1
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Omta AW, Liefer JD, Finkel ZV, Irwin AJ, Sher D, Follows MJ. A model of time-dependent macromolecular and elemental composition of phytoplankton. J Theor Biol 2024; 592:111883. [PMID: 38908474 DOI: 10.1016/j.jtbi.2024.111883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024]
Abstract
Phytoplankton Chl:C:N:P ratios are important from both an ecological and a biogeochemical perspective. We show that these elemental ratios can be represented by a phytoplankton physiological model of low complexity that includes major cellular macromolecular pools. In particular, our model resolves time-dependent intracellular pools of chlorophyll, proteins, nucleic acids, carbohydrates/lipids, and N and P storage. Batch culture data for two diatom and two prasinophyte species are used to constrain parameters that represent specific allocation traits and strategies. A key novelty is the simultaneous estimation of physiological parameters for two phytoplankton groups of such different sizes. The number of free parameters is reduced by assuming (i) allometric scaling for maximum uptake rates, (ii) shared half-saturation constants for synthesis of functional macromolecules, (iii) shared exudation rates of functional macromolecules across the species. The rationale behind this assumption is that across the different species, the same or similar processes, enzymes, and metabolites play a role in key physiological processes. For the turnover numbers of macromolecular synthesis and storage exudation rates, differences between diatoms and prasinophytes need to be taken into account to obtain a good fit. Our model fits suggest that the parameters related to storage dynamics dominate the differences in the C:N:P ratios between the different phytoplankton groups. Since descriptions of storage dynamics are still incomplete and imprecise, predictions of C:N:P ratios by phytoplankton models likely have a large uncertainty.
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Affiliation(s)
- Anne Willem Omta
- Department of Earth, Environmental, and Planetary Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Justin D Liefer
- Department of Biology, Mount Allison University, 63B York Street, Sackville, E4L 1A5, New Brunswick, Canada
| | - Zoe V Finkel
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, B3H 4R2, Nova Scotia, Canada
| | - Andrew J Irwin
- Department of Mathematics and Statistics, Dalhousie University, 6316 Coburg Road, Halifax, B3H 4R2, Nova Scotia, Canada
| | - Daniel Sher
- Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel 31905, Haifa, Israel
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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2
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Foresi N, De Marco MA, Del Castello F, Ramirez L, Nejamkin A, Calo G, Grimsley N, Correa-Aragunde N, Martínez-Noël GMA. The tiny giant of the sea, Ostreococcus's unique adaptations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108661. [PMID: 38735153 DOI: 10.1016/j.plaphy.2024.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina.
| | - María Agustina De Marco
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | | | - Leonor Ramirez
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Andres Nejamkin
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina
| | - Gonzalo Calo
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | - Nigel Grimsley
- CNRS, LBBM, Sorbonne Université OOB, 1 Avenue de Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | | | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina.
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3
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Wang L, Liu L, Zhao J, Li C, Wu H, Zhao H, Wu Q. Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111843. [PMID: 37648115 DOI: 10.1016/j.plantsci.2023.111843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.
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Affiliation(s)
- Lei Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Linling Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China.
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4
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Steinke N, Vidal‐Melgosa S, Schultz‐Johansen M, Hehemann J. Biocatalytic quantification of α-glucan in marine particulate organic matter. Microbiologyopen 2022; 11:e1289. [PMID: 35765187 PMCID: PMC9134812 DOI: 10.1002/mbo3.1289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/06/2022] [Indexed: 12/04/2022] Open
Abstract
Marine algae drive the marine carbon cycle, converting carbon dioxide into organic material. A major component of this produced biomass is a variety of glycans. Marine α-glucans include a range of storage glycans from red and green algae, bacteria, fungi, and animals. Although these compounds are likely to account for a high amount of the carbon stored in the oceans they have not been quantified in marine samples so far. Here we present a method to extract and quantify α-glucans (and compare it with the β-glucan laminarin) in particulate organic matter from algal cultures and environmental samples using sequential physicochemical extraction and enzymes as α-glucan-specific probes. This enzymatic assay is more specific and less susceptible to side reactions than chemical hydrolysis. Using HPAEC-PAD to detect the hydrolysis products allows for a glycan quantification in particulate marine samples down to a concentration of ≈2 µg/L. We measured glucans in three cultured microalgae as well as in marine particulate organic matter from the North Sea and western North Atlantic Ocean. While the β-glucan laminarin from diatoms and brown algae is an essential component of marine carbon turnover, our results further indicate the significant contribution of starch-like α-glucans to marine particulate organic matter. Henceforth, the combination of glycan-linkage-specific enzymes and chromatographic hydrolysis product detection can provide a powerful tool in the exploration of marine glycans and their role in the global carbon cycle.
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Affiliation(s)
- Nicola Steinke
- MARUM—Center for Marine Environmental Sciences, Faculty of Biology and ChemistryUniversity of BremenBremenGermany
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Silvia Vidal‐Melgosa
- MARUM—Center for Marine Environmental Sciences, Faculty of Biology and ChemistryUniversity of BremenBremenGermany
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Mikkel Schultz‐Johansen
- MARUM—Center for Marine Environmental Sciences, Faculty of Biology and ChemistryUniversity of BremenBremenGermany
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Jan‐Hendrik Hehemann
- MARUM—Center for Marine Environmental Sciences, Faculty of Biology and ChemistryUniversity of BremenBremenGermany
- Max Planck Institute for Marine MicrobiologyBremenGermany
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5
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Bachy C, Wittmers F, Muschiol J, Hamilton M, Henrissat B, Worden AZ. The Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:585-616. [PMID: 35259927 DOI: 10.1146/annurev-arplant-071921-100530] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
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Affiliation(s)
- Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jan Muschiol
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Hamilton
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille Université (AMU), Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratories, Woods Hole, Massachusetts, USA
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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6
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Wang Y, Ral JP, Saulnier L, Kansou K. How Does Starch Structure Impact Amylolysis? Review of Current Strategies for Starch Digestibility Study. Foods 2022; 11:foods11091223. [PMID: 35563947 PMCID: PMC9104245 DOI: 10.3390/foods11091223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
In vitro digestibility of starch is a common analysis in human nutrition research, and generally consists of performing the hydrolysis of starch by α-amylase in specific conditions. Similar in vitro assays are also used in other research fields, where different methods can be used. Overall, the in vitro hydrolysis of native starch is a bridge between all of these methods. In this literature review, we examine the use of amylolysis assays in recent publications investigating the complex starch structure-amylolysis relation. This review is divided in two parts: (1) a brief review of the factors influencing the hydrolysis of starch and (2) a systematic review of the experimental designs and methods used in publications for the period 2016–2020. The latter reports on starch materials, factors investigated, characterization of the starch hydrolysis kinetics and data analysis techniques. This review shows that the dominant research strategy favors the comparison between a few starch samples most frequently described through crystallinity, granule type, amylose and chain length distribution with marked characteristics. This strategy aims at circumventing the multifactorial aspect of the starch digestion mechanism by focusing on specific features. An alternative strategy relies on computational approaches such as multivariate statistical analysis and machine learning techniques to decipher the role of each factor on amylolysis. While promising to address complexity, the limited use of a computational approach can be explained by the small size of the experimental datasets in most publications. This review shows that key steps towards the production of larger datasets are already available, in particular the generalization of rapid hydrolysis assays and the development of quantification approaches for most analytical results.
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Affiliation(s)
- Yuzi Wang
- INRAE, UR1268, Biopolymers, Interactions & Assemblies (BIA), 44316 Nantes, France; (Y.W.); (L.S.)
| | - Jean-Philippe Ral
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia;
| | - Luc Saulnier
- INRAE, UR1268, Biopolymers, Interactions & Assemblies (BIA), 44316 Nantes, France; (Y.W.); (L.S.)
| | - Kamal Kansou
- INRAE, UR1268, Biopolymers, Interactions & Assemblies (BIA), 44316 Nantes, France; (Y.W.); (L.S.)
