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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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2
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Thappeta Y, Cañas-Duarte SJ, Kallem T, Fragasso A, Xiang Y, Gray W, Lee C, Cegelski L, Jacobs-Wagner C. Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590186. [PMID: 38659787 PMCID: PMC11042326 DOI: 10.1101/2024.04.19.590186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacterium Escherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and 13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.
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Affiliation(s)
- Yashna Thappeta
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Silvia J. Cañas-Duarte
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Till Kallem
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Alessio Fragasso
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yingjie Xiang
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - William Gray
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - Cheyenne Lee
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | | | - Christine Jacobs-Wagner
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
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3
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Lin Z, Jiang S, Zwe YH, Zhang K, Li D. Glycogen plays a key role in survival of Salmonella Typhimurium on dry surfaces and in low-moisture foods. Food Res Int 2024; 175:113714. [PMID: 38128983 DOI: 10.1016/j.foodres.2023.113714] [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: 10/05/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Salmonella enterica is known to survive in desiccate environments and is often associated with low-moisture foods (LMFs). In this work, S. Typhimurium ATCC 14028 was found to survive better by achieving the least reductions (3.17 ± 0.20 Log CFU reduction) compared to S. Tennessee ATCC 10722 (3.82 ± 0.13 Log CFU reduction) and S. Newport ATCC 6962 (6.03 ± 0.36 Log CFU reduction) after 30 days on surfaces with a relative humidity of 49% at ambient temperature. A metabolomic analysis revealed that S. Typhimurium was still active in energy metabolism after 24 h in the desiccate environment and glycogen, an energy reserve, was drastically reduced. We followed up on the glycogen levels over 30 days and found indeed a sharp decline on the first day. However, the glycogens detected on day 7 were significantly higher (P < 0.05) and thereafter remained stable above the original levels until day 30. The expression levels of both glycogen anabolism- and catabolism-related genes (csrA, glgA, glgC, glgX) were significantly up-regulated at all tested points (P < 0.05). The glgA and glgC insertion mutants displayed weaker survivability on both dry surfaces and in representative LMFs (flour and milk powder) compared to the wild-type strain. This work highlights the role of glycogen during different periods of desiccation, which may bring novel insight into mitigating Salmonella by disrupting glycogen metabolism.
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Affiliation(s)
- Zejia Lin
- Department of Food Science & Technology, National University of Singapore, Singapore 117543, Singapore
| | - Shaoqian Jiang
- Department of Food Science & Technology, National University of Singapore, Singapore 117543, Singapore
| | - Ye Htut Zwe
- Department of Food Science & Technology, National University of Singapore, Singapore 117543, Singapore; National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
| | - Kexin Zhang
- Department of Food Science & Technology, National University of Singapore, Singapore 117543, Singapore
| | - Dan Li
- Department of Food Science & Technology, National University of Singapore, Singapore 117543, Singapore.
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4
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Bogdan DF, Baricz AI, Chiciudean I, Bulzu PA, Cristea A, Năstase-Bucur R, Levei EA, Cadar O, Sitar C, Banciu HL, Moldovan OT. Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania. Front Microbiol 2023; 14:962452. [PMID: 36825091 PMCID: PMC9941645 DOI: 10.3389/fmicb.2023.962452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania). Materials and Methods To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water. Results and Discussion Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Leșu Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, γ-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and α-cyclodextrin), carbohydrates (α-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.
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Affiliation(s)
- Diana Felicia Bogdan
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania,Institute for Research, Development and Innovation in Applied Natural Sciences, Cluj-Napoca, Romania,*Correspondence: Diana Felicia Bogdan, ✉
| | - Andreea Ionela Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Iulia Chiciudean
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Paul-Adrian Bulzu
- Biology Centre CAS, Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Laboratory of Microbial Ecology and Evolution, Ceske Budejovice, Czechia
| | - Adorján Cristea
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ruxandra Năstase-Bucur
- Emil Racovita Institute of Speleology, Cluj-Napoca Department, Cluj-Napoca, Romania,Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Erika Andrea Levei
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Oana Cadar
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Cristian Sitar
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania,Zoological Museum, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania,Centre for Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania,Horia Leonard Banciu, ✉
| | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj-Napoca Department, Cluj-Napoca, Romania,Romanian Institute of Science and Technology, Cluj-Napoca, Romania,Centro Nacional de Investigación sobre la Evolución Humana, CENIEH, Burgos, Spain
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5
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Microbial storage and its implications for soil ecology. THE ISME JOURNAL 2022; 16:617-629. [PMID: 34593996 PMCID: PMC8857262 DOI: 10.1038/s41396-021-01110-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]
Abstract
Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.
