Sulfoquinovose Metabolism in Marine Algae
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Sulfite Dehydrogenases in Organotrophic Bacteria : Enzymes
Sulfite dehydrogenases in organotrophic bacteria: enzymes, genes and regulation. Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Fachbereich Biologie vorgelegt von Sabine Lehmann Tag der mündlichen Prüfung: 10. April 2013 1. Referent: Prof. Dr. Bernhard Schink 2. Referent: Prof. Dr. Andrew W. B. Johnston So eine Arbeit wird eigentlich nie fertig, man muss sie für fertig erklären, wenn man nach Zeit und Umständen das möglichste getan hat. (Johann Wolfgang von Goethe, Italienische Reise, 1787) DANKSAGUNG An dieser Stelle möchte ich mich herzlich bei folgenden Personen bedanken: . Prof. Dr. Alasdair M. Cook (Universität Konstanz, Deutschland), der mir dieses Thema und seine Laboratorien zur Verfügung stellte, . Prof. Dr. Bernhard Schink (Universität Konstanz, Deutschland), für seine spontane und engagierte Übernahme der Betreuung, . Prof. Dr. Andrew W. B. Johnston (University of East Anglia, UK), für seine herzliche und bereitwillige Aufnahme in seiner Arbeitsgruppe, seiner engagierten Unter- stützung, sowie für die Übernahme des Koreferates, . Prof. Dr. Frithjof C. Küpper (University of Aberdeen, UK), für seine große Hilfsbereitschaft bei der vorliegenden Arbeit und geplanter Manuskripte, als auch für die mentale Unterstützung während der letzten Jahre! Desweiteren möchte ich herzlichst Dr. David Schleheck für die Übernahme des Koreferates der mündlichen Prüfung sowie Prof. Dr. Alexander Bürkle, für die Übernahme des Prüfungsvorsitzes sowie für seine vielen hilfreichen Ratschläge danken! Ein herzliches Dankeschön geht an alle beteiligten Arbeitsgruppen der Universität Konstanz, der UEA und des SAMS, ganz besonders möchte ich dabei folgenden Personen danken: . Dr. David Schleheck und Karin Denger, für die kritische Durchsicht dieser Arbeit, der durch und durch sehr engagierten Hilfsbereitschaft bei Problemen, den zahlreichen wissenschaftlichen Diskussionen und für die aufbauenden Worte, . -
Permanent Draft Genome Sequence of Sulfoquinovose-Degrading Pseudomonas Putida Strain SQ1 Ann-Katrin Felux1,2, Paolo Franchini1,3 and David Schleheck1,2*
Erschienen in: Standards in Genomic Sciences ; 10 (2015). - 42 Felux et al. Standards in Genomic Sciences (2015) 10:42 DOI 10.1186/s40793-015-0033-x SHORT GENOME REPORT Open Access Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1 Ann-Katrin Felux1,2, Paolo Franchini1,3 and David Schleheck1,2* Abstract Pseudomonas putida SQ1 was isolated for its ability to utilize the plant sugar sulfoquinovose (6-deoxy-6-sulfoglucose) for growth, in order to define its SQ-degradation pathway and the enzymes and genes involved. Here we describe the features of the organism, together with its draft genome sequence and annotation. The draft genome comprises 5,328,888 bp and is predicted to encode 5,824 protein-coding genes; the overall G + C content is 61.58 %. The genome annotation is being used for identification of proteins that might be involved in SQ degradation by peptide fingerprinting-mass spectrometry. Keywords: Pseudomonas putida SQ1, aerobic, Gram-negative, Pseudomonadaceae, plant sulfolipid, organosulfonate, sulfoquinovose biodegradation Introduction sediment of pre-Alpine Lake Constance, Germany [13]. Pseudomonas putida strain SQ1 belongs to the family of SQ is the polar headgroup of the plant sulfolipid sulfo- Pseudomonadaceae in the class of Gammaproteobac- quinovosyl diacylglycerol, which is present in the teria. The genus Pseudomonas was first described by photosynthetic membranes of all higher plants, mosses, Migula (in the year 1894 [1]) and the species Pseudo- ferns and algae and most photosynthetic bacteria [14]. monas putida by Trevisan (in 1889 [2]). P. putida strain SQ is one of the most abundant organosulfur com- KT2440 was the first strain whose genome had been se- pounds in the biosphere, following glutathione, cyst- quenced (in 2002 [3]), and it is the most well-studied P. -
The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis
This is a repository copy of The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/170966/ Version: Accepted Version Article: Sharma, Mahima orcid.org/0000-0003-3960-2212, Abayakoon, Palika, Epa, Ruwan et al. (9 more authors) (2021) The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. ACS Central Science. ISSN 2374-7943 https://doi.org/10.1021/acscentsci.0c01285 Reuse This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) licence. This licence only allows you to download this work and share it with others as long as you credit the authors, but you can’t change the article in any way or use it commercially. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis Mahima Sharma,1 Palika Abayakoon,2 Ruwan Epa,2 Yi Jin,1 James P. Lingford,3,4 Tomohiro Shimada,5 Masahiro Nakano,6 Janice W.-Y. Mui,2 Akira Ishihama,7 Ethan D. Goddard- Borger,*,3,4 Gideon J. Davies,*,1 Spencer J. Williams*,2 1York Structural Biology Laboratory, Department of Chemistry, University of York YO10 5DD, U.K. 2School of Chemistry and -