- Correspondence: ; Tel.: +33-02-40-67-51-49
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7
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Figueroa CM, Asencion Diez MD, Ballicora MA, Iglesias AA. Structure, function, and evolution of plant ADP-glucose pyrophosphorylase. PLANT MOLECULAR BIOLOGY 2022; 108:307-323. [PMID: 35006475 DOI: 10.1007/s11103-021-01235-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023]
Abstract
This review outlines research performed in the last two decades on the structural, kinetic, regulatory and evolutionary aspects of ADP-glucose pyrophosphorylase, the regulatory enzyme for starch biosynthesis. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the pathway of glycogen and starch synthesis in bacteria and plants, respectively. Plant ADP-Glc PPase is a heterotetramer allosterically regulated by metabolites and post-translational modifications. In this review, we focus on the three-dimensional structure of the plant enzyme, the amino acids that bind the regulatory molecules, and the regions involved in transmitting the allosteric signal to the catalytic site. We provide a model for the evolution of the small and large subunits, which produce heterotetramers with distinct catalytic and regulatory properties. Additionally, we review the various post-translational modifications observed in ADP-Glc PPases from different species and tissues. Finally, we discuss the subcellular localization of the enzyme found in grain endosperm from grasses, such as maize and rice. Overall, this work brings together research performed in the last two decades to better understand the multiple mechanisms involved in the regulation of ADP-Glc PPase. The rational modification of this enzyme could improve the yield and resilience of economically important crops, which is particularly important in the current scenario of climate change and food shortage.
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Affiliation(s)
- Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA.
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina.
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8
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Hedin N, Velazquez MB, Barchiesi J, Gomez-Casati DF, Busi MV. CBM20CP, a novel functional protein of starch metabolism in green algae. PLANT MOLECULAR BIOLOGY 2022; 108:363-378. [PMID: 34546521 DOI: 10.1007/s11103-021-01190-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/20/2021] [Indexed: 05/29/2023]
Abstract
Ostreococcus tauri is a picoalga that contains a small and compact genome, which resembles that of higher plants in the multiplicity of enzymes involved in starch synthesis (ADP-glucose pyrophosphorylase, ADPGlc PPase; granule bound starch synthase, GBSS; starch synthases, SSI, SSII, SSIII; and starch branching enzyme, SBE, between others), except starch synthase IV (SSIV). Although its genome is fully sequenced, there are still many genes and proteins to which no function was assigned. Here, we identify the OT_ostta06g01880 gene that encodes CBM20CP, a plastidial protein which contains a central carbohydrate binding domain of the CBM20 family, and a coiled coil domain at the C-terminus that lacks catalytic activity. We demonstrate that CBM20CP has the ability to bind starch, amylose and amylopectin with different affinities. Furthermore, this protein interacts with OsttaSSIII-B, increasing its binding to starch granules, its catalytic efficiency and promoting granule growth. The results allow us to postulate a functional role for CBM20CP in starch metabolism in green algae. KEY MESSAGE: CBM20CP, a plastidial protein that has a modular structure but lacks catalytic activity, regulates the synthesis of starch in Ostreococcus tauri.
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Affiliation(s)
- Nicolas Hedin
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Maria B Velazquez
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Julieta Barchiesi
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Maria V Busi
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
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9
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Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsley N, Piganeau G. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190089. [PMID: 31587637 DOI: 10.1098/rstb.2019.0089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- L Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, université Paris Saclay, 9105 Evry, France
| | | | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
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10
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Liefer JD, Garg A, Fyfe MH, Irwin AJ, Benner I, Brown CM, Follows MJ, Omta AW, Finkel ZV. The Macromolecular Basis of Phytoplankton C:N:P Under Nitrogen Starvation. Front Microbiol 2019; 10:763. [PMID: 31057501 PMCID: PMC6479212 DOI: 10.3389/fmicb.2019.00763] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
Biogeochemical cycles in the ocean are strongly affected by the elemental stoichiometry (C:N:P) of phytoplankton, which largely reflects their macromolecular content. A greater understanding of how this macromolecular content varies among phytoplankton taxa and with resource limitation may strengthen physiological and biogeochemical modeling efforts. We determined the macromolecular basis (protein, carbohydrate, lipid, nucleic acids, pigments) of C:N:P in diatoms and prasinophytes, two globally important phytoplankton taxa, in response to N starvation. Despite their differing cell sizes and evolutionary histories, the relative decline in protein during N starvation was similar in all four species studied and largely determined variations in N content. The accumulation of carbohydrate and lipid dominated the increase in C content and C:N in all species during N starvation, but these processes differed greatly between diatoms and prasinophytes. Diatoms displayed far greater accumulation of carbohydrate with N starvation, possibly due to their greater cell size and storage capacity, resulting in larger increases in C content and C:N. In contrast, the prasinophytes had smaller increases in C and C:N that were largely driven by lipid accumulation. Variation in C:P and N:P was species-specific and mainly determined by residual P pools, which likely represent intracellular storage of inorganic P and accounted for the majority of cellular P in all species throughout N starvation. Our findings indicate that carbohydrate and lipid accumulation may play a key role in determining the environmental and taxonomic variability in phytoplankton C:N. This quantitative assessment of macromolecular and elemental content spanning several marine phytoplankton species can be used to develop physiological models for ecological and biogeochemical applications.
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Affiliation(s)
- Justin D. Liefer
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Aneri Garg
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Matthew H. Fyfe
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Andrew J. Irwin
- Department of Mathematics and Computer Science, Mount Allison University, Sackville, NB, Canada
| | - Ina Benner
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Christopher M. Brown
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
| | - Michael J. Follows
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Anne Willem Omta
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Zoe V. Finkel
- Department of Geography and Environment, Mount Allison University, Sackville, NB, Canada
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11
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Peng H, Zhai L, Xu S, Xu P, He C, Xiao Y, Gao Y. Efficient Hydrolysis of Raw Microalgae Starch by an α-Amylase (AmyP) of Glycoside Hydrolase Subfamily GH13_37. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12748-12755. [PMID: 30441891 DOI: 10.1021/acs.jafc.8b03524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microalgae starch is receiving increasing attention as a renewable feedstock for biofuel production. Raw microalgae starch from Tetraselmis subcordiformis was proven to be very efficiently hydrolyzed by an α-amylase (AmyP) of glycoside hydrolase subfamily GH13_37 below the temperature of gelatinization (40 °C). The hydrolysis degree reached 74.4 ± 2.2% for 4% raw microalgae starch and 53.2 ± 1.7% for 8% raw microalgae starch after only 2 h. The hydrolysis efficiency was significantly stimulated by calcium ions. The enzyme catalysis of AmyP and its mutants (Q306A and E347A) suggested that calcium ions contributed to the hydrolysis of cyclic structures in raw microalgae starch by a distinctive calcium-binding site Ca2 of AmyP. The study explored raw microalgae starch as a new resource for cold enzymatic hydrolysis and extended our knowledge on the function of calcium in amylolytic enzyme.
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Affiliation(s)
- Hui Peng
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Lu Zhai
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Suo Xu
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Peng Xu
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Yazhong Xiao
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Yi Gao
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
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12
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Tzabari M, Lerner A, Iluz D, Haspel C. Sensitivity study on the effect of the optical and physical properties of coated spherical particles on linear polarization in clear to semi-turbid waters. APPLIED OPTICS 2018; 57:5806-5822. [PMID: 30118052 DOI: 10.1364/ao.57.005806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/10/2018] [Indexed: 06/08/2023]
Abstract
The influence of internal inhomogeneities within hydrosol particles on the polarization characteristics of light is investigated by combining an accurate coated sphere (core-shell) single-scattering model with a radiative transfer model that employs Stokes formalism and considers refraction of direct solar radiation at the air-water interface followed by single scattering. A Junge particle size distribution is assumed. Variations in what we call the "linear polarization phase function" (the degree of linear polarization as a function of scattering angle and the E-vector orientation as a function of scattering angle) are examined as a function of variations in the characteristics of the hydrosol particles. An extensive sensitivity study on the influence of variations in the real and imaginary parts of the refractive index of both the core and shell of the hydrosol particles and on the influences of variations in the ratio between the core radius and shell radius is conducted, varying the values of these parameters over the entire parameter space documented in the literature for actual hydrosol particles. In addition, calculations are conducted for specific parameter combinations in order to demonstrate the influence of some of the most important groups of hydrosols, namely, phytoplankton, gas bubbles, carbonaceous hydrosols, and mineral hydrosols, on the polarization field under water. Variations as a function of solar zenith angle are also investigated. Due to the assumption of single scattering, the results presented are relevant to conditions of low wind speed and a low scattering optical depth and/or low single-scattering albedo within the water body (clear to semi-turbid waters at shallow geometric depths and/or moderate to strong absorption within the water body) outside of Snell's window. Possible implications for aquatic animal polarization vision, for light polarization pollution, and for remote sensing are discussed.
