DOCSLIB.ORG

Investigating Protein-Protein Interactions in the Chlorophyll Biosynthesis Pathway

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Investigating Protein-Protein Interactions in the Chlorophyll Biosynthesis Pathway Investigating Protein-Protein Interactions in the Chlorophyll Biosynthesis Pathway Sarah Louise Hollingshead A thesis submitted for the degree of Doctor of Philosophy Department of Molecular Biology and Biotechnology University of Sheffield December 2013 Summary Summary The production of chemical energy from light energy is arguably the most important reaction known, which makes photosynthesis one of the most important processes on Earth. Nearly all life depends on the energy derived from light, and it is this process that supports Earths oxygenated atmosphere. Photosynthesis is initiated by the absorption of light, which is performed by specialised pigment molecules known as the chlorophylls. These are highly specialised pigment molecules that belong to the tetrapyrrole family, which also includes vitamin B12, sirohaem and haem. Chlorophyll is synthesised via a series of chemical reactions collectively known as chlorophyll biosynthesis. Whilst the majority of enzymes required for chlorophyll biosynthesis are known and have, to some extent, been characterised, one enzyme, the magnesium protoporphyrin IX monomethylester cyclase (cyclase), remains an enigma. This enzyme catalyses the formation of the 5th isocyclic ring, altering the colour of the tetrapyrrole molecule from red to green. Despite being known for over 60 years, only one subunit of the cyclase has been identified. This is the catalytic or AcsF subunit, which contains a distinctive di-iron motif and is absolutely conserved across all known oxygenic photosynthetic organisms. One of the focuses of this work was to identify other subunits of the cyclase. This led to the discovery of Ycf54, a protein that is highly conserved among oxygenic photosynthetic organisms, which is essential for chlorophyll accumulation in Synechocystis sp. PCC6803. The latter half of this thesis focuses on investigating the structural and functional characteristics of Synechocystis Ycf54; a protein that had previously not been investigated. This work lead the identification of three residues in Ycf54 (D39, F40 and R82), which are required for protochlorophyllide synthesis and chlorophyll formation in Synechocystis, and the observation that these residues are all required for Ycf54 to interact with the catalytic (AcsF) subunit of the cyclase. Additionally, the crystal structure of wild type Synechocystis Ycf54 to a resolution of 1.2 Å, and the structures of two Ycf54 mutants (A9G and R82A), which have an in vivo phenotype were obtained using molecular replacement. Furthermore this work presents the first investigations into the previously unknown protein Slr0483 in Synechocystis. This protein contains the conserved C-terminal membrane anchoring CAAD (Cyanobacterial Aminoacyl-tRNA synthetases Appended Domain) domain and is found in all of the oxygenic photosynthetic organisms investigated. The experiments reported in this thesis show that Slr0483 is essential for photosystem stability and accumulation in Synechocystis and that this protein interacts with the chlorophyll biosynthesis enzymes protoporphyrin IX oxidase, protoporphyrin IX methyltransferase, the i Summary cyclase subunit Sll1214 and the geranylgeranyl reductase ChlP, as well as the haem biosynthesis enzyme ferrochelatase. Leading to the hypothesis that Slr0483 may serve as a membrane anchor, localising the enzymes required for chlorophyll and haem biosynthesis, to the sites where these tetrapyrroles are required in the thylakoid membrane (i.e. next to the sites of photosystem and cytochrome assembly). i Acknowledgements Acknowledgements Firstly, I would like to thank my supervisor Professor Neil Hunter FRS for his continued support and advice throughout the four years I’ve been with the lab. Thanks in particular for not rejecting my rather late plea for a PhD, for jetting me off to several exotic conference locations and for lots of useful scientific discussions. In relation to this work I’d like to thank Drs: Daniel Canniffe for introducing me to Synechocystis, lending me so many of his strains and teaching me how to use the HPLC, Phil Jackson for all his invaluable help, time and patience with the mass spectrometry, Roman Sobotka for sharing his knowledge on all things Synechocystis and Amanda Brindley for all her help and advice with