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6
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Cohen H, Adani B, Cohen E, Piscon B, Azriel S, Desai P, Bähre H, McClelland M, Rahav G, Gal-Mor O. The ancestral stringent response potentiator, DksA has been adapted throughout Salmonella evolution to orchestrate the expression of metabolic, motility, and virulence pathways. Gut Microbes 2022; 14:1997294. [PMID: 34923900 PMCID: PMC8726615 DOI: 10.1080/19490976.2021.1997294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DksA is a conserved RNA polymerase-binding protein known to play a key role in the stringent response of proteobacteria species, including many gastrointestinal pathogens. Here, we used RNA-sequencing of Escherichia coli, Salmonella bongori and Salmonella enterica serovar Typhimurium, together with phenotypic comparison to study changes in the DksA regulon, during Salmonella evolution. Comparative RNA-sequencing showed that under non-starved conditions, DksA controls the expression of 25%, 15%, and 20% of the E. coli, S. bongori, and S. enterica genes, respectively, indicating that DksA is a pleiotropic regulator, expanding its role beyond the canonical stringent response. We demonstrate that DksA is required for the growth of these three enteric bacteria species in minimal medium and controls the expression of the TCA cycle, glycolysis, pyrimidine biosynthesis, and quorum sensing. Interestingly, at multiple steps during Salmonella evolution, the type I fimbriae and various virulence genes encoded within SPIs 1, 2, 4, 5, and 11 have been transcriptionally integrated under the ancestral DksA regulon. Consequently, we show that DksA is necessary for host cells invasion by S. Typhimurium and S. bongori and for intracellular survival of S. Typhimurium in bone marrow-derived macrophages (BMDM). Moreover, we demonstrate regulatory inversion of the conserved motility-chemotaxis regulon by DksA, which acts as a negative regulator in E. coli, but activates this pathway in S. bongori and S. enterica. Overall, this study demonstrates the regulatory assimilation of multiple horizontally acquired virulence genes under the DksA regulon and provides new insights into the evolution of virulence genes regulation in Salmonella spp.
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Affiliation(s)
- Helit Cohen
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Boaz Adani
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Emiliano Cohen
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Bar Piscon
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Shalhevet Azriel
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Prerak Desai
- Janssen Research & Development, LLC, Raritan, New Jersey, USA,Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Heike Bähre
- Hannover Medical School, Research Core Unit Metabolomics, Hannover, Germany
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Galia Rahav
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel,Contact Ohad Gal-Mor The Infectious Diseases Research Laboratory Sheba Medical Cente, Tel-Hashomer, Israel
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7
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Surface Glucan Structures in Aeromonas spp. Mar Drugs 2021; 19:md19110649. [PMID: 34822520 PMCID: PMC8625153 DOI: 10.3390/md19110649] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 01/24/2023] Open
Abstract
Aeromonas spp. are generally found in aquatic environments, although they have also been isolated from both fresh and processed food. These Gram-negative, rod-shaped bacteria are mostly infective to poikilothermic animals, although they are also considered opportunistic pathogens of both aquatic and terrestrial homeotherms, and some species have been associated with gastrointestinal and extraintestinal septicemic infections in humans. Among the different pathogenic factors associated with virulence, several cell-surface glucans have been shown to contribute to colonization and survival of Aeromonas pathogenic strains, in different hosts. Lipopolysaccharide (LPS), capsule and α-glucan structures, for instance, have been shown to play important roles in bacterial–host interactions related to pathogenesis, such as adherence, biofilm formation, or immune evasion. In addition, glycosylation of both polar and lateral flagella has been shown to be mandatory for flagella production and motility in different Aeromonas strains, and has also been associated with increased bacterial adhesion, biofilm formation, and induction of the host proinflammatory response. The main aspects of these structures are covered in this review.
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8
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Structural basis of glycogen metabolism in bacteria. Biochem J 2019; 476:2059-2092. [PMID: 31366571 DOI: 10.1042/bcj20170558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The evolution of metabolic pathways is a major force behind natural selection. In the spotlight of such process lies the structural evolution of the enzymatic machinery responsible for the central energy metabolism. Specifically, glycogen metabolism has emerged to allow organisms to save available environmental surplus of carbon and energy, using dedicated glucose polymers as a storage compartment that can be mobilized at future demand. The origins of such adaptive advantage rely on the acquisition of an enzymatic system for the biosynthesis and degradation of glycogen, along with mechanisms to balance the assembly and disassembly rate of this polysaccharide, in order to store and recover glucose according to cell energy needs. The first step in the classical bacterial glycogen biosynthetic pathway is carried out by the adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase. This allosteric enzyme synthesizes ADP-glucose and acts as a point of regulation. The second step is carried out by the glycogen synthase, an enzyme that generates linear α-(1→4)-linked glucose chains, whereas the third step catalyzed by the branching enzyme produces α-(1→6)-linked glucan branches in the polymer. Two enzymes facilitate glycogen degradation: glycogen phosphorylase, which functions as an α-(1→4)-depolymerizing enzyme, and the debranching enzyme that catalyzes the removal of α-(1→6)-linked ramifications. In this work, we rationalize the structural basis of glycogen metabolism in bacteria to the light of the current knowledge. We describe and discuss the remarkable progress made in the understanding of the molecular mechanisms of substrate recognition and product release, allosteric regulation and catalysis of all those enzymes.