Marine Species Distributions: from Data to Predictive Models
Marine Species Distributions: From data to predictive models Samuel Bosch Promoter: Prof. Dr. Olivier De Clerck Thesis submitted in partial fulfilment of the requirements for the degree of Doctor (PhD) in Science – Biology Academic year 2016-2017 Members of the examination committee Prof. Dr. Olivier De Clerck - Ghent University (Promoter)* Prof. Dr. Tom Moens – Ghent University (Chairman) Prof. Dr. Elie Verleyen – Ghent University (Secretary) Prof. Dr. Frederik Leliaert – Botanic Garden Meise / Ghent University Dr. Tom Webb – University of Sheffield Dr. Lennert Tyberghein - Vlaams Instituut voor de Zee * non-voting members Financial support This thesis was funded by the ERANET INVASIVES project (EU FP7 SEAS-ERA/INVASIVES SD/ER/010) and by VLIZ as part of the Flemish contribution to the LifeWatch ESFRI. Table of contents Chapter 1 General Introduction 7 Chapter 2 Fishing for data and sorting the catch: assessing the 25 data quality, completeness and fitness for use of data in marine biogeographic databases Chapter 3 sdmpredictors: an R package for species distribution 49 modelling predictor datasets Chapter 4 In search of relevant predictors for marine species 61 distribution modelling using the MarineSPEED benchmark dataset Chapter 5 Spatio-temporal patterns of introduced seaweeds in 97 European waters, a critical review Chapter 6 A risk assessment of aquarium trade introductions of 119 seaweed in European waters Chapter 7 Modelling the past, present and future distribution of 147 invasive seaweeds in Europe Chapter 8 General discussion 179 References 193 Summary 225 Samenvatting 229 Acknowledgements 233 Chapter 1 General Introduction 8 | C h a p t e r 1 Species distribution modelling Throughout most of human history knowledge of species diversity and their respective distributions was an essential skill for survival and civilization. -
Investigating the Impacts of Marine Invasive Non-Native Species
Natural England Commissioned Report NECR223 Investigating the Impacts of Marine Invasive Non-Native Species First published 14 September 2016 www.gov.uk/natural -england Foreword Natural England commission a range of reports from external contractors to provide evidence and advice to assist us in delivering our duties. The views in this report are those of the authors and do not necessarily represent those of Natural England. Background Non-native species can become invasive, altering worm F. enigmaticus and the leathery sea-squirt S. local ecology and out-competing native species. clava. However, we currently lack evidence on the impacts The focus of this report to provide evidence on that some of these species have on the environment, potential susceptibility of MPA features in particular in particular to features of Marine Protected Areas and the generation of a matrix tool which can be and how best to incorporate the presence and adapted in future to incorporate more species and potential impacts caused by invasive non-native new information will provide our staff and others with species (INNS) in the assessment of site condition. overview of potential risks and priorities. This The Improvement Programme for England’s Natura information will feed into the guidance being 2000 sites (IPENS) identified INNS as a key issue developed on the condition assessment process as it impacting our Natura 2000 sites. The theme plan of will help staff to assess the potential threats of key actions includes gathering evidence on impacts invasive species on the MPA. to encourage uptake of best practice and also Finally, the information gathered in this report will be gathering evidence to help determine priority species provided to the GB Non Native Species Secretariat to to address. -
The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis
The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis Mahima Sharma,1 Palika Abayakoon,2 Ruwan Epa,2 Yi Jin,1 James P. Lingford,3,4 Tomohiro Shimada,5 Masahiro Nakano,6 Janice W.-Y. Mui,2 Akira Ishihama,7 Ethan D. Goddard- Borger,*,3,4 Gideon J. Davies,*,1 Spencer J. Williams*,2 1York Structural Biology Laboratory, Department of Chemistry, University of York YO10 5DD, U.K. 2School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia 3ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia 4Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia 5Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan 6Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan 7Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan Keywords: metabolism; sulfur cycle; enzyme mechanism; glycobiology; structural biology 1 Abstract: The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolises SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden- Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase and sulfofructose-1-phosphate (SFP) aldolase. Our data shows that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. -