protein purification. A huge thank you to Sophie Bliss for all her help with the crystallography and introducing me to crystal trials, polishing cover slips, CCP4 and PyMOL (such fun!), Dave Armstrong for doing the NMR analysis on my mystery pigment (I couldn’t have done that without you) and Jana Kopecna for her help with clear native gels. Thanks to the whole of E12/E11 in its entirety for being a lovely bunch of people to work with and for making work enjoyable. In particular, I would like to thank Mo and Lizzy for keeping everything going. Jack, Dan, Paul, Lizzie and Gooch for all their great lab banter and the Dave’s for generally being great chaps. Thanks for Katie for keeping me fuelled with lunch, Starbucks coffee and muffins. Finally, thanks to all of the friends I’ve met in Sheffield over the last three years. Especially to Sophie, Abi, Simon, Katie and many bottles of sauvignon blank, for keeping me sane with our Wednesday drinking sessions and for helping me escape from the algae to go procure ice-creams and duck watch in the park. ii Table of contents Table of contents Summary __________________________________________________________________________________________________ 1 Acknowledgements ______________________________________________________________________________________ 2 1. Introduction ____________________________________________________________________________________________ 1 1.1 Photosynthesis __________________________________________________________________________ 1 1.2 The origins of photosynthesis and photosynthetic bacteria _____________________ 3 1.2.1 The evolution of photosynthesis _______________________________________________ 6 1.3 Synechocystis as a model organism __________________________________________________ 9 1.4 Tetrapyrroles____________________________________________________________________________ 9 1.4.1 Formation of δ-aminolaevulinic acid ___________________________________________ 15 1.4.2 Condensation of δ-aminolaevulinic acid to porphobilinogen ________________________ 21 1.4.3 Porphobilinogen deaminase and uroporphyrinogen III synthase _____________________ 23 1.4.4 Uroporphyrinogen III to coproporphyrinogen III __________________________________ 27 1.4.5 Coproporphyrinogen III to protoporphyrinogen IX ________________________________ 28 1.4.6 Protoporphyrinogen IX to protoporphyrin IX_____________________________________ 31 1.4.7 The branch-point of haem and chlorophyll biosynthesis ___________________________ 33 1.4.8 S-adenosyl-L-methionine Mg-protoporphyrin IX methyltransferase __________________ 46 1.4.9 Mg-protoporphyrin IX monomethylester cyclase _________________________________ 49 1.4.10 Protochlorophyllide reductase _______________________________________________ 55 1.4.11 Divinyl reductase __________________________________________________________ 62 1.4.12 Geranylgeranyl reductase and chlorophyll synthase ______________________________ 64 1.5 Aims ______________________________________________________________________________________67 2. Materials and methods _____________________________________________________________________________ 69 2.1 Standard buffers, reagents and media _____________________________________________69 2.2 E. coli strains and plasmids ___________________________________________________________69 2.2.1 Chemically competent E. coli cells _____________________________________________ 69 2.2.2 Transformation of chemically competent E. coli cells ______________________________ 70 2.3 Synechocystis strains _________________________________________________________________70 2.3.1 Transformation of Synechocystis sp PCC6803 ____________________________________ 70 2.3.2 Construction of Synechocystis knock-out mutants ________________________________ 71 2.4 Nucleic acid manipulation ____________________________________________________________71 2.4.1 Preparation of plasmid DNA __________________________________________________ 71 2.4.2 Polymerase chain reaction (PCR) ______________________________________________ 71 2.4.3 Restriction enzyme digests ___________________________________________________ 72 iv Table of contents 2.4.4 Agarose gel electrophoresis of DNA ____________________________________________ 72 2.4.5 Recovery of DNA from agarose gels ____________________________________________ 72 2.4.6 Ligation of DNA into vectors __________________________________________________ 73 2.4.7 DNA sequencing ____________________________________________________________ 73 2.4.8 Reverse