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9
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Yi T, Lim HJ, Lee SJ, Lee KH, Kim DM. Synthesis of (R,R)-2,3-butanediol from starch in a hybrid cell-free reaction system. J IND ENG CHEM 2018. [DOI: 10.1016/j.jiec.2018.06.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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Tian Y, Xu W, Zhang W, Zhang T, Guang C, Mu W. Amylosucrase as a transglucosylation tool: From molecular features to bioengineering applications. Biotechnol Adv 2018; 36:1540-1552. [PMID: 29935268 DOI: 10.1016/j.biotechadv.2018.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/10/2018] [Accepted: 06/15/2018] [Indexed: 02/04/2023]
Abstract
Amylosucrase (EC 2.4.1.4, ASase), an outstanding sucrose-utilizing transglucosylase in the glycoside hydrolase family 13, can produce glucans with only α-1,4 linkages. Generally, on account of a double-displacement mechanism, ASase can catalyze polymerization, isomerization, and hydrolysis reactions with sucrose as the sole substrate, and has transglycosylation capacity to attach glucose molecules from sucrose to extra glycosyl acceptors. Based on extensive enzymology research, this review presents the characteristics of various ASases, including their microbial metabolism, preparation, and enzymatic properties, and exhibits structure-based strategies in the improvement of activity, specificity, and thermostability. As a vital transglucosylation tool of producing sugars, carbohydrate-based bioactive compounds, and materials, the bioengineering applications of ASases are also systematically summarized.
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Affiliation(s)
- Yuqing Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
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11
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Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems. Int J Microbiol 2018; 2018:6234931. [PMID: 29977299 PMCID: PMC5994298 DOI: 10.1155/2018/6234931] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/10/2018] [Accepted: 04/23/2018] [Indexed: 11/18/2022] Open
Abstract
Information on the biodegradation potential of lake and river microbial communities is essential for watershed management. The water draining into the lake ecosystems often carries a significant amount of suspended sediments, which are transported by rivers and streams from the local drainage basin. The organic carbon processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and apprehend some of these variabilities in the sediments, we sampled six sites: three from the Saint Clair River (SC1, SC2, and SC3) and three from Lake Saint Clair in the spring, summer, fall, and winter of 2016. Here, we investigated the shifts in metabolic profiles of sediment microbial communities, along Saint Clair River and Lake Saint Clair using Biolog EcoPlates, which test for the oxidation of 31 carbon sources. The number of utilized substrates was generally higher in the river sediments (upstream) than in the lake sediments (downstream), suggesting a shift in metabolic activities among microbial assemblages. Seasonal and site-specific differences were also found in the numbers of utilized substrates, which were similar in the summer and fall, and spring and winter. The sediment microbial communities in the summer and fall showed more versatile substrate utilization patterns than spring and winter communities. The functional fingerprint analyses clearly distinguish the sediment microbial communities from the lake sites (downstream more polluted sites), which showed a potential capacity to use more complex carbon substrates such as polymers. This study establishes a close linkage between physical and chemical properties (temperature and organic matter content) of lake and river sediments and associated microbial functional activities.
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12
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Bhutada G, Kavšcek M, Ledesma-Amaro R, Thomas S, Rechberger GN, Nicaud JM, Natter K. Sugar versus fat: elimination of glycogen storage improves lipid accumulation in Yarrowia lipolytica. FEMS Yeast Res 2018; 17:3798535. [PMID: 28475761 PMCID: PMC5812513 DOI: 10.1093/femsyr/fox020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/12/2017] [Indexed: 01/01/2023] Open
Abstract
Triacylglycerol (TAG) and glycogen are the two major metabolites for carbon storage in most eukaryotic organisms. We investigated the glycogen metabolism of the oleaginous Yarrowia lipolytica and found that this yeast accumulates up to 16% glycogen in its biomass. Assuming that elimination of glycogen synthesis would result in an improvement of lipid accumulation, we characterized and deleted the single gene coding for glycogen synthase, YlGSY1. The mutant was grown under lipogenic conditions with glucose and glycerol as substrates and we obtained up to 60% improvement in TAG accumulation compared to the wild-type strain. Additionally, YlGSY1 was deleted in a background that was already engineered for high lipid accumulation. In this obese background, TAG accumulation was also further increased. The highest lipid content of 52% was found after 3 days of cultivation in nitrogen-limited glycerol medium. Furthermore, we constructed mutants of Y. lipolytica and Saccharomyces cerevisiae that are deleted for both glycogen and TAG synthesis, demonstrating that the ability to store carbon is not essential. Overall, this work showed that glycogen synthesis is a competing pathway for TAG accumulation in oleaginous yeasts and that deletion of the glycogen synthase has beneficial effects on neutral lipid storage.