Circular Spectropolarimetric Sensing of Higher Plant and Algal Chloroplast Structural Variations
Photosynthesis Research (2019) 140:129–139 https://doi.org/10.1007/s11120-018-0572-2 ORIGINAL ARTICLE Circular spectropolarimetric sensing of higher plant and algal chloroplast structural variations C. H. Lucas Patty1 · Freek Ariese2 · Wybren Jan Buma3 · Inge Loes ten Kate4 · Rob J. M. van Spanning5 · Frans Snik6 Received: 7 June 2018 / Accepted: 4 August 2018 / Published online: 23 August 2018 © The Author(s) 2018 Abstract Photosynthetic eukaryotes show a remarkable variability in photosynthesis, including large differences in light-harvesting proteins and pigment composition. In vivo circular spectropolarimetry enables us to probe the molecular architecture of photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological and structural information. In the present study, we have measured the circular polarizance of several multicellular green, red, and brown algae and higher plants, which show large variations in circular spectropolarimetric signals with differences in both spectral shape and magnitude. Many of the algae display spectral characteristics not previously reported, indicating a larger variation in molecular organization than previously assumed. As the strengths of these signals vary by three orders of magnitude, these results also have important implications in terms of detectability for the use of circular polarization as a signature of life. Keywords Circular polarization · Photosynthesis · Chloroplast · Chlorophyll · Algae Introduction other, called homochirality, therefore serves as a unique and unambiguous biosignature (Schwieterman et al. 2018). Terrestrial biochemistry is based upon chiral molecules. Many larger, more complex biomolecules and biomolecu- In their most simple form, these molecules can occur in a lar architectures are chiral too and the structure and func- left-handed and a right-handed version called enantiom- tioning of biological systems is largely determined by their ers. -
New Intermediates, Pathways, Enzymes and Genes in the Microbial Metabolism of Organosulfonates
New intermediates, pathways, enzymes and genes in the microbial metabolism of organosulfonates Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Fachbereich Biologie vorgelegt von Sonja Luise Weinitschke Konstanz, Dezember 2009 Tag der mündlichen Prüfung: 26.02.2010 1. Referent: Prof. Dr. Alasdair M. Cook 2. Referent: Prof. Dr. Bernhard Schink „In der Wissenschaft gleichen wir alle nur den Kindern, die am Rande des Wissens hier und da einen Kiesel aufheben, während sich der weite Ozean des Unbekannten vor unseren Augen erstreckt.“ Sir Isaac Newton Meiner Familie gewidmet Contributions during my PhD thesis to other projects than mentioned in the main Chapters: Denger, K., S. Weinitschke, T. H. M. Smits, D. Schleheck and A. M. Cook (2008). Bacterial sulfite dehydrogenases in organotrophic metabolism: separation and identification in Cupriavidus necator H16 and in Delftia acidovorans SPH-1. Microbiology 154: 256-263. Krejčík, Z., K. Denger, S. Weinitschke, K. Hollemeyer, V. Pačes, A. M. Cook and T. H. M. Smits (2008). Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch. Microbiol. 190: 159-168. Denger, K., J. Mayer, M. Buhmann, S. Weinitschke, T. H. M. Smits and A. M. Cook (2009). Bifurcated degradative pathway of 3-sulfolactate in Roseovarius nubinhibens ISM via sulfoacetaldehyde acetyltransferase and (S)-cysteate sulfo-lyase. J. Bacteriol. 191: 5648-5656. An erster Stelle möchte ich mich herzlich bei Prof. Dr. Alasdair M. Cook bedanken für die Betreuung und die Möglichkeit, an einem so interessanten Projekt forschen zu dürfen. Mein herzlicher Dank gilt außerdem… … Prof. -
Narragansett Bay Research Reserve Technical Reports Series 2011:4
Narragansett Bay Research Reserve Technical Report Technical A protocol for rapidly monitoring macroalgae in the Narragansett Bay Research Reserve 1 2011:4 Kenneth B. Raposa, Ph.D. Research Coordinator, NBNERR Brandon Russell University of Connecticut Ashley Bertrand US EPA Atlantic Ecology Division November 2011 Technical Report Series 2011:4 Introduction Macroalgae (i.e., seaweed) is an important source of primary production in shallow estuarine systems, and at low to moderate biomass levels it serves as important refuge and forage habitat for nekton (Sogard and Able 1991; Kingsford 1995; Raposa and Oviatt 2000). Macroalgae is typically nitrogen limited in estuaries and it can therefore respond rapidly when anthropogenic nutrient inputs increase (Nelson et al. 2003). Under eutrophic conditions, macroalgae can shade and outcompete eelgrass and other submerged aquatic vegetation (SAV) species and lead to hypoxic and anoxic conditions that can alter estuarine ecosystem function (Peckol et al. 1994; Raffaelli et al. 1998). Macroalgae is therefore an excellent indicator of current estuarine condition and of how these systems respond to changes in the amount of anthropogenic nitrogen inputs. Narragansett Bay is an urban estuary in Rhode Island, USA that receives high levels of nitrogen inputs from waste-water treatment facilities (WWTFs), mostly into the Providence River at the head of the Bay (Pruell et al. 2006). As a result, excessive summertime macroalgal blooms dominated by green algae (e.g., Ulva spp.) are a conspicuous and problematic occurrence in many parts of the upper Bay and in constricted, shallow coves and embayments (Granger et al. 2000). Many of these same areas also experience periods of bottom hypoxia during summer, but the degree to which this is caused by macroalgae has not been quantified. -