transcription PCR ____________________________________________________ 73 2.5 Analysis of protein_____________________________________________________________________ 74 2.5.1 Polyacrylamide gel electrophoresis (PAGE) ______________________________________ 74 2.5.2 Western blot analysis of protein _______________________________________________ 74 2.5.3 Immunodetection __________________________________________________________ 75 2.5.4 Determination of protein concentration _________________________________________ 75 2.5.5 Analysis of proteins by mass spectrometry: whole solution digest ____________________ 76 2.5.6 Analysis of proteins by mass spectrometry: in-gel digestion _________________________ 77 2.5.7 Analysis of protein complexes
Load more

Recommended publications
  • Pufc Gene Targeted PCR Primers for Identification and Classification of Marine Photosynthetic Bacterium Rhodovulum Sulfidophilum
    Acta Scientific MICROBIOLOGY (ISSN: 2581-3226) Volume 4 Issue 2 February 2021 Research Article pufC Rhodovulum sulfidophilum Gene Targeted PCR Primers for Identification and Classification of Marine Photosynthetic Bacterium Aoi Koga, Nao Yamauchi, Mayu Imamura, Mina Urata, Tomomi Received: Kurayama, Ranko Iwai, Shuhei Hayashi, Shinjiro Yamamoto and January 28, 2021 Hitoshi Miyasaka* Published: December 30, 2020 © All rights are reserved by Hitoshi Department of Applied Life Science, Sojo University, Nishiku, Japan Miyasaka., et al. *Corresponding Author: Sojo University, Nishiku, Japan. Hitoshi Miyasaka, Department of Applied Life Science, DOI: 10.31080/ASMI.2020.04.0770 Abstract Rhodovulum sulfidophilum - The marine non-sulfur purple photosynthetic bacterium has a wide application potential in the fields sify various R. sulfidophilum strains, we designed a PCR primer set targeting pufC of aquaculture, renewable energy production, environmental protection, and biomaterial production. To detect, identify and clas pufC R. sulfidophilum gene encoding one of the photosystem proteins. - Nucleotide sequence alignment of the genes from five strains revealed that the 3’ region of this gene is rich in ious R. sulfidophilum pufC gene. For the validation of this nucleotide substitutions (approximately 10 substitutions/100 bp), making it suitable for the identification and classification of var R. sulfidophilum strains. strains. We designed a primer set that amplified 0.7 kb of the 3’ region of primerKeywords: set, we used fish fecal DNA as Rhodovulumthe PCR templates, sulfidophilum and successfully identified and classified several Photosynthetic Bacteria; ; PCR; Fish Fecal DNA Introduction R. sulfidophilum Rho- Marsupenaeus japonicus classified several strains from the intestinal tracts dovulum sulfidophilum The marine non-sulfur purple photosynthetic bacterium of some fish and kuruma shrimps ( ).
    [Show full text]
  • Itraq-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves
    Article iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves Fang Dong 1,2, Yuanzhi Shi 1,2, Meiya Liu 1,2, Kai Fan 1,2, Qunfeng Zhang 1,2,* and Jianyun Ruan 1,2 1 Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; [email protected] (F.D.); [email protected] (Y.S.); [email protected] (M.L.); [email protected] (K.F.); [email protected] (J.R.) 2 Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, Hangzhou 310008, China * Correspondence: [email protected]; Tel.: +86-571-8527-0665 Received: 7 November 2018; Accepted: 5 December 2018; Published: 7 December 2018 Abstract: To uncover mechanism of highly weakened carbon metabolism in chlorotic tea (Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar “Huangjinya”. A total of 2110 proteins were identified in “Huangjinya”, and 173 proteins showed differential accumulations between the chlorotic and normal green leaves. Of these, 19 proteins were correlated with RNA expression levels, based on integrated analyses of the transcriptome and proteome. Moreover, the results of our analysis of differentially expressed proteins suggested that primary carbon metabolism (i.e., carbohydrate synthesis and transport) was inhibited in chlorotic tea leaves. The differentially expressed genes and proteins combined with photosynthetic phenotypic data indicated that 4-coumarate-CoA ligase (4CL) showed a major effect on repressing flavonoid metabolism, and abnormal developmental chloroplast inhibited the accumulation of chlorophyll and flavonoids because few carbon skeletons were provided as a result of a weakened primary carbon metabolism.