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Affiliation(s)
- Govindprasad Bhutada
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Martin Kavšcek
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gerald N Rechberger
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.,Omics Center Graz, BioTechMed Graz, 8010 Graz, Austria
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
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13
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Wilson WA, Pradhan P, Madhan N, Gist GC, Brittingham A. Glycogen synthase from the parabasalian parasite Trichomonas vaginalis: An unusual member of the starch/glycogen synthase family. Biochimie 2017; 138:90-101. [PMID: 28465215 DOI: 10.1016/j.biochi.2017.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/28/2017] [Indexed: 01/13/2023]
Abstract
Trichomonas vaginalis, a parasitic protist, is the causative agent of the common sexually-transmitted infection trichomoniasis. The organism has long been known to synthesize substantial glycogen as a storage polysaccharide, presumably mobilizing this compound during periods of carbohydrate limitation, such as might be encountered during transmission between hosts. However, little is known regarding the enzymes of glycogen metabolism in T. vaginalis. We had previously described the identification and characterization of two forms of glycogen phosphorylase in the organism. Here, we measure UDP-glucose-dependent glycogen synthase activity in cell-free extracts of T. vaginalis. We then demonstrate that the TVAG_258220 open reading frame encodes a glycosyltransferase that is presumably responsible for this synthetic activity. We show that expression of TVAG_258220 in a yeast strain lacking endogenous glycogen synthase activity is sufficient to restore glycogen accumulation. Furthermore, when TVAG_258220 is expressed in bacteria, the resulting recombinant protein has glycogen synthase activity in vitro, transferring glucose from either UDP-glucose or ADP-glucose to glycogen and using both substrates with similar affinity. This protein is also able to transfer glucose from UDP-glucose or ADP-glucose to maltose and longer oligomers of glucose but not to glucose itself. However, with these substrates, there is no evidence of processivity and sugar transfer is limited to between one and three glucose residues. Taken together with our earlier work on glycogen phosphorylase, we are now well positioned to define both how T. vaginalis synthesizes and utilizes glycogen, and how these processes are regulated.
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Affiliation(s)
- Wayne A Wilson
- Department of Biochemistry & Nutrition, Des Moines University, Des Moines, IA 50312, USA.
| | - Prajakta Pradhan
- Department of Microbiology & Immunology, Des Moines University, Des Moines, IA 50312, USA
| | - Nayasha Madhan
- Department of Microbiology & Immunology, Des Moines University, Des Moines, IA 50312, USA
| | - Galen C Gist
- Department of Microbiology & Immunology, Des Moines University, Des Moines, IA 50312, USA
| | - Andrew Brittingham
- Department of Microbiology & Immunology, Des Moines University, Des Moines, IA 50312, USA
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14
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Bhutada G, Kavšček M, Ledesma-Amaro R, Thomas S, Rechberger GN, Nicaud JM, Natter K. Sugar versus fat: elimination of glycogen storage improves lipid accumulation inYarrowia lipolytica. FEMS Yeast Res 2017. [DOI: 10.1093/femsle/fox020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Govindprasad Bhutada
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Martin Kavšček
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gerald N. Rechberger
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
- Omics Center Graz, BioTechMed Graz, 8010 Graz, Austria
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
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15
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Klotz A, Forchhammer K. Glycogen, a major player for bacterial survival and awakening from dormancy. Future Microbiol 2017; 12:101-104. [DOI: 10.2217/fmb-2016-0218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Alexander Klotz
- Interfaculty Institute of Microbiology & Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology & Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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16
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Abstract
Glycogen accumulation occurs in Escherichia coli and Salmonella enterica serovar Typhimurium as well as in many other bacteria. Glycogen will be formed when there is an excess of carbon under conditions in which growth is limited because of the lack of a growth nutrient, e.g., a nitrogen source. This review describes the enzymatic reactions involved in glycogen synthesis and the allosteric regulation of the first enzyme, ADP-glucose pyrophosphorylase. The properties of the enzymes involved in glycogen synthesis, ADP-glucose pyrophosphorylase, glycogen synthase, and branching enzyme are also characterized. The data describing the genetic regulation of the glycogen synthesis are also presented. An alternate pathway for glycogen synthesis in mycobacteria is also described.