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Barchiesi J, Velazquez MB, Palopoli N, Iglesias AA, Gomez-Casati DF, Ballicora MA, Busi MV. Starch Synthesis in Ostreococcus tauri: The Starch-Binding Domains of Starch Synthase III-B Are Essential for Catalytic Activity. FRONTIERS IN PLANT SCIENCE 2018; 9:1541. [PMID: 30410499 PMCID: PMC6210743 DOI: 10.3389/fpls.2018.01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/02/2018] [Indexed: 05/06/2023]
Abstract
Starch is the major energy storage carbohydrate in photosynthetic eukaryotes. Several enzymes are involved in building highly organized semi-crystalline starch granules, including starch-synthase III (SSIII), which is widely conserved in photosynthetic organisms. This enzyme catalyzes the extension of the α-1,4 glucan chain and plays a regulatory role in the synthesis of starch. Interestingly, unlike most plants, the unicellular green alga Ostreococcus tauri has three SSIII isoforms. In the present study, we describe the structure and function of OsttaSSIII-B, which has a similar modular organization to SSIII in higher plants, comprising three putative starch-binding domains (SBDs) at the N-terminal region and a C-terminal catalytic domain (CD). Purified recombinant OsttaSSIII-B displayed a high affinity toward branched polysaccharides such as glycogen and amylopectin, and to ADP-glucose. Lower catalytic activity was detected for the CD lacking the associated SBDs, suggesting that they are necessary for enzyme function. Moreover, analysis of enzyme kinetic and polysaccharide-binding parameters of site-directed mutants with modified conserved aromatic amino acid residues W122, Y124, F138, Y147, W279, and W304, belonging to the SBDs, revealed their importance for polysaccharide binding and SS activity. Our results suggest that OT_ostta13g01200 encodes a functional SSIII comprising three SBD domains that are critical for enzyme function.
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Affiliation(s)
- Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Belen Velazquez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and CONICET, Bernal, Argentina
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET- Universidad Nacional del Litoral) and Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
| | - Miguel Angel Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Maria Victoria Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Rosario, Argentina
- *Correspondence: Maria Victoria Busi,
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Hedin N, Barchiesi J, Gomez-Casati DF, Iglesias AA, Ballicora MA, Busi MV. Identification and characterization of a novel starch branching enzyme from the picoalgae Ostreococcus tauri. Arch Biochem Biophys 2017; 618:52-61. [DOI: 10.1016/j.abb.2017.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/16/2017] [Accepted: 02/18/2017] [Indexed: 01/26/2023]
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15
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Barchiesi J, Hedin N, Iglesias AA, Gomez-Casati DF, Ballicora MA, Busi MV. Identification of a novel starch synthase III from the picoalgae Ostreococcus tauri. Biochimie 2016; 133:37-44. [PMID: 28003125 DOI: 10.1016/j.biochi.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 12/08/2016] [Indexed: 01/07/2023]
Abstract
Hydrosoluble glycogen is the major energy storage compound in bacteria, archaea, fungi, and animal cells. In contrast, photosynthetic eukaryotes have evolved to build a highly organized semicrystalline granule of starch. Several enzymes are involved in polysaccharide synthesis, among which glycogen or starch synthase catalyze the elongation of the α-1,4-glucan chain. Ostreococcus tauri, accumulates a single starch granule and contains three starch synthase III (SSIII) isoforms, known as OsttaSSIII-A, OsttaSSIII-B and OsttaSSIII-C. After amino acids sequence analysis we found that OsttaSSIII-C lacks starch-binding domains, being 49% identical to the catalytic region of the SSIII from Arabidopsis thaliana and 32% identical to the entire Escherichia coli glycogen synthase. The recombinant, highly purified OsttaSSIII-C exhibited preference to use as a primer branched glycans (such as rabbit muscle glycogen and amylopectin), rather than amylose. Also, the enzyme displayed a high affinity toward ADP-glucose. We found a marked conservation of the amino acids located in the catalytic site, and specifically determined the role of residues R270, K275 and E352 by site-directed mutagenesis. Results show that these residues are important for OsttaSSIII-C activity, suggesting a strong similarity between the active site of the O. tauri SSIII-C isoform and other bacterial glycogen synthases.
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Affiliation(s)
- Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - Nicolás Hedin
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, 3000, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 405 Flanner Hall, 1068 W Sheridan Road, Chicago, IL 60660, USA
| | - María V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina.
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Toyosawa Y, Kawagoe Y, Matsushima R, Crofts N, Ogawa M, Fukuda M, Kumamaru T, Okazaki Y, Kusano M, Saito K, Toyooka K, Sato M, Ai Y, Jane JL, Nakamura Y, Fujita N. Deficiency of Starch Synthase IIIa and IVb Alters Starch Granule Morphology from Polyhedral to Spherical in Rice Endosperm. PLANT PHYSIOLOGY 2016; 170:1255-70. [PMID: 26747287 PMCID: PMC4775109 DOI: 10.1104/pp.15.01232] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/07/2016] [Indexed: 05/03/2023]
Abstract
Starch granule morphology differs markedly among plant species. However, the mechanisms controlling starch granule morphology have not been elucidated. Rice (Oryza sativa) endosperm produces characteristic compound-type granules containing dozens of polyhedral starch granules within an amyloplast. Some other cereal species produce simple-type granules, in which only one starch granule is present per amyloplast. A double mutant rice deficient in the starch synthase (SS) genes SSIIIa and SSIVb (ss3a ss4b) produced spherical starch granules, whereas the parental single mutants produced polyhedral starch granules similar to the wild type. The ss3a ss4b amyloplasts contained compound-type starch granules during early developmental stages, and spherical granules were separated from each other during subsequent amyloplast development and seed dehydration. Analysis of glucan chain length distribution identified overlapping roles for SSIIIa and SSIVb in amylopectin chain synthesis, with a degree of polymerization of 42 or greater. Confocal fluorescence microscopy and immunoelectron microscopy of wild-type developing rice seeds revealed that the majority of SSIVb was localized between starch granules. Therefore, we propose that SSIIIa and SSIVb have crucial roles in determining starch granule morphology and in maintaining the amyloplast envelope structure. We present a model of spherical starch granule production.
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Affiliation(s)
- Yoshiko Toyosawa
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Yasushi Kawagoe
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Ryo Matsushima
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Naoko Crofts
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Masahiro Ogawa
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Masako Fukuda
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Toshihiro Kumamaru
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Yozo Okazaki
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Miyako Kusano
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Kazuki Saito
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Kiminori Toyooka
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Mayuko Sato
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Yongfeng Ai
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Jay-Lin Jane
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Yasunori Nakamura
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
| | - Naoko Fujita
- Department of Biological Production, Akita Prefectural University, Akita City, Akita 010-0195, Japan (Y.T., N.C., Y.N., N.F.);Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan (Y.K.);Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan (R.M.);Department of General Education, Yamaguchi Prefectural University, Yamaguchi 753-8502, Japan (M.O.);Plant Genetic Resources, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (M.F., T.K.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (Y.O., M.K., K.S., K.T., M.S.);Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (K.S.); andDepartment of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011-1120 (Y.A., J.-L.J.)
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Mock T, Daines SJ, Geider R, Collins S, Metodiev M, Millar AJ, Moulton V, Lenton TM. Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. GLOBAL CHANGE BIOLOGY 2016; 22:61-75. [PMID: 25988950 PMCID: PMC4949645 DOI: 10.1111/gcb.12983] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 05/17/2023]
Abstract
The advent of genomic-, transcriptomic- and proteomic-based approaches has revolutionized our ability to describe marine microbial communities, including biogeography, metabolic potential and diversity, mechanisms of adaptation, and phylogeny and evolutionary history. New interdisciplinary approaches are needed to move from this descriptive level to improved quantitative, process-level understanding of the roles of marine microbes in biogeochemical cycles and of the impact of environmental change on the marine microbial ecosystem. Linking studies at levels from the genome to the organism, to ecological strategies and organism and ecosystem response, requires new modelling approaches. Key to this will be a fundamental shift in modelling scale that represents micro-organisms from the level of their macromolecular components. This will enable contact with omics data sets and allow acclimation and adaptive response at the phenotype level (i.e. traits) to be simulated as a combination of fitness maximization and evolutionary constraints. This way forward will build on ecological approaches that identify key organism traits and systems biology approaches that integrate traditional physiological measurements with new insights from omics. It will rely on developing an improved understanding of ecophysiology to understand quantitatively environmental controls on microbial growth strategies. It will also incorporate results from experimental evolution studies in the representation of adaptation. The resulting ecosystem-level models can then evaluate our level of understanding of controls on ecosystem structure and function, highlight major gaps in understanding and help prioritize areas for future research programs. Ultimately, this grand synthesis should improve predictive capability of the ecosystem response to multiple environmental drivers.