    [Show full text]
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
    [Show full text]
  • Hyperbilirubinemia
    Porphyrins Porphyrins (Porphins) are cyclic tetrapyrol compounds formed by the linkage )). of four pyrrole rings through methenyl bridges (( HC In the reduced porphyrins (Porphyrinogens) the linkage of four pyrrole rings (tetrapyrol) through methylene bridges (( CH2 )) The characteristic property of porphyrins is the formation of complexes with the metal ion bound to nitrogen atoms of the pyrrole rings. e.g. Heme (iron porphyrin). Proteins which contain heme ((hemoproteins)) are widely distributed e.g. Hemoglobin, Myoglobin, Cytochromes, Catalase & Tryptophan pyrrolase. Natural porphyrins have substituent side chains on the eight hydrogen atoms numbered on the pyrrole rings. These side chains are: CH 1-Methyl-group (M)… (( 3 )) 2-Acetate-group (A)… (( CH2COOH )) 3-Propionate-group (P)… (( CH2CH2COOH )) 4-Vinyl-group (V)… (( CH CH2 )) Porphyrins with asymmetric arrangement of the side chains are classified as type III porphyrins while those with symmetric arrangement of the side chains are classified as type I porphyrins. Only types I & III are present in nature & type III series is more important because it includes heme. 1 Heme Biosynthesis Heme biosynthesis occurs through the following steps: 1-The starting reaction is the condensation between succinyl-CoA ((derived from citric acid cycle in the mitochondria)) & glycine, this reaction is a rate limiting reaction in the hepatic heme synthesis, it occurs in the mitochondria & is catalyzed by ALA synthase (Aminolevulinate synthase) enzyme in the presence of pyridoxal phosphate as a cofactor. The product of this reaction is α-amino-β-ketoadipate which is rapidly decarboxylated to form δ-aminolevulinate (ALA). 2-In the cytoplasm condensation reaction between two molecules of ALA is catalyzed by ALA dehydratase enzyme to form two molecules of water & one 2 molecule of porphobilinogen (PBG) which is a precursor of pyrrole.
    [Show full text]
  • Porphyrins & Bile Pigments
    Bio. 2. ASPU. Lectu.6. Prof. Dr. F. ALQuobaili Porphyrins & Bile Pigments • Biomedical Importance These topics are closely related, because heme is synthesized from porphyrins and iron, and the products of degradation of heme are the bile pigments and iron. Knowledge of the biochemistry of the porphyrins and of heme is basic to understanding the varied functions of hemoproteins in the body. The porphyrias are a group of diseases caused by abnormalities in the pathway of biosynthesis of the various porphyrins. A much more prevalent clinical condition is jaundice, due to elevation of bilirubin in the plasma, due to overproduction of bilirubin or to failure of its excretion and is seen in numerous diseases ranging from hemolytic anemias to viral hepatitis and to cancer of the pancreas. • Metalloporphyrins & Hemoproteins Are Important in Nature Porphyrins are cyclic compounds formed by the linkage of four pyrrole rings through methyne (==HC—) bridges. A characteristic property of the porphyrins is the formation of complexes with metal ions bound to the nitrogen atom of the pyrrole rings. Examples are the iron porphyrins such as heme of hemoglobin and the magnesium‐containing porphyrin chlorophyll, the photosynthetic pigment of plants. • Natural Porphyrins Have Substituent Side Chains on the Porphin Nucleus The porphyrins found in nature are compounds in which various side chains are substituted for the eight hydrogen atoms numbered in the porphyrin nucleus. As a simple means of showing these substitutions, Fischer proposed a shorthand formula in which the methyne bridges are omitted and a porphyrin with this type of asymmetric substitution is classified as a type III porphyrin.