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17
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Weiner M, Tröndle J, Albermann C, Sprenger GA, Weuster-Botz D. Carbon storage in recombinantEscherichia coliduring growth on glycerol and lactic acid. Biotechnol Bioeng 2014; 111:2508-19. [DOI: 10.1002/bit.25306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/20/2014] [Accepted: 05/27/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Michael Weiner
- Lehrstuhl für Bioverfahrenstechnik; Technische Universität München; Garching Germany
| | - Julia Tröndle
- Lehrstuhl für Bioverfahrenstechnik; Technische Universität München; Garching Germany
| | | | - Georg A. Sprenger
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart Germany
| | - Dirk Weuster-Botz
- Lehrstuhl für Bioverfahrenstechnik; Technische Universität München; Garching Germany
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18
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Lutz C, Erken M, Noorian P, Sun S, McDougald D. Environmental reservoirs and mechanisms of persistence of Vibrio cholerae. Front Microbiol 2013; 4:375. [PMID: 24379807 PMCID: PMC3863721 DOI: 10.3389/fmicb.2013.00375] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/21/2013] [Indexed: 12/23/2022] Open
Abstract
It is now well accepted that Vibrio cholerae, the causative agent of the water-borne disease cholera, is acquired from environmental sources where it persists between outbreaks of the disease. Recent advances in molecular technology have demonstrated that this bacterium can be detected in areas where it has not previously been isolated, indicating a much broader, global distribution of this bacterium outside of endemic regions. The environmental persistence of V. cholerae in the aquatic environment can be attributed to multiple intra- and interspecific strategies such as responsive gene regulation and biofilm formation on biotic and abiotic surfaces, as well as interactions with a multitude of other organisms. This review will discuss some of the mechanisms that enable the persistence of this bacterium in the environment. In particular, we will discuss how V. cholerae can survive stressors such as starvation, temperature, and salinity fluctuations as well as how the organism persists under constant predation by heterotrophic protists.
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Affiliation(s)
- Carla Lutz
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia
| | - Martina Erken
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia ; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| | - Parisa Noorian
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia
| | - Shuyang Sun
- The Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore
| | - Diane McDougald
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia ; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
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19
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Tuncel A, Okita TW. Improving starch yield in cereals by over-expression of ADPglucose pyrophosphorylase: expectations and unanticipated outcomes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 211:52-60. [PMID: 23987811 DOI: 10.1016/j.plantsci.2013.06.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 05/09/2023]
Abstract
Significant improvements in crop productivity are required to meet the nutritional requirements of a growing world population. This challenge is magnified by an increased demand for bioenergy as a means to mitigate carbon inputs into the environment. Starch is a major component of the harvestable organs of many crop plants, and various endeavors have been taken to improve the yields of starchy organs through the manipulation of starch synthesis. Substantial efforts have centered on the starch regulatory enzyme ADPglucose pyrophosphorylase (AGPase) due to its pivotal role in starch biosynthesis. These efforts include over-expression of this enzyme in cereal plants such as maize, rice and wheat as well as potato and cassava, as they supply the bulk of the staple food worldwide. In this perspective, we describe efforts to increase starch yields in cereal grains by first providing an introduction about the importance of source-sink relationship and the motives behind the efforts to alter starch biosynthesis and turnover in leaves. We then discuss the catalytic and regulatory properties of AGPase and the molecular approaches used to enhance starch synthesis by manipulation of this process during grain filling using seed-specific promoters. Several studies have demonstrated increases in starch content per seed using endosperm-specific promoters, but other studies have demonstrated an increase in seed number with only marginal impact on seed weight. Potential mechanisms that may be responsible for this paradoxical increase in seed number will also be discussed. Finally, we describe current efforts and future prospects to improve starch yield in cereals. These efforts include further enhancement of starch yield in rice by augmenting the process of ADPglucose transport into amyloplast as well as other enzymes involved in photoassimilate partitioning in seeds.