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Affiliation(s)
- Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Stuart J. Daines
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
| | - Richard Geider
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Sinead Collins
- Ashworth LaboratoriesEdinburgh UniversityEH9 3JFEdinburghUK
| | - Metodi Metodiev
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Andrew J. Millar
- SynthSys and School of Biological SciencesEdinburgh UniversityEH9 3BFEdinburghUK
| | - Vincent Moulton
- School of Computing SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Timothy M. Lenton
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
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Barchiesi J, Hedin N, Gomez-Casati DF, Ballicora MA, Busi MV. Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms. BMC Res Notes 2015; 8:613. [PMID: 26510916 PMCID: PMC4625611 DOI: 10.1186/s13104-015-1598-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Starch-binding domains are key modules present in several enzymes involved in polysaccharide metabolism. These non-catalytic modules have already been described as essential for starch-binding and the catalytic activity of starch synthase III from the higher plant Arabidopsis thaliana. In Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, there are three SSIII isoforms, known as Ostta SSIII-A, SSIII-B and SSIII-C. RESULTS In this work, using in silico and in vitro characterization techniques, we have demonstrated that Ostta SSIII-A, SSIII-B and SSIII-C contain two, three and no starch-binding domains, respectively. Additionally, our phylogenetic analysis has indicated that OsttaSSIII-B, presenting three N-terminal SBDs, is the isoform more closely related to higher plant SSIII. Furthermore, the sequence alignment and homology modeling data gathered showed that both the main 3-D structures of all the modeled domains obtained and the main amino acid residues implicated in starch binding are well conserved in O. tauri SSIII starch-binding domains. In addition, adsorption assays showed that OsttaSSIII-A D2 and SSIII-B D2 domains are the two that make the greatest contribution to amylose and amylopectin binding, while OsttaSSIII-B D1 is also important for starch binding. CONCLUSIONS The results presented here suggest that differences between OsttaSSIII-A and SSIII-B SBDs in the number of and binding of amino acid residues may produce differential affinities for each isoform to polysaccharides. Increasing the knowledge about SBDs may lead to their employment in biomedical and industrial applications.
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Affiliation(s)
- Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Nicolás Hedin
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 405 Flanner Hall, 1068 W Sheridan Road, Chicago, IL, 60660, USA.
| | - María V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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Affiliation(s)
- María V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
- IIB - Universidad Nacional de General San Martín (UNSAM); San Martín Buenos Aires Argentina
| | - Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
- IIB - Universidad Nacional de General San Martín (UNSAM); San Martín Buenos Aires Argentina
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Suzuki E, Suzuki R. Variation of Storage Polysaccharides in Phototrophic Microorganisms. J Appl Glycosci (1999) 2013. [DOI: 10.5458/jag.jag.jag-2012_016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Brust H, Orzechowski S, Fettke J, Steup M. Starch Synthesizing Reactions and Paths: in vitro and in vivo Studies. J Appl Glycosci (1999) 2013. [DOI: 10.5458/jag.jag.jag-2012_018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Abstract
Starch is the major non-structural carbohydrate in plants. It serves as an important store of carbon that fuels plant metabolism and growth when they are unable to photosynthesise. This storage can be in leaves and other green tissues, where it is degraded during the night, or in heterotrophic tissues such as roots, seeds and tubers, where it is stored over longer time periods. Arabidopsis accumulates starch in many of its tissues, but mostly in its leaves during the day. It has proven to be a powerful genetic system for discovering how starch is synthesised and degraded, and new proteins and processes have been discovered. Such work has major significance for our starch crops, whose yield and quality could be improved by the application of this knowledge. Research into Arabidopsis starch metabolism has begun to reveal how its daily turnover is integrated into the rest of metabolism and adapted to the environmental conditions. Furthermore, Arabidopsis mutant lines deficient in starch metabolism have been employed as tools to study other biological processes ranging from sugar sensing to gravitropism and flowering time control. This review gives a detailed account of the use of Arabidopsis to study starch metabolism. It describes the major discoveries made and presents an overview of our understanding today, together with some as-yet unresolved questions.
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Affiliation(s)
- Sebastian Streb
- Institute of Agricultural Sciences, Department of Biology, ETH
Zurich, Universitätstrasse 2, Zurich, Switzerland
| | - Samuel C. Zeeman
- Institute of Agricultural Sciences, Department of Biology, ETH
Zurich, Universitätstrasse 2, Zurich, Switzerland
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Streb S, Zeeman SC. Starch metabolism in Arabidopsis. THE ARABIDOPSIS BOOK 2012; 10:e0160. [PMID: 23393426 DOI: 10.199/tab.e0160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Starch is the major non-structural carbohydrate in plants. It serves as an important store of carbon that fuels plant metabolism and growth when they are unable to photosynthesise. This storage can be in leaves and other green tissues, where it is degraded during the night, or in heterotrophic tissues such as roots, seeds and tubers, where it is stored over longer time periods. Arabidopsis accumulates starch in many of its tissues, but mostly in its leaves during the day. It has proven to be a powerful genetic system for discovering how starch is synthesised and degraded, and new proteins and processes have been discovered. Such work has major significance for our starch crops, whose yield and quality could be improved by the application of this knowledge. Research into Arabidopsis starch metabolism has begun to reveal how its daily turnover is integrated into the rest of metabolism and adapted to the environmental conditions. Furthermore, Arabidopsis mutant lines deficient in starch metabolism have been employed as tools to study other biological processes ranging from sugar sensing to gravitropism and flowering time control. This review gives a detailed account of the use of Arabidopsis to study starch metabolism. It describes the major discoveries made and presents an overview of our understanding today, together with some as-yet unresolved questions.
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Affiliation(s)
- Sebastian Streb
- Institute of Agricultural Sciences, Department of Biology, ETH Zurich, Universitätstrasse 2, Zurich, Switzerland
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Lin Q, Huang B, Zhang M, Zhang X, Rivenbark J, Lappe RL, James MG, Myers AM, Hennen-Bierwagen TA. Functional interactions between starch synthase III and isoamylase-type starch-debranching enzyme in maize endosperm. PLANT PHYSIOLOGY 2012; 158:679-92. [PMID: 22193705 PMCID: PMC3271759 DOI: 10.1104/pp.111.189704] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 12/20/2011] [Indexed: 05/09/2023]
Abstract
This study characterized genetic interactions between the maize (Zea mays) genes dull1 (du1), encoding starch synthase III (SSIII), and isa2, encoding a noncatalytic subunit of heteromeric isoamylase-type starch-debranching enzyme (ISA1/ISA2 heteromer). Mutants lacking ISA2 still possess the ISA1 homomeric enzyme. Eight du1(-) mutations were characterized, and structural changes in amylopectin resulting from each were measured. In every instance, the same complex pattern of alterations in discontinuous spans of chain lengths was observed, which cannot be explained solely by a discrete range of substrates preferred by SSIII. Homozygous double mutants were constructed containing the null mutation isa2-339 and either du1-Ref, encoding a truncated SSIII protein lacking the catalytic domain, or the null allele du1-R4059. In contrast to the single mutant parents, double mutant endosperms affected in both SSIII and ISA2 were starch deficient and accumulated phytoglycogen. This phenotype was previously observed only in maize sugary1 mutants impaired for the catalytic subunit ISA1. ISA1 homomeric enzyme complexes assembled in both double mutants and were enzymatically active in vitro. Thus, SSIII is required for normal starch crystallization and the prevention of phytoglycogen accumulation when the only isoamylase-type debranching activity present is ISA1 homomer, but not in the wild-type condition, when both ISA1 homomer and ISA1/ISA2 heteromer are present. Previous genetic and biochemical analyses showed that SSIII also is required for normal glucan accumulation when the only isoamylase-type debranching enzyme activity present is ISA1/ISA heteromer. These data indicate that isoamylase-type debranching enzyme and SSIII work in a coordinated fashion to repress phytoglycogen accumulation.
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Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri. J Proteomics 2011; 74:2060-70. [DOI: 10.1016/j.jprot.2011.05.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/03/2011] [Accepted: 05/17/2011] [Indexed: 01/02/2023]
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Yun MS, Umemoto T, Kawagoe Y. Rice debranching enzyme isoamylase3 facilitates starch metabolism and affects plastid morphogenesis. PLANT & CELL PHYSIOLOGY 2011; 52:1068-82. [PMID: 21551159 PMCID: PMC3110883 DOI: 10.1093/pcp/pcr058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 04/25/2011] [Indexed: 05/04/2023]
Abstract
Debranching enzymes, which hydrolyze α-1 and 6-glucosidic linkages in α-polyglucans, play a dual role in the synthesis and degradation of starch in plants. A transposon-inserted rice mutant of isoamylase3 (isa3) contained an increased amount of starch in the leaf blade at the end of the night, indicating that ISA3 plays a role in the degradation of transitory starch during the night. An epitope-tagged ISA3 expressed in Escherichia coli exhibited hydrolytic activity on β-limit dextrin and amylopectin. We investigated whether ISA3 plays a role in amyloplast development and starch metabolism in the developing endosperm. ISA3-green fluorescent protein (GFP) fusion protein expressed under the control of the rice ISA3 promoter was targeted to the amyloplast stroma in the endosperm. Overexpression of ISA3 in the sugary1 mutant, which is deficient in ISA1 activity, did not convert water-soluble phytoglycogen to starch granules, indicating that ISA1 and ISA3 are not functionally redundant. Both overexpression and loss of function of ISA3 in the endosperm generated pleomorphic amyloplasts and starch granules. Furthermore, chloroplasts in the leaf blade of isa3 seedlings were large and pleomorphic. These results suggest that ISA3 facilitates starch metabolism and affects morphological characteristics of plastids in rice.
