorylation: Regulation by Redox Balance* by Subir K
VOL. 49, 1963 BIOCHEMISTRY: BOSE AND GEST 337 12 Hanson, L. A., and I. Berggird, Clin. Chim. Acta, 7, 828 (1962). 13 Stevenson, G. T., J. Clin. Invest., 41, 1190 (1962). 14 Burtin, P., L. Hartmann, R. Fauvert, and P. Grabar, Rev. franc. etudes clin. et biol., 1, 17 (1956). 15 Korngold, L., and R. Lipari, Cancer, 9, 262 (1956). 16Lowry, 0. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall, J. Biol. Chem., 193, 265 (1951). 17 Muller-Eberhard, H. J., Scand. J. Clin. and Lab. Invest., 12, 33 (1960). 18 Bergg&rd, I., Arkiv Kemi, 18, 291 (1962). 19 BerggArd, I., Arkiv Kemi, 18, 315 (1962). 20 Flodin, P., Dextran Gels and Their Application in Gel Filtration (Uppsala: Pharmacia, 1962). 21 Dische, Z., and L. B. Shettles, J. Biol. Chem., 175, 595 (1948). 22 Kunkel, H. G., and R. Trautman, in Electrophoresis, ed. M. Bier (New York: Academic Press, 1959), p. 225. 23Fleischman, J. B., R. H. Pain, and R. R. Porter, Arch. Biochem. Biophys., Suppl. 1, 174 (1962). 24 Porter, R. R., Biochem. J., 73, 119 (1959). 25 Edelman, G. M., J. F. Heremans, M.-Th. Heremans, and H. G. Kunkel, J. Exptl. Med., 112, 203 (1960). 26 Scheidegger, J. J., Intern. Arch. Allergy Appl. Immunol., 7, 103 (1955). 27 Yphantis, D. A., American Chemical Society, 140th meeting, Chicago, Abstracts of Papers, 1961, p. ic. 28 Gally, J. A. and G. M. Edelman, Biochim. Biophys. Acta, 60, 499 (1962). 29 Webb, T., B. Rose, and A. H. Sehon, Can. J. Biochem. Physiol., 36, 1159 (1958). -
Characterization of Methanosarcina Barkeri MST and 227, Methanosarcina Mazei S-6T, and Methanosarcina Vacuolata Z-76IT GLORIA M
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1991, p. 267-274 Vol. 41, No. 2 0020-7713/91/020267-08$02.OO/O Copyright 0 1991, International Union of Microbiological Societies Characterization of Methanosarcina barkeri MST and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-76IT GLORIA M. MAESTROJUAN' AND DAVID R. BOONE172* Departments of Environmental Science and Engineering' and Chemical and Biological Science,2 Oregon Graduate Institute, 19600 N.W. von Neumann Drive, Beaverton, Oregon 97006-1999 Members of the genus Methanosarcina are recognized as major aceticlastic methanogens, and several species which thrive in low-salt, pH-neutral culture medium at mesophilic temperatures have been described. However, the environmental conditions which support the fastest growth of these species (Methanosarcina barkeri MST [T = type strain] and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-761T) have not been reported previously. Although the members of the genus Methanosarcina are widely assumed to grow best at pH values near neutrality, we found that some strains prefer acidic pH values. M. vacuolata and the two strains of M. barkeri which we tested were acidophilic when they were grown on H, plus methanol, growing most rapidly at pH 5 and growing at pH values as low as 4.3. M. mazei grew best at pH values near neutrality. We found that all of the strains tested grew most rapidly at 37 to 42°C on all of the growth substrates which we tested. None of the strains was strongly halophilic, although the growth of some strains was slightly stimulated by small amounts of added NaCI. -
The Archaeal Concept and the World It Lives In: a Retrospective
Carl R. Woese (center) with His Majesty Carl XVI Gustaf of Sweden and Queen Silvia on the occassion of his receiving the 2003 Crafoord Prize, given by the Royal Swedish Academy of Sciences. Photo credit: Royal Swedish Academy of Sciences. Photosynthesis Research 80: 361–372, 2004. 363 © 2004 Kluwer Academic Publishers. Printed in the Netherlands. Personal perspective The archaeal concept and the world it lives in: a retrospective Carl R. Woese Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemical and Life Sciences Laboratory, 601 South Goodwin Ave, Urbana, IL 61801-3709, USA (e-mail: [email protected]; fax: +1-217-244-6697) Received 9 July 2003; accepted in revised form 30 August 2003 Key words: archaea, evolution, genomics, molecular phylogeny, phylogenetic reconstruction, ribosomal RNA Abstract The present retrospective concerns the discovery and development of the archaea, the so-called ‘third form of life’ that no one anticipated and many did not, and still do not want. In its birth pangs, which the archaea had a plenty, the concept encountered biology unmasked; for it ran up against some of the key struts in the 20th century biological edifice. Consequently, the history of the development of the archaeal concept provides an excellent window on certain of the weaknesses in the 20th century biology paradigm, weaknesses that have now led that paradigm to a conceptual dead end. On the other hand, the archaeal concept has also provided us one of the pillars on which a new holistic paradigm for biology can be built. So, it would seem of value to retrace some of the twists and turns in the history of the development of the archaeal concept. -