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Affiliation(s)
- Aytug Tuncel
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, United States
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20
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Gründel M, Scheunemann R, Lockau W, Zilliges Y. Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology (Reading) 2012; 158:3032-3043. [DOI: 10.1099/mic.0.062950-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marianne Gründel
- Humboldt-Universität zu Berlin, Institute of Biology/Biochemistry of Plants, Chausseestr. 117, 10115 Berlin, Germany
| | - Ramon Scheunemann
- Humboldt-Universität zu Berlin, Institute of Biology/Biochemistry of Plants, Chausseestr. 117, 10115 Berlin, Germany
| | - Wolfgang Lockau
- Humboldt-Universität zu Berlin, Institute of Biology/Biochemistry of Plants, Chausseestr. 117, 10115 Berlin, Germany
| | - Yvonne Zilliges
- Humboldt-Universität zu Berlin, Institute of Biology/Biochemistry of Plants, Chausseestr. 117, 10115 Berlin, Germany
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21
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Wang J, Qi P, Wei Y, Liu D, Fedak G, Zheng Y. Molecular characterization and functional analysis of elite genes in wheat and its related species. J Genet 2011; 89:539-54. [PMID: 21273706 DOI: 10.1007/s12041-010-0074-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The tribe Triticeae includes major cereal crops (bread wheat, durum wheat, triticale, barley and rye), as well as abundant forage and lawn grasses. Wheat and its wild related species possess numerous favourable genes for yield improvement, grain quality enhancement, biotic and abiotic stress resistance, and constitute a giant gene pool for wheat improvement. In recent years, significant progress on molecular characterization and functional analysis of elite genes in wheat and its related species have been achieved. In this paper, we review the cloned functional genes correlated with grain quality, biotic and abiotic stress resistance, photosystem and nutrition utilization in wheat and its related species.
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Affiliation(s)
- Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Yaan 625014, Sichuan, People's Republic of China
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22
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23
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Eydallin G, Montero M, Almagro G, Sesma MT, Viale AM, Muñoz FJ, Rahimpour M, Baroja-Fernández E, Pozueta-Romero J. Genome-wide screening of genes whose enhanced expression affects glycogen accumulation in Escherichia coli. DNA Res 2010; 17:61-71. [PMID: 20118147 PMCID: PMC2853380 DOI: 10.1093/dnares/dsp028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Using a systematic and comprehensive gene expression library (the ASKA library), we have carried out a genome-wide screening of the genes whose increased plasmid-directed expression affected glycogen metabolism in Escherichia coli. Of the 4123 clones of the collection, 28 displayed a glycogen-excess phenotype, whereas 58 displayed a glycogen-deficient phenotype. The genes whose enhanced expression affected glycogen accumulation were classified into various functional categories including carbon sensing, transport and metabolism, general stress and stringent responses, factors determining intercellular communication, aggregative and social behaviour, nitrogen metabolism and energy status. Noteworthy, one-third of them were genes about which little or nothing is known. We propose an integrated metabolic model wherein E. coli glycogen metabolism is highly interconnected with a wide variety of cellular processes and is tightly adjusted to the nutritional and energetic status of the cell. Furthermore, we provide clues about possible biological roles of genes of still unknown functions.
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Affiliation(s)
- Gustavo Eydallin
- Instituto de Agrobiotecnología, Universidad Pública de Navarra/Gobierno de Navarra/Consejo Superior de Investigaciones Científicas, Mutiloako etorbidea zenbaki gabe, Mutiloabeiti, Nafarroa, Spain
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24
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Oliveira LR, Marcelino FC, Barcellos FG, Rodrigues EP, Megías M, Hungria M. The nodC, nodG, and glgX genes of Rhizobium tropici strain PRF 81. Funct Integr Genomics 2009; 10:425-31. [DOI: 10.1007/s10142-009-0151-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 11/15/2009] [Accepted: 11/15/2009] [Indexed: 10/20/2022]
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25
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Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes. Biochem J 2009; 424:129-41. [PMID: 19702577 DOI: 10.1042/bj20090980] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using the Keio collection of gene-disrupted mutants of Escherichia coli, we have recently carried out a genome-wide screening of the genes affecting glycogen metabolism. Among the mutants identified in the study, Delta mgtA, Delta phoP and Delta phoQ cells, all lacking genes that are induced under low extracellular Mg2+ conditions, displayed glycogen-deficient phenotypes. In this work we show that these mutants accumulated normal glycogen levels when the culture medium was supplemented with submillimolar Mg2+ concentrations. Expression analyses conducted in wild-type, Delta phoP and Delta phoQ cells showed that the glgCAP operon is under PhoP-PhoQ control in the submillimolar Mg2+ concentration range. Subsequent screening of the Keio collection under non-limiting Mg2+ allowed the identification of 183 knock-out mutants with altered glycogen levels. The stringent and general stress responses, end-turnover of tRNA, intracellular AMP levels, and metabolism of amino acids, iron, carbon and sulfur were major determinants of glycogen levels. glgC::lacZY expression analyses using mutants representing different functional categories revealed that the glgCAP operon belongs to the RelA regulon. We propose an integrated metabolic model wherein glycogen metabolism is (a) tightly controlled by the energy and nutritional status of the cell and (b) finely regulated by changes in environmental Mg2+ occurring at the submillimolar concentration range.