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Affiliation(s)
- Min-Soo Yun
- Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Japan
- Present address: Food Resource Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, 305-8642 Japan
| | - Takayuki Umemoto
- Rice Quality Research Team, National Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, 305-8518, Japan
- Present address: National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira, Sapporo, 062-8555 Japan
| | - Yasushi Kawagoe
- Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Japan
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Genome diversity in the smallest marine photosynthetic eukaryotes. Res Microbiol 2011; 162:570-7. [PMID: 21540104 DOI: 10.1016/j.resmic.2011.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 03/02/2011] [Indexed: 02/04/2023]
Abstract
Unicellular algae of the class Mamiellophyceae are widespread in our oceans and their apparent uniformity conceals an impressive array of biologically distinct species. Each of the five complete genomes analysed so far reveals densely packed coding sequences, with strong evolutionary divergence from its nearest phylogenetically defined neighbours. These species lie at the base of the green lineage, but various metabolic processes reflect their marine life-styles and distinguish them from land plants, including a high proportion of selenoprotein enzymes and C4 photosynthesis. They all possess two unusual chromosomes, with lower GC content and atypical gene content, whose function so far remains enigmatic.
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Ball S, Colleoni C, Cenci U, Raj JN, Tirtiaux C. The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1775-801. [PMID: 21220783 DOI: 10.1093/jxb/erq411] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Solid semi-crystalline starch and hydrosoluble glycogen define two distinct physical states of the same type of storage polysaccharide. Appearance of semi-crystalline storage polysaccharides appears linked to the requirement of unicellular diazotrophic cyanobacteria to fuel nitrogenase and protect it from oxygen through respiration of vast amounts of stored carbon. Starch metabolism itself resulted from the merging of the bacterial and eukaryote pathways of storage polysaccharide metabolism after endosymbiosis of the plastid. This generated the three Archaeplastida lineages: the green algae and land plants (Chloroplastida), the red algae (Rhodophyceae), and the glaucophytes (Glaucophyta). Reconstruction of starch metabolism in the common ancestor of Archaeplastida suggests that polysaccharide synthesis was ancestrally cytosolic. In addition, the synthesis of cytosolic starch from the ADP-glucose exported from the cyanobacterial symbiont possibly defined the original metabolic flux by which the cyanobiont provided photosynthate to its host. Additional evidence supporting this scenario include the monophyletic origin of the major carbon translocators of the inner membrane of eukaryote plastids which are sisters to nucleotide-sugar transporters of the eukaryote endomembrane system. It also includes the extent of enzyme subfunctionalization that came as a consequence of the rewiring of this pathway to the chloroplasts in the green algae. Recent evidence suggests that, at the time of endosymbiosis, obligate intracellular energy parasites related to extant Chlamydia have donated important genes to the ancestral starch metabolism network.
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Affiliation(s)
- Steven Ball
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Bâtiment C9, Cité Scientifique, F-59655 Villeneuve d'Ascq, France.
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Sorokina O, Corellou F, Dauvillée D, Sorokin A, Goryanin I, Ball S, Bouget FY, Millar AJ. Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. BMC SYSTEMS BIOLOGY 2011; 5:36. [PMID: 21352558 PMCID: PMC3056741 DOI: 10.1186/1752-0509-5-36] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Accepted: 02/26/2011] [Indexed: 11/10/2022]
Abstract
Background The storage of photosynthetic carbohydrate products such as starch is subject to complex regulation, effected at both transcriptional and post-translational levels. The relevant genes in plants show pronounced daily regulation. Their temporal RNA expression profiles, however, do not predict the dynamics of metabolite levels, due to the divergence of enzyme activity from the RNA profiles. Unicellular phytoplankton retains the complexity of plant carbohydrate metabolism, and recent transcriptomic profiling suggests a major input of transcriptional regulation. Results We used a quasi-steady-state, constraint-based modelling approach to infer the dynamics of starch content during the 12 h light/12 h dark cycle in the model alga Ostreococcus tauri. Measured RNA expression datasets from microarray analysis were integrated with a detailed stoichiometric reconstruction of starch metabolism in O. tauri in order to predict the optimal flux distribution and the dynamics of the starch content in the light/dark cycle. The predicted starch profile was validated by experimental data over the 24 h cycle. The main genetic regulatory targets within the pathway were predicted by in silico analysis. Conclusions A single-reaction description of starch production is not able to account for the observed variability of diurnal activity profiles of starch-related enzymes. We developed a detailed reaction model of starch metabolism, which, to our knowledge, is the first attempt to describe this polysaccharide polymerization while preserving the mass balance relationships. Our model and method demonstrate the utility of a quasi-steady-state approach for inferring dynamic metabolic information in O. tauri directly from time-series gene expression data.
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Affiliation(s)
- Oksana Sorokina
- School of Biological Sciences, The University of Edinburgh King's Buildings, Mayfield Road, Edinburgh EH9 3JH, UK.
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Battaglia E, Benoit I, van den Brink J, Wiebenga A, Coutinho PM, Henrissat B, de Vries RP. Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. BMC Genomics 2011; 12:38. [PMID: 21241472 PMCID: PMC3032700 DOI: 10.1186/1471-2164-12-38] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 01/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses. RESULTS Carbohydrate Active enzyme (CAZy) annotation of the R. oryzae identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs) and a high number of glycosyl transferases (GTs) and carbohydrate esterases (CEs). A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars), chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of R. oryzae to its environment. CONCLUSIONS CAZy analyses of the genome of the zygomycete fungus R. oryzae and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota.
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Affiliation(s)
- Evy Battaglia
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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D'Hulst C, Mérida A. The priming of storage glucan synthesis from bacteria to plants: current knowledge and new developments. THE NEW PHYTOLOGIST 2010; 188:13-21. [PMID: 20618917 DOI: 10.1111/j.1469-8137.2010.03361.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Starch is the main polymer in which carbon and energy are stored in land plants, algae and some cyanobacteria. It plays a crucial role in the physiology of these organisms and also represents an important polymer for humans, in terms of both diet and nonfood industry uses. Recent efforts have elucidated most of the steps involved in the synthesis of starch. However, the process that initiates the synthesis of the starch granule remains unclear. Here, we outline the similarities between the synthesis of starch and the synthesis of glycogen, the other widespread and abundant glucose-based polymer in living cells. We place special emphasis on the mechanisms of initiation of the glycogen granule and current knowledge concerning the initiation of the starch granule. We also discuss recent discoveries regarding the function of starch synthases in the priming of the starch granule and possible interactions with other elements of the starch synthesis machinery.
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Affiliation(s)
- Christophe D'Hulst
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS/USTL, IFR 147, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
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Zeeman SC, Kossmann J, Smith AM. Starch: its metabolism, evolution, and biotechnological modification in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:209-34. [PMID: 20192737 DOI: 10.1146/annurev-arplant-042809-112301] [Citation(s) in RCA: 576] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bioethanol production. Here, we review recent advances in research in three key areas. First, we assess progress in identifying the enzymatic machinery required for the synthesis of amylopectin, the glucose polymer responsible for the insoluble nature of starch. Second, we discuss the pathways of starch degradation, focusing on the emerging role of transient glucan phosphorylation in plastids as a mechanism for solubilizing the surface of the starch granule. We contrast this pathway in leaves with the degradation of starch in the endosperm of germinated cereal seeds. Third, we consider the evolution of starch biosynthesis in plants from the ancestral ability to make glycogen. Finally, we discuss how this basic knowledge has been utilized to improve and diversify starch crops.