    [Show full text]
  • UROPORPHYRINOGEN HII COSYNTHETASE in HUMAN Hemolysates from Five Patientswith Congenital Erythropoietic Porphyriawas Much Lower
    UROPORPHYRINOGEN HII COSYNTHETASE IN HUMAN CONGENITAL ERYTHROPOIETIC PORPHYRIA * BY GIOVANNI ROMEO AND EPHRAIM Y. LEVIN DEPARTMENT OF PEDIATRICS, THE JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE Communicated by William L. Straus, Jr., April 24, 1969 Abstract.-Activity of the enzyme uroporphyrinogen III cosynthetase in hemolysates from five patients with congenital erythropoietic porphyria was much lower than the activity in control samples. The low cosynthetase activity in patients was not due to the presence of a free inhibitor or some competing en- zymatic activity, because hemolysates from porphyric subjects did not interfere either with the cosynthetase activity of hemolysates from normal subjects or with cosynthetase prepared from hematopoietic mouse spleen. This partial deficiency of cosynthetase in congenital erythropoietic porphyria corresponds to that shown previously in the clinically similar erythropoietic porphyria of cattle and explains the overproduction of uroporphyrin I in the human disease. Erythropoietic porphyria is a rare congenital disorder of man and cattle, characterized by photosensitivity, erythrodontia, hemolytic anemia, and por- phyrinuria.1 Many of the clinical manifestations of the disease can be explained by the production in marrow, deposition in tissues, and excretion in the urine and feces, of large amounts of uroporphyrin I and coproporphyrin I, which are products of the spontaneous oxidation of uroporphyrinogen I and its decarboxyl- ated derivative, coproporphyrinogen I. In cattle, the condition is inherited
    [Show full text]
  • Properties of Chlorophyllase from Capsicum Annuum L. Fruits
    Properties of Chlorophyllase from Capsicum annuum L. Fruits Dámaso Hornero-Méndez and Marí a Isabel Mínguez-Mosquera* Departamento de Biotecnologia de Alimentos, Instituto de la Grasa (CSIC), Av. Padre Garcia Tejero, 4, 41012-Sevilla, SPAIN. Fax: +34-954691262. E-mail: [email protected] * Author for correspondence and reprint requests Z. Naturforsch. 56c, 1015-1021 (2001); received June 27/August 6 , 2001 Chlorophyll, Chlorophyllase, Capsicum annuum The in vitro properties of semi-purified chlorophyllase (chlorophyll-chlorophyllido hy­ drolase, EC 3.1.1.14) from Capsicum annuum fruits have been studied. The enzyme showed an optimum of activity at pH 8.5 and 50 °C. Substrate specificity was studied for chlorophyll (Chi) a, Chi b, pheophytin (Phe) a and Phe b, with K m values of 10.70, 4.04, 2.67 and 6.37 ^im respectively. Substrate inhibition was found for Phe b at concentrations higher than 5 ^m. Chlorophyllase action on Chi a ’ and Chi b' was also studied but no hydrolysis was observed, suggesting that the mechanism of action depends on the configuration at C-132 in the chloro­ phyll molecule, with the enzyme acting only on compounds with R132 stereochemistry. The effect of various metals (Mg2+, Hg2+, Cu2+, Zn2+, Co , Fe2+ and Fe3+) was also investigated, and a general inhibitory effect was found, this being more marked for Hg2+ and Fe2+. Func­ tional groups such as -SH and -S-S- seemed to participate in the formation of the enzyme- substrate complex. Chelating ion and the carbonyl group at C3 appeared to be important in substrate recognition by the enzyme.
    [Show full text]
  • Structure of Pigment Metabolic Pathways and Their Contributions to White Tepal Color Formation of Chinese Narcissus Tazetta Var
    International Journal of Molecular Sciences Article Structure of Pigment Metabolic Pathways and Their Contributions to White Tepal Color Formation of Chinese Narcissus tazetta var. chinensis cv Jinzhanyintai Yujun Ren † ID , Jingwen Yang †, Bingguo Lu, Yaping Jiang, Haiyang Chen, Yuwei Hong, Binghua Wu and Ying Miao * Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; [email protected] (Y.R.); [email protected] (J.Y.); [email protected] (B.L.); [email protected] (Y.J.); [email protected] (H.C.); [email protected] (Y.H.); [email protected] (B.W.) * Correspondence: [email protected]; Tel.:/Fax: +86-591-8639-2987 † These authors contributed equally to this work. Received: 7 August 2017; Accepted: 4 September 2017; Published: 8 September 2017 Abstract: Chinese narcissus (Narcissus tazetta var. chinensis) is one of the ten traditional flowers in China and a famous bulb flower in the world flower market. However, only white color tepals are formed in mature flowers of the cultivated varieties, which constrains their applicable occasions. Unfortunately, for lack of genome information of narcissus species, the explanation of tepal color formation of Chinese narcissus is still not clear. Concerning no genome information, the application of transcriptome profile to dissect biological phenomena in plants was reported to be effective. As known, pigments are metabolites of related metabolic pathways, which dominantly decide flower color. In this study, transcriptome profile and pigment metabolite analysis methods were used in the most widely cultivated Chinese narcissus “Jinzhanyintai” to discover the structure of pigment metabolic pathways and their contributions to white tepal color formation during flower development and pigmentation processes.