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26
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Abstract
The accumulation of glycogen occurs in Escherichia coli and Salmonella enterica serovar Typhimurium as well as in many other bacteria. Glycogen will be formed when there is an excess of carbon under conditions in which growth is limited due to the lack of a growth nutrient, e.g., a nitrogen source. The structural genes of the glycogen biosynthetic enzymes of E. coli and S. serovar Typhimurium have been cloned previously, and that has provided insights in the genetic regulation of glycogen synthesis. An important aspect of the regulation of glycogen synthesis is the allosteric regulation of the ADP-Glc PPase. The current information, views, and concepts regarding the regulation of enzyme activity and the expression of the glycogen biosynthetic enzymes are presented in this review. The recent information on the amino acid residues critical for the activity of both glycogen synthase and branching enzyme (BE) is also presented. The residue involved in catalysis in the E. coli ADP-Glc PPase was determined by comparing a predicted structure of the enzyme with the known three-dimensional structures of sugar-nucleotide PPase domains. The molecular cloning of the E. coliglg K-12 structural genes greatly facilitated the subsequent study of the genetic regulation of bacterial glycogen biosynthesis. Results from studies of glycogen excess E. coli B mutants SG3 and AC70R1, which exhibit enhanced levels of the enzymes in the glycogen synthesis pathway (i.e., they are derepressed mutants), suggested that glycogen synthesis is under negative genetic regulation.
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27
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Bourassa L, Camilli A. Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae. Mol Microbiol 2009; 72:124-38. [PMID: 19226328 DOI: 10.1111/j.1365-2958.2009.06629.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pathogenic Vibrio cholerae cycle between the nutrient-rich human intestinal tract and nutrient-poor aquatic environments and currently few bacterial factors are known that aid in the transition between these disparate environments. We hypothesized that the ability to store carbon as glycogen would facilitate both bacterial fitness in the aquatic environment and transmission of V. cholerae to new hosts. To investigate the role of glycogen in V. cholerae transmission, we constructed mutants that cannot store or degrade glycogen. Here, we provide the first report of glycogen metabolism in V. cholerae and demonstrate that glycogen prolongs survival in nutrient-poor environments that are known ecological niches of V. cholerae, including pond water and rice-water stool. Additionally, glycogen contributes to the pathogenesis of V. cholerae in a transmission model of cholera. A role for glycogen in the transmission of V. cholerae is further supported by the presence of glycogen granules in rice-water stool vibrios from cholera patients, indicating that glycogen is stored during human infection. Collectively, our findings indicate that glycogen metabolism is critical for V. cholerae to transition between host and aquatic environments.
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Affiliation(s)
- Lori Bourassa
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
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28
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Cho KM, Lim WJ, Math RK, Asraful Islam SM, Hong SJ, Kim H, Yun HD. Comparative analysis of the glg operons of Pectobacterium chrysanthemi PY35 and other prokaryotes. J Mol Evol 2008; 67:1-12. [PMID: 18594899 DOI: 10.1007/s00239-008-9103-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 03/06/2008] [Indexed: 11/25/2022]
Abstract
A chromosomal region of Pectobacterium chrysanthemi PY35 that contains of genes for glycogen synthesis was isolated from a cosmid library. The operon consists of glycogen branching enzyme (glgB), glycogen debranching enzyme (glgX), ADP-glucose pyrophosphorylase (glgC), glycogen synthase (glgA), and glycogen phosphorylase (glgP) genes. Gene organization is similar to that of Escherichia coli. The purified ADP-glucose pyrophosphorylase (GlgC) was activated by fructose 1,6-bisphosphate and inhibited by AMP. The constructed glgX::Omega mutant failed to integrate into the chromosome of P. chrysanthemi by marker exchange. Phylogenetic analysis based on the 16S rDNA and the amino acid sequence of Glg enzymes showed correlation with other bacteria. gamma-Proteobacteria have the glgX gene instead of the bacilli glgD gene in the glg operon. The possible evolutionary implications of the results among the prokaryotes are discussed.