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Kuhn ML, Falaschetti CA, Ballicora MA. Ostreococcus tauri ADP-glucose pyrophosphorylase reveals alternative paths for the evolution of subunit roles. J Biol Chem 2009; 284:34092-102. [PMID: 19737928 DOI: 10.1074/jbc.m109.037614] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ADP-glucose pyrophosphorylase controls starch synthesis in plants and is an interesting case to study the evolution and differentiation of roles in heteromeric enzymes. It includes two homologous subunits, small (S) and large (L), that originated from a common photosynthetic eukaryotic ancestor. In present day organisms, these subunits became complementary after loss of certain roles in a process described as subfunctionalization. For instance, the potato tuber enzyme has a noncatalytic L subunit that complements an S subunit with suboptimal allosteric properties. To understand the evolution of catalysis and regulation in this family, we artificially synthesized both subunit genes from the unicellular alga Ostreococcus tauri. This is among the most ancient species in the green lineage that diverged from the ancestor of all green plants and algae. After heterologous gene expression, we purified and characterized the proteins. The O. tauri enzyme was not redox-regulated, suggesting that redox regulation of ADP-glucose pyrophosphorylases appeared later in evolution. The S subunit had a typical low apparent affinity for the activator 3-phosphoglycerate, but it was atypically defective in the catalytic efficiency (V(max)/K(m)) for the substrate Glc-1-P. The L subunit needed the S subunit for soluble expression. In the presence of a mutated S subunit (to avoid interference), the L subunit had a high apparent affinity for 3-phosphoglycerate and substrates suggesting a leading role in catalysis. Therefore, the subfunctionalization of the O. tauri enzyme was different from previously described cases. To the best of our knowledge, this is the first biochemical description of a system with alternative subfunctionalization paths.
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Affiliation(s)
- Misty L Kuhn
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, USA
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Serrato AJ, Yubero-Serrano EM, Sandalio LM, Muñoz-Blanco J, Chueca A, Caballero JL, Sahrawy M. cpFBPaseII, a novel redox-independent chloroplastic isoform of fructose-1,6-bisphosphatase. PLANT, CELL & ENVIRONMENT 2009; 32:811-27. [PMID: 19220782 DOI: 10.1111/j.1365-3040.2009.01960.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A full-length FBPase cDNA has been isolated from Fragaria x ananassa (strawberry) corresponding to a novel putative chloroplastic FBPase but lacking the regulatory redox domain, a characteristic of the plastidial isoenzyme (cpFBPaseI). Another outstanding feature of this novel isoform, called cpFBPaseII, is the absence of the canonical active site. Enzymatic assays with cpFBPaseII evidenced clear Mg(2+)-dependent FBPase activity and a K(m) for fructose-1,6-bisphosphate (FBP) of 1.3 mM. Immunolocalization experiments and chloroplast isolation confirmed that the new isoenzyme is located in the stroma. Nevertheless, unlike cpFBPaseI, which is redox activated, cpFBPaseII did not increase its activity in the presence of either DTT or thioredoxin f (TRX f) and is resistant to H(2)O(2) inactivation. Additionally, the novel isoform was able to complement the growth deficiency of the yeast FBP1 deletion fed with a non-fermentable carbon source. Furthermore, orthologues are restricted to land plants, suggesting that cpFBPaseII is a novel and an intriguing chloroplastic FBPase that emerged late in the evolution of photosynthetic organisms, possibly because of a pressing need of land plants.
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Reininga JM, Nielsen D, Purugganan MD. Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana. Mol Ecol 2009; 18:2844-55. [PMID: 19457201 DOI: 10.1111/j.1365-294x.2009.04206.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Molecular population genetic analysis of three chromosomal regions in Arabidopsis thaliana suggested that balancing selection might operate to maintain variation at three novel candidate adaptive trait genes, including SOLUBLE STARCH SYNTHASE I (SSI), PLASTID TRANSCRIPTIONALLY ACTIVE 7(PTAC7), and BELL-LIKE HOMEODOMAIN 10 (BLH10). If balanced polymorphisms are indeed maintained at these loci, then we would expect to observe functional variation underlying the previously detected signatures of selection. We observe multiple replacement polymorphisms within and in the 32 amino acids just upstream of the protein-protein interacting BELL domain at the BLH10 locus. While no clear protein sequence differences are found between allele types in SSI and PTAC7, these two genes show evidence for allele-specific variation in expression levels. Geographical patterns of allelic differentiation seem consistent with population stratification in this species and a significant longitudinal cline was observed at all three candidate loci. These data support a hypothesis of balancing selection at all three candidate loci and provide a basis for more detailed functional work by identifying possible functional differences that might be selectively maintained.
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Affiliation(s)
- Jennifer M Reininga
- Department of Genetics, Box 7614, North Carolina State University, Raleigh, NC 27695, USA
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Leterrier M, Holappa LD, Broglie KE, Beckles DM. Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications. BMC PLANT BIOLOGY 2008; 8:98. [PMID: 18826586 PMCID: PMC2576272 DOI: 10.1186/1471-2229-8-98] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 09/30/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Starch is of great importance to humans as a food and biomaterial, and the amount and structure of starch made in plants is determined in part by starch synthase (SS) activity. Five SS isoforms, SSI, II, III, IV and Granule Bound SSI, have been identified, each with a unique catalytic role in starch synthesis. The basic mode of action of SSs is known; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete. To gain a better understanding of the differences in SS sequences that underscore their specificity, the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done. RESULTS The wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement. The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock. Phylogenetic analysis showed that in plants, SSIV is closely related to SSIII, while SSI, SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation. Further, identified differences at the amino acid level in their glycosyltransferase domains, predicted secondary structures, global conformations and conserved residues might be indicative of intragroup functional associations. CONCLUSION Based on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases (GSs), it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI, SSI and SSII. In GBSSI, the Ile485 residue may partially explain that enzyme's unique catalytic features. The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly.
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MESH Headings
- Amino Acid Sequence
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Cloning, Molecular
- DNA, Complementary/genetics
- Evolution, Molecular
- Expressed Sequence Tags
- Gene Expression
- Gene Library
- Genes, Plant
- Genome, Plant
- Molecular Sequence Data
- Phylogeny
- Plant Leaves/enzymology
- Plant Leaves/genetics
- Plant Proteins/genetics
- Protein Structure, Secondary
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Starch Synthase/genetics
- Triticum/enzymology
- Triticum/genetics
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Affiliation(s)
- Marina Leterrier
- Department of Plant Sciences, One Peter Shield Avenue, University of California, Davis, CA 95616-8617, USA
| | - Lynn D Holappa
- Department of Plant Sciences, One Peter Shield Avenue, University of California, Davis, CA 95616-8617, USA
- Department of Organismic & Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge MA 02138, USA
| | - Karen E Broglie
- DuPont-Pioneer, Crop Genetics Research, Experimental Station, Wilmington, DE 19808, USA
| | - Diane M Beckles
- Department of Plant Sciences, One Peter Shield Avenue, University of California, Davis, CA 95616-8617, USA
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Zhang X, Szydlowski N, Delvallé D, D'Hulst C, James MG, Myers AM. Overlapping functions of the starch synthases SSII and SSIII in amylopectin biosynthesis in Arabidopsis. BMC PLANT BIOLOGY 2008; 8:96. [PMID: 18811962 PMCID: PMC2566982 DOI: 10.1186/1471-2229-8-96] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 09/23/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND The biochemical mechanisms that determine the molecular architecture of amylopectin are central in plant biology because they allow long-term storage of reduced carbon. Amylopectin structure imparts the ability to form semi-crystalline starch granules, which in turn provides its glucose storage function. The enzymatic steps of amylopectin biosynthesis resemble those of the soluble polymer glycogen, however, the reasons for amylopectin's architectural distinctions are not clearly understood. The multiplicity of starch biosynthetic enzymes conserved in plants likely is involved. For example, amylopectin chain elongation in plants involves five conserved classes of starch synthase (SS), whereas glycogen biosynthesis typically requires only one class of glycogen synthase. RESULTS Null mutations were characterized in AtSS2, which codes for SSII, and mutant lines were compared to lines lacking SSIII and to an Atss2, Atss3 double mutant. Loss of SSII did not affect growth rate or starch quantity, but caused increased amylose/amylopectin ratio, increased total amylose, and deficiency in amylopectin chains with degree of polymerization (DP) 12 to DP28. In contrast, loss of both SSII and SSIII caused slower plant growth and dramatically reduced starch content. Extreme deficiency in DP12 to DP28 chains occurred in the double mutant, far more severe than the summed changes in SSII- or SSIII-deficient plants lacking only one of the two enzymes. CONCLUSION SSII and SSIII have partially redundant functions in determination of amylopectin structure, and these roles cannot be substituted by any other conserved SS, specifically SSI, GBSSI, or SSIV. Even though SSIII is not required for the normal abundance of glucan chains of DP12 to DP18, the enzyme clearly is capable of functioning in production such chains. The role of SSIII in producing these chains cannot be detected simply by analysis of an individual mutation. Competition between different SSs for binding to substrate could in part explain the specific distribution of glucan chains within amylopectin.