A Sulfoglycolytic Entner-Doudoroff Pathway in Rhizobium Leguminosarum Bv
This is a repository copy of A sulfoglycolytic Entner-Doudoroff pathway in Rhizobium leguminosarum bv. trifolii SRDI565. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/161920/ Version: Accepted Version Article: Li, Jinling, Epa, Ruwan, Scott, Nichollas E et al. (8 more authors) (2020) A sulfoglycolytic Entner-Doudoroff pathway in Rhizobium leguminosarum bv. trifolii SRDI565. Applied and Environmental Microbiology. ISSN 0099-2240 https://doi.org/10.1128/AEM.00750-20 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ 1 A sulfoglycolytic Entner-Doudoroff pathway in Rhizobium leguminosarum bv. trifolii 2 SRDI565 3 4 Jinling Li,1 Ruwan Epa,1 Nichollas E. Scott,3 Dominic Skoneczny,4 Mahima Sharma,5 5 Alexander J.D. Snow,5 James P. Lingford,2 Ethan D. Goddard-Borger,2 Gideon J. Davies,5 6 Malcolm J. McConville,4 Spencer J. Williams1* 7 8 1School of -
Arxiv:1808.08033V1 [Q-Bio.BM] 24 Aug 2018
Circular spectropolarimetric sensing of higher plant and algal chloroplast structural variations C.H. Lucas Patty1*, Freek Ariese2, Wybren Jan Buma3, Inge Loes ten Kate4, Rob J.M. van Spanning5, Frans Snik6 1 Molecular Cell Physiology, VU Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands 2 LaserLaB, VU Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands 3 HIMS, Photonics group, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands 4 Department of Earth Sciences, Utrecht University, Budapestlaan 4, 3584 CD Utrecht, The Netherlands 5 Systems Bioinformatics, VU Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands 6 Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden, The Netherlands *[email protected] Abstract Photosynthetic eukaryotes show a remarkable variability in photosynthesis, in- cluding large differences in light harvesting proteins and pigment composition. In vivo circular spectropolarimetry enables us to probe the molecular architecture of photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological and structural information. In the present study we have measured the circular polarizance of several multicellular green, red and brown algae and higher plants, which show large variations in circular spectropo- larimetric signals with differences in both spectral shape and magnitude. Many of the algae display spectral characteristics not previously reported, indicating a larger variation in molecular organization than previously assumed. As the strengths of these signals vary by three orders of magnitude, these results also have important implications in terms of detectability for the use of circular polarization as a signature of life. -
DNA Barcoding
Botanica Marina 2020; 63(3): 253–272 Review Angela G. Bartolo*, Gabrielle Zammit, Akira F. Peters and Frithjof C. Küpper The current state of DNA barcoding of macroalgae in the Mediterranean Sea: presently lacking but urgently required https://doi.org/10.1515/bot-2019-0041 Received 12 June, 2019; accepted 18 February, 2020; online first 28 Introduction March, 2020 This review delves into the current state of DNA barcod- Abstract: This review article explores the state of DNA ing of macroalgae with a focus on the Mediterranean Sea. barcoding of macroalgae in the Mediterranean Sea. Data To this end, data from the Barcode of Life Data System from the Barcode of Life Data System (BOLD) were utilised (BOLD) were researched and a literature review was con- in conjunction with a thorough bibliographic review. Our ducted. The study concludes that there is a lack of genetic findings indicate that from around 1124 records of algae data for these organisms. This article discusses the steps in the Mediterranean Sea, only 114 species have been required for improving DNA-based methods in this region. barcoded. We thus conclude that there are insufficient Algae including macrophytes and phytoplankton are macroalgal genetic data from the Mediterranean and the base of marine food webs, provide oxygen to aquatic that this area would greatly benefit from studies involv- environments and humans, can be used as biological indi- ing DNA barcoding. Such research would contribute to cators, and are a potential food source which is underuti- resolving numerous questions about macroalgal system- lised in most parts of the world (Wolf 2012).