Characterization of Methanosarcina Mazei JL01 Isolated from Holocene
Proceedings Characterization of Methanosarcina mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta associata GLS2T † Viktoriia Oshurkova 1,*, Olga Troshina 1, Vladimir Trubitsyn 1, Yana Ryzhmanova 1, Olga Bochkareva 2 and Viktoria Shcherbakova 1 1 Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, prospect Nauki 5, Pushchino, 142290 Moscow, Russia; [email protected] (O.T.); [email protected] (V.T.); [email protected] (Y.R.); [email protected] (V.S.) 2 Institute of Science and Technology (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria; [email protected] * Correspondence: [email protected] † Presented at the 1st International Electronic Conference on Microbiology, 2–30 November 2020; Available online: https://ecm2020.sciforum.net/. Published: 18 December 2020 Abstract: A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic. After long-term extensive cultivation at 15 °C, it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate, and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stain-positive. Optimum conditions for growth were 24–28 °C, pH 6.8–7.3, and 0.075–0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein- coding genes revealed 16S rRNA’s close relation to Methanosarcina mazei S-6T (similarity 99.5%). -
Reducing the Genetic Code Induces Massive Rearrangement of the Proteome
Reducing the genetic code induces massive rearrangement of the proteome Patrick O’Donoghuea,b, Laure Pratc, Martin Kucklickd, Johannes G. Schäferc, Katharina Riedele, Jesse Rinehartf,g, Dieter Söllc,h,1, and Ilka U. Heinemanna,1 Departments of aBiochemistry and bChemistry, The University of Western Ontario, London, ON N6A 5C1, Canada; Departments of cMolecular Biophysics and Biochemistry, fCellular and Molecular Physiology, and hChemistry, and gSystems Biology Institute, Yale University, New Haven, CT 06520; dDepartment of Microbiology, Technical University of Braunschweig, Braunschweig 38106, Germany; and eDivision of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald 17487, Germany Contributed by Dieter Söll, October 22, 2014 (sent for review September 29, 2014; reviewed by John A. Leigh) Expanding the genetic code is an important aim of synthetic Opening codons by reducing the genetic code is highly biology, but some organisms developed naturally expanded ge- promising, but it is unknown how removing 1 amino acid from netic codes long ago over the course of evolution. Less than 1% of the genetic code might impact the proteome or cellular viability. all sequenced genomes encode an operon that reassigns the stop Many genetic code variations are found in nature (15), including codon UAG to pyrrolysine (Pyl), a genetic code variant that results stop or sense codon reassignments, codon recoding, and natural from the biosynthesis of Pyl-tRNAPyl. To understand the selective code expansion (16). Pyrrolysine (Pyl) is a rare example of nat- advantage of genetically encoding more than 20 amino acids, we ural genetic code expansion. Evidence for genetically encoded constructed a markerless tRNAPyl deletion strain of Methanosarcina Pyl is found in <1% of all sequenced genomes (17). -
Photosynthesis
ENVIRONMENTAL PLANT PHYSIOLOGY SESSION 3 Photosynthesis An understanding of the biochemical processes of photosynthesis is needed to allow us to understand how plants respond to changing environmental conditions. This session looks at the details of the physiology and considers how plants can adapt these processes. If you studied the foundation degree with Myerscough previously you will recognise that much of these session notes are a very similar to those provided for the Plant Biology Module. The difference is not in the content but in the level of understanding required! Page Introduction to Photosynthesis 2 First catch your light! 