    [Show full text]
  • Infection by a Giant Virus (Aav) Induces Widespread Physiological Reprogramming in Aureococcus Anophagefferens CCMP1984 – a Harmful Bloom Algae
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-19-2018 Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae Mohammad Moniruzzaman University of Tennessee, Knoxville Eric R. Gann University of Tennessee, Knoxville Steven W. Wilhelm University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Recommended Citation Moniruzzaman, Mohammad, Eric R. Gann, and Steven W. Wilhelm. “Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae.” Frontiers in Microbiology 9 (2018). https://doi.org/10.3389/fmicb.2018.00752. This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. fmicb-09-00752 April 18, 2018 Time: 16:59 # 1 ORIGINAL RESEARCH published: 19 April 2018 doi: 10.3389/fmicb.2018.00752 Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae Mohammad Moniruzzaman1,2, Eric R. Gann1 and Steven W. Wilhelm1* 1 Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States, 2 Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA, United States While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, “giant” dsDNA viruses have been found to Edited by: be associated with important ecological processes, including the collapse of algal Akio Adachi, Tokushima University, Japan blooms.
    [Show full text]
  • Biochemistry I Enzymes
    BIOCHEMISTRY I 3rd. Stage Lec. ENZYMES Biomedical Importance: Enzymes, which catalyze the biochemical reactions, are essential for life. They participate in the breakdown of nutrients to supply energy and chemical building blocks; the assembly of those building blocks into proteins, DNA, membranes, cells, and tissues; and the harnessing of energy to power cell motility, neural function, and muscle contraction. The vast majority of enzymes are proteins. Notable exceptions include ribosomal RNAs and a handful of RNA molecules imbued with endonuclease or nucleotide ligase activity known collectively as ribozymes. The ability to detect and to quantify the activity of specific enzymes in blood, other tissue fluids, or cell extracts provides information that complements the physician’s ability to diagnose and predict the prognosis of many diseases. Further medical applications include changes in the quantity or in the catalytic activity of key enzymes that can result from genetic defects, nutritional deficits, tissue damage, toxins, or infection by viral or bacterial pathogens (eg, Vibrio cholerae). Medical scientists address imbalances in enzyme activity by using pharmacologic agents to inhibit specific enzymes and are investigating gene therapy as a means to remedy deficits in enzyme level or function. In addition to serving as the catalysts for all metabolic processes, their impressive catalytic activity, substrate specificity, and stereospecificity enable enzymes to fulfill key roles in additional processes related to human health and well-being. Proteases and amylases augment the capacity of detergents to remove dirt and stains, and enzymes play important roles in producing or enhancing the nutrient value of food products for both humans and animals.
    [Show full text]
  • Title a Marine Photosynthetic Microbial Cell Factory As a Platform
    A marine photosynthetic microbial cell factory as a platform Title for spider silk production Foong, Choon Pin; Higuchi-Takeuchi, Mieko; Malay, Ali D.; Author(s) Oktaviani, Nur Alia; Thagun, Chonprakun; Numata, Keiji Citation Communications Biology (2020), 3 Issue Date 2020-07-08 URL http://hdl.handle.net/2433/252537 © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included Right in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Type Journal Article Textversion publisher Kyoto University ARTICLE https://doi.org/10.1038/s42003-020-1099-6 OPEN A marine photosynthetic microbial cell factory as a platform for spider silk production Choon Pin Foong1,2, Mieko Higuchi-Takeuchi1, Ali D. Malay 1, Nur Alia Oktaviani1, Chonprakun Thagun1 & ✉ Keiji Numata 1,2 1234567890():,; Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracted great interest as promising platforms for economical and sustainable production of bioenergy, biochemicals, and biopolymers.
    [Show full text]
  • (10) Patent No.: US 8119385 B2
    US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
    [Show full text]