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Affiliation(s)
- Xiaoli Zhang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
- The Ohio State University, Center for Biostatistics, M200 Starling Loving Hall, 320 W. 10th Avenue, Columbus, OH 43210, USA
| | - Nicolas Szydlowski
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, IFR 147, Bâtiment C9, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
| | - David Delvallé
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, IFR 147, Bâtiment C9, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
| | - Christophe D'Hulst
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 du CNRS, IFR 147, Bâtiment C9, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
| | - Martha G James
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Alan M Myers
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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Vaulot D, Eikrem W, Viprey M, Moreau H. The diversity of small eukaryotic phytoplankton (≤3 μm) in marine ecosystems. FEMS Microbiol Rev 2008; 32:795-820. [DOI: 10.1111/j.1574-6976.2008.00121.x] [Citation(s) in RCA: 304] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Hennen-Bierwagen TA, Liu F, Marsh RS, Kim S, Gan Q, Tetlow IJ, Emes MJ, James MG, Myers AM. Starch biosynthetic enzymes from developing maize endosperm associate in multisubunit complexes. PLANT PHYSIOLOGY 2008; 146:1892-908. [PMID: 18281416 PMCID: PMC2287357 DOI: 10.1104/pp.108.116285] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2008] [Accepted: 02/11/2008] [Indexed: 05/18/2023]
Abstract
Mutations affecting specific starch biosynthetic enzymes commonly have pleiotropic effects on other enzymes in the same metabolic pathway. Such genetic evidence indicates functional relationships between components of the starch biosynthetic system, including starch synthases (SSs), starch branching enzymes (BEs), and starch debranching enzymes; however, the molecular explanation for these functional interactions is not known. One possibility is that specific SSs, BEs, and/or starch debranching enzymes associate physically with each other in multisubunit complexes. To test this hypothesis, this study sought to identify stable associations between three separate SS polypeptides (SSI, SSIIa, and SSIII) and three separate BE polypeptides (BEI, BEIIa, and BEIIb) from maize (Zea mays) amyloplasts. Detection methods included in vivo protein-protein interaction tests in yeast (Saccharomyces cerevisiae) nuclei, immunoprecipitation, and affinity purification using recombinant proteins as the solid phase ligand. Eight different instances were detected of specific pairs of proteins associating either directly or indirectly in the same multisubunit complex, and direct, pairwise interactions were indicated by the in vivo test in yeast. In addition, SSIIa, SSIII, BEIIa, and BEIIb all comigrated in gel permeation chromatography in a high molecular mass form of approximately 600 kD, and SSIIa, BEIIa, and BEIIb also migrated in a second high molecular form, lacking SSIII, of approximately 300 kD. Monomer forms of all four proteins were also detected by gel permeation chromatography. The 600- and 300-kD complexes were stable at high salt concentration, suggesting that hydrophobic effects are involved in the association between subunits.
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Affiliation(s)
- Tracie A Hennen-Bierwagen
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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41
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Dennis ES, Ellis J, Green A, Llewellyn D, Morell M, Tabe L, Peacock W. Genetic contributions to agricultural sustainability. Philos Trans R Soc Lond B Biol Sci 2008; 363:591-609. [PMID: 17656342 PMCID: PMC2610172 DOI: 10.1098/rstb.2007.2172] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The current tools of enquiry into the structure and operation of the plant genome have provided us with an understanding of plant development and function far beyond the state of knowledge that we had previously. We know about key genetic controls repressing or stimulating the cascades of gene expression that move a plant through stages in its life cycle, facilitating the morphogenesis of vegetative and reproductive tissues and organs. The new technologies are enabling the identification of key gene activity responses to the range of biotic and abiotic challenges experienced by plants. In the past, plant breeders produced new varieties with changes in the phases of development, modifications of plant architecture and improved levels of tolerance and resistance to environmental and biotic challenges by identifying the required phenotypes in a few plants among the large numbers of plants in a breeding population. Now our increased knowledge and powerful gene sequence-based diagnostics provide plant breeders with more precise selection objectives and assays to operate in rationally planned crop improvement programmes. We can expect yield potential to increase and harvested product quality portfolios to better fit an increasing diversity of market requirements. The new genetics will connect agriculture to sectors beyond the food, feed and fibre industries; agri-business will contribute to public health and will provide high-value products to the pharmaceutical industry as well as to industries previously based on petroleum feedstocks and chemical modification processes.
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Affiliation(s)
| | | | | | | | | | | | - W.J Peacock
- CSIRO Plant IndustryGPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
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42
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Early gene duplication within chloroplastida and its correspondence with relocation of starch metabolism to chloroplasts. Genetics 2008; 178:2373-87. [PMID: 18245855 DOI: 10.1534/genetics.108.087205] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The endosymbiosis event resulting in the plastid of photosynthetic eukaryotes was accompanied by the appearance of a novel form of storage polysaccharide in Rhodophyceae, Glaucophyta, and Chloroplastida. Previous analyses indicated that starch synthesis resulted from the merging of the cyanobacterial and the eukaryotic storage polysaccharide metabolism pathways. We performed a comparative bioinformatic analysis of six algal genome sequences to investigate this merger. Specifically, we analyzed two Chlorophyceae, Chlamydomonas reinhardtii and Volvox carterii, and four Prasinophytae, two Ostreococcus strains and two Micromonas pusilla strains. Our analyses revealed a complex metabolic pathway whose intricacies and function seem conserved throughout the green lineage. Comparison of this pathway to that recently proposed for the Rhodophyceae suggests that the complexity that we observed is unique to the green lineage and was generated when the latter diverged from the red algae. This finding corresponds well with the plastidial location of starch metabolism in Chloroplastidae. In contrast, Rhodophyceae and Glaucophyta produce and store starch in the cytoplasm and have a lower complexity pathway. Cytoplasmic starch synthesis is currently hypothesized to represent the ancestral state of storage polysaccharide metabolism in Archaeplastida. The retargeting of components of the cytoplasmic pathway to plastids likely required a complex stepwise process involving several rounds of gene duplications. We propose that this relocation of glucan synthesis to the plastid facilitated evolution of chlorophyll-containing light-harvesting complex antennae by playing a protective role within the chloroplast.
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Shimonaga T, Konishi M, Oyama Y, Fujiwara S, Satoh A, Fujita N, Colleoni C, Buléon A, Putaux JL, Ball SG, Yokoyama A, Hara Y, Nakamura Y, Tsuzuki M. Variation in Storage α-Glucans of the Porphyridiales (Rhodophyta). ACTA ACUST UNITED AC 2008; 49:103-16. [DOI: 10.1093/pcp/pcm172] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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44
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Pathway of cytosolic starch synthesis in the model glaucophyte Cyanophora paradoxa. EUKARYOTIC CELL 2007; 7:247-57. [PMID: 18055913 DOI: 10.1128/ec.00373-07] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The nature of the cytoplasmic pathway of starch biosynthesis was investigated in the model glaucophyte Cyanophora paradoxa. The storage polysaccharide granules are shown to be composed of both amylose and amylopectin fractions, with a chain length distribution and crystalline organization similar to those of green algae and land plant starch. A preliminary characterization of the starch pathway demonstrates that Cyanophora paradoxa contains several UDP-glucose-utilizing soluble starch synthase activities related to those of the Rhodophyceae. In addition, Cyanophora paradoxa synthesizes amylose with a granule-bound starch synthase displaying a preference for UDP-glucose. A debranching enzyme of isoamylase specificity and multiple starch phosphorylases also are evidenced in the model glaucophyte. The picture emerging from our biochemical and molecular characterizations consists of the presence of a UDP-glucose-based pathway similar to that recently proposed for the red algae, the cryptophytes, and the alveolates. The correlative presence of isoamylase and starch among photosynthetic eukaryotes is discussed.
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45
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Henderson GP, Gan L, Jensen GJ. 3-D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell. PLoS One 2007; 2:e749. [PMID: 17710148 PMCID: PMC1939878 DOI: 10.1371/journal.pone.0000749] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 07/16/2007] [Indexed: 01/11/2023] Open
Abstract
The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes.