3 The Light Dependent Reaction 7 The Light Independent Reaction 11 Photosynthesis and the Environment 12 Alternative Carbon Fixation Strategies 16 Further Reading 19 LEARNING OUTCOMES You need to be able to describe the biochemical basis of photosynthesis including: • Describing the role of chloroplasts and chlorophyll • Describing the steps of the light reaction and stating its products • Describing the Calvin cycle or light independent reaction and stating its products • Describing the role and position of the electron transport chain • Identify the effects of environmental factors on the rate of photosynthesis and explain how these relate to your field of study • Describe adaptations used by plants to continue photosynthesis in conditions of environmental stress such as hot arid conditions or shade conditions 1 Introduction to Photosynthesis The sun is the main source of energy to all living things. Light energy from the sun is converted to the chemical energy of organic molecules by green plants by a complicated pathway of reactions called photosynthesis. -
Quantum Efficiency of Photosynthetic Energy Conversion (Photosynthesis/Photophosphorylation/Ferredoxin) RICHARD K
Proc. Natl. Acad. Sd. USA Vol. 74, No. 8, pp. 3377-81, August 1977 Biophysics Quantum efficiency of photosynthetic energy conversion (photosynthesis/photophosphorylation/ferredoxin) RICHARD K. CHAIN AND DANIEL I. ARNON Department of Cell Physiology, University of California, Berkeley, Berkeley, California 94720 Contributed by Daniel I. Arnon, June 7,1977 ABSTRACT The quantum efficiency of photosynthetic with cyclic and noncyclic photophosphorylation and a "dark," energy conversion was investigated in isolated spinach chlo- enzymatic phase concerned with the assimilation of CO2 (8). roplasts by measurements of the quantum requirements of ATP has established that the formation by cyclic and noncyclic photophosphorylation cata- Fractionation of chloroplasts (9) light lyzed by ferredoxin. ATP formation had a requirement of about phase is localized in the membrane fraction (grana) that is 2 quanta per 1 ATP at 715 nm (corresponding to a requirement separable from the soluble stroma fraction which contains the of 1 quantum per electron) and a requirement of 4 quanta per enzymes of CO2 assimilation (10). Thus, in isolated and frac- ATP (corresponding to a requirement of 2 quanta per electron) tionated chloroplasts, investigations of photosynthetic quantum at 554 nm. When cyclic and noncyclic photophosphorylation efficiency can be focused solely on cyclic and noncyclic pho-. were operating concurrently at 554 nm, a total of about 12 account the conversion of quanta was required to generate the two NADPH and three ATP tophosphorylation, which jointly for needed for the assimilation of one CO2 to the level of glu- photon energy into chemical energy without the subsequent cose. or concurrent reactions of biosynthesis and respiration that cannot be avoided in whole cells. -
Consequences of the Structure of the Cytochrome B6 F Complex for Its Charge Transfer Pathways ⁎ William A
Biochimica et Biophysica Acta 1757 (2006) 339–345 http://www.elsevier.com/locate/bba Review Consequences of the structure of the cytochrome b6 f complex for its charge transfer pathways ⁎ William A. Cramer , Huamin Zhang Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA Received 17 January 2006; received in revised form 30 March 2006; accepted 24 April 2006 Available online 4 May 2006 Abstract At least two features of the crystal structures of the cytochrome b6 f complex from the thermophilic cyanobacterium, Mastigocladus laminosus and a green alga, Chlamydomonas reinhardtii, have implications for the pathways and mechanism of charge (electron/proton) transfer in the complex: (i) The narrow 11×12 Å portal between the p-side of the quinone exchange cavity and p-side plastoquinone/quinol binding niche, through which all Q/QH2 must pass, is smaller in the b6 f than in the bc1 complex because of its partial occlusion by the phytyl chain of the one bound chlorophyll a molecule in the b6 f complex. Thus, the pathway for trans-membrane passage of the lipophilic quinone is even more labyrinthine in the b6 f than in the bc1 complex. (ii) A unique covalently bound heme, heme cn, in close proximity to the n-side b heme, is present in the b6 f complex. The b6 f structure implies that a Q cycle mechanism must be modified to include heme cn as an intermediate between heme bn and plastoquinone bound at a different site than in the bc1 complex. In addition, it is likely that the heme bn–cn couple participates in photosytem + I-linked cyclic electron transport that requires ferredoxin and the ferredoxin: NADP reductase.