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Affiliation(s)
- Gregory P. Henderson
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Lu Gan
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Grant J. Jensen
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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46
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Georgelis N, Braun EL, Shaw JR, Hannah LC. The two AGPase subunits evolve at different rates in angiosperms, yet they are equally sensitive to activity-altering amino acid changes when expressed in bacteria. THE PLANT CELL 2007; 19:1458-72. [PMID: 17496118 PMCID: PMC1913735 DOI: 10.1105/tpc.106.049676] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The rate of protein evolution is generally thought to reflect, at least in part, the proportion of amino acids within the protein that are needed for proper function. In the case of ADP-glucose pyrophosphorylase (AGPase), this premise led to the hypothesis that, because the AGPase small subunit is more conserved compared with the large subunit, a higher proportion of the amino acids of the small subunit are required for enzyme activity compared with the large subunit. Evolutionary analysis indicates that the AGPase small subunit has been subject to more intense purifying selection than the large subunit in the angiosperms. However, random mutagenesis and expression of the maize (Zea mays) endosperm AGPase in bacteria show that the two AGPase subunits are equally predisposed to enzyme activity-altering amino acid changes when expressed in one environment with a single complementary subunit. As an alternative hypothesis, we suggest that the small subunit exhibits more evolutionary constraints in planta than does the large subunit because it is less tissue specific and thus must form functional enzyme complexes with different large subunits. Independent approaches provide data consistent with this alternative hypothesis.
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Affiliation(s)
- Nikolaos Georgelis
- Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32610-0245, USA
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47
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Roldán I, Wattebled F, Mercedes Lucas M, Delvallé D, Planchot V, Jiménez S, Pérez R, Ball S, D'Hulst C, Mérida A. The phenotype of soluble starch synthase IV defective mutants of Arabidopsis thaliana suggests a novel function of elongation enzymes in the control of starch granule formation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:492-504. [PMID: 17217470 DOI: 10.1111/j.1365-313x.2006.02968.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
All plants and green algae synthesize starch through the action of the same five classes of elongation enzymes: the starch synthases. Arabidopsis mutants defective for the synthesis of the soluble starch synthase IV (SSIV) type of elongation enzyme have now been characterized. The mutant plants displayed a severe growth defect but nonetheless accumulated near to normal levels of polysaccharide storage. Detailed structural analysis has failed to yield any change in starch granule structure. However, the number of granules per plastid has dramatically decreased leading to a large increase in their size. These results, which distinguish the SSIV mutants from all other mutants reported to date, suggest a specific function of this enzyme class in the control of granule numbers. We speculate therefore that SSIV could be selectively involved in the priming of starch granule formation.
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Affiliation(s)
- Isaac Roldán
- Instituto de Bioquímica Vegetal y Fotosíntesis. CSIC-US. Avda Américo Vespucio 49. Isla de la Cartuja, 41092-Sevilla, Spain
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48
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Ral JP, Colleoni C, Wattebled F, Dauvillée D, Nempont C, Deschamps P, Li Z, Morell MK, Chibbar R, Purton S, d'Hulst C, Ball SG. Circadian clock regulation of starch metabolism establishes GBSSI as a major contributor to amylopectin synthesis in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2006; 142:305-17. [PMID: 16844835 PMCID: PMC1557617 DOI: 10.1104/pp.106.081885] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 07/03/2006] [Indexed: 05/10/2023]
Abstract
Chlamydomonas reinhardtii displays a diurnal rhythm of starch content that peaks in the middle of the night phase if the algae are provided with acetate and CO(2) as a carbon source. We show that this rhythm is controlled by the circadian clock and is tightly correlated to ADP-glucose pyrophosphorylase activity. Persistence of this rhythm depends on the presence of either soluble starch synthase III or granule-bound starch synthase I (GBSSI). We show that both enzymes play a similar function in synthesizing the long glucan fraction that interconnects the amylopectin clusters. We demonstrate that in log phase-oscillating cultures, GBSSI is required to obtain maximal polysaccharide content and fully compensates for the loss of soluble starch synthase III. A point mutation in the GBSSI gene that prevents extension of amylopectin chains, but retains the enzyme's normal ability to extend maltooligosaccharides, abolishes the function of GBSSI both in amylopectin and amylose synthesis and leads to a decrease in starch content in oscillating cultures. We propose that GBSSI has evolved as a major enzyme of amylopectin synthesis and that amylose synthesis comes as a secondary consequence of prolonged synthesis by GBSSI in arrhythmic systems. Maintenance in higher plant leaves of circadian clock control of GBSSI transcription is discussed.
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Affiliation(s)
- Jean-Philippe Ral
- Unité de Glycobiologie Structurale et Fonctionnelle, Unité Mixte de Recherche 8576, Centre National de la Recherche Scientifique, Université des Sciences et Technologies de Lille, Institut Fédératif de Recherche, 59655 Villeneuve d'Ascq cedex, France
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49
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Derelle E, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piégu B, Ball SG, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y, Moreau H. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A 2006; 103:11647-52. [PMID: 16868079 PMCID: PMC1544224 DOI: 10.1073/pnas.0604795103] [Citation(s) in RCA: 539] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Indexed: 02/06/2023] Open
Abstract
The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C(4) photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.
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Affiliation(s)
- Evelyne Derelle
- Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Université Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France
| | - Conchita Ferraz
- Institut de Génétique Humaine, Unité Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France
| | - Stephane Rombauts
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and
| | - Pierre Rouzé
- Laboratoire Associé de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Alexandra Z. Worden
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149
| | - Steven Robbens
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and
| | - Frédéric Partensky
- Station Biologique, Unité Mixte de Recherche 7144, Centre National de la Recherche Scientifique–Université Pierre et Marie Curie-Paris 6, BP74, 29682 Roscoff Cedex, France
| | - Sven Degroeve
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and
- Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sophie Echeynié
- Institut de Génétique Humaine, Unité Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France
| | - Richard Cooke
- Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique–Université de Perpignan, 52, Avenue de Villeneuve, 66860 Perpignan, France
| | - Yvan Saeys
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and
| | - Jan Wuyts
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and
| | - Kamel Jabbari
- Département de Biologie, Formation de Recherche en Evolution 2910, Centre National de la Recherche Scientifique–Ecole Normale Supérieure, 46 Rue d’Ulm, 75230 Paris Cedex 05, France; and
| | - Chris Bowler
- Laboratoire de Chimie Biologique, Unité Mixte de Recherche 8765, Centre National de la Recherche Scientifique–Université Sciences et Technologies de Lille, 59655 Villeneuve d’Ascq, France
| | - Olivier Panaud
- Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique–Université de Perpignan, 52, Avenue de Villeneuve, 66860 Perpignan, France
| | - Benoît Piégu
- Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique–Université de Perpignan, 52, Avenue de Villeneuve, 66860 Perpignan, France
| | - Steven G. Ball
- Laboratoire de Chimie Biologique, Unité Mixte de Recherche 8765, Centre National de la Recherche Scientifique–Université Sciences et Technologies de Lille, 59655 Villeneuve d’Ascq, France
| | - Jean-Philippe Ral
- Laboratoire de Chimie Biologique, Unité Mixte de Recherche 8765, Centre National de la Recherche Scientifique–Université Sciences et Technologies de Lille, 59655 Villeneuve d’Ascq, France
| | - François-Yves Bouget
- Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Université Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France
| | - Gwenael Piganeau
- Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Université Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France
| | - Bernard De Baets
- Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - André Picard
- Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Université Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France
| | - Michel Delseny
- Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique–Université de Perpignan, 52, Avenue de Villeneuve, 66860 Perpignan, France
| | - Jacques Demaille
- Institut de Génétique Humaine, Unité Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France
| | - Yves Van de Peer
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and
| | - Hervé Moreau
- Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Université Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France
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Delvallé D, Dumez S, Wattebled F, Roldán I, Planchot V, Berbezy P, Colonna P, Vyas D, Chatterjee M, Ball S, Mérida A, D'Hulst C. Soluble starch synthase I: a major determinant for the synthesis of amylopectin in Arabidopsis thaliana leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 43:398-412. [PMID: 16045475 DOI: 10.1111/j.1365-313x.2005.02462.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A minimum of four soluble starch synthase families have been documented in all starch-storing green plants. These activities are involved in amylopectin synthesis and are extremely well conserved throughout the plant kingdom. Mutants or transgenic plants defective for SSII and SSIII isoforms have been previously shown to have a large and specific impact on the synthesis of amylopectin while the function of the SSI type of enzymes has remained elusive. We report here that Arabidopsis mutants, lacking a plastidial starch synthase isoform belonging to the SSI family, display a major and novel type of structural alteration within their amylopectin. Comparative analysis of beta-limit dextrins for both wild type and mutant amylopectins suggests a specific and crucial function of SSI during the synthesis of transient starch in Arabidopsis leaves. Considering our own characterization of SSI activity and the previously described kinetic properties of maize SSI, our results suggest that the function of SSI is mainly involved in the synthesis of small outer chains during amylopectin cluster synthesis.
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Affiliation(s)
- David Delvallé
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS/USTL, IFR 118, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
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