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Affiliation(s)
- Kye Man Cho
- Division of Applied Life Science (BK21 Program), Graduate School of Gyeongsang National University, Chinju 660-701, Republic of Korea
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29
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Morán-Zorzano MT, Alonso-Casajús N, Muñoz FJ, Viale AM, Baroja-Fernández E, Eydallin G, Pozueta-Romero J. Occurrence of more than one important source of ADPglucose linked to glycogen biosynthesis in Escherichia coli and Salmonella. FEBS Lett 2007; 581:4423-9. [PMID: 17719035 DOI: 10.1016/j.febslet.2007.08.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 07/30/2007] [Accepted: 08/06/2007] [Indexed: 10/22/2022]
Abstract
To explore the possible occurrence of sources, other than GlgC, of ADPglucose linked to bacterial glycogen biosynthesis we characterized Escherichia coli and Salmonella DeltaglgCAP deletion mutants lacking the whole glycogen biosynthetic machinery. These mutants displayed the expected glycogen-less phenotype but accumulated ADPglucose. Importantly, DeltaglgCAP cells expressing the glycogen synthase encoding glgA gene accumulated glycogen. Protein chromatographic separation of crude extracts of DeltaglgCAP mutants and subsequent activity measurement analyses revealed that these cells possess various proteins catalyzing the conversion of glucose-1-phosphate into ADPglucose. Collectively these findings show that enterobacteria possess more than one important source of ADPglucose linked to glycogen biosynthesis.
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Affiliation(s)
- María T Morán-Zorzano
- Instituto de Agrobiotecnología, (CSIC, UPNA, Gobierno de Navarra), Mutiloako etorbidea zenbaki gabe, 31192 Mutiloabeti, Nafarroa, Spain
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30
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Eydallin G, Viale AM, Morán-Zorzano MT, Muñoz FJ, Montero M, Baroja-Fernández E, Pozueta-Romero J. Genome-wide screening of genes affecting glycogen metabolism in Escherichia coli K-12. FEBS Lett 2007; 581:2947-53. [PMID: 17543954 DOI: 10.1016/j.febslet.2007.05.044] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 05/11/2007] [Accepted: 05/15/2007] [Indexed: 11/19/2022]
Abstract
A systematic and comprehensive gene-disrupted mutant collection of E. coli K-12 was used to identify genes whose deletions affect glycogen accumulation. Of the 3985 non-essential gene mutants of the collection, 35 displayed a glycogen-excess phenotype, whereas 30 displayed either glycogen-less or glycogen-deficient phenotypes. The genes whose deletions affect glycogen accumulation were classified into various functional categories, including energy production, envelope composition and integrity, protein translation and stability, transport of inorganic ions and nucleotides, and metabolism of carbohydrates and amino acids. The overall data indicate that glycogen metabolism is highly interconnected with a wide variety of cellular processes in E. coli.
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Affiliation(s)
- Gustavo Eydallin
- Instituto de Agrobiotecnología, Universidad Pública de Navarra, Gobierno de Navarra, Consejo Superior de Investigaciones Científicas, Mutiloako etorbidea zenbaki gabe, Mutiloabeiti, Nafarroa, Spain
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31
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Seibold G, Dempf S, Schreiner J, Eikmanns BJ. Glycogen formation in Corynebacterium glutamicum and role of ADP-glucose pyrophosphorylase. Microbiology (Reading) 2007; 153:1275-1285. [PMID: 17379737 DOI: 10.1099/mic.0.2006/003368-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycogen is generally assumed to serve as a major reserve polysaccharide in bacteria. In this work, glycogen accumulation in the amino acid producer Corynebacterium glutamicum was characterized, expression of the C. glutamicum glgC gene, encoding the key enzyme in glycogen synthesis, ADP-glucose (ADP-Glc) pyrophosphorylase, was analysed, and the relevance of this enzyme for growth, survival, amino acid production and osmoprotection was investigated. C. glutamicum cells grown in medium containing the glycolytic substrates glucose, sucrose or fructose showed rapid glycogen accumulation (up to 90 mg per g dry weight) in the early exponential growth phase and degradation of the polymer when the sugar became limiting. In contrast, no glycogen was detected in cells grown on the gluconeogenic substrates acetate or lactate. In accordance with these results, the specific activity of ADP-Glc pyrophosphorylase was 20-fold higher in glucose-grown than in acetate- or lactate-grown cells. Expression analysis suggested that this carbon-source-dependent regulation might be only partly due to transcriptional control of the glgC gene. Inactivation of the chromosomal glgC gene led to the absence of ADP-Glc pyrophosphorylase activity, to a complete loss of intracellular glycogen in all media tested and to a distinct lag phase when the cells were inoculated in minimal medium containing 750 mM sodium chloride. However, the growth of C. glutamicum, its survival in the stationary phase and its glutamate and lysine production were not affected by glgC inactivation under either condition tested. These results indicate that intracellular glycogen formation is not essential for growth and survival of and amino acid production by C. glutamicum and that ADP-Glc pyrophosphorylase activity might be advantageous for fast adaptation of C. glutamicum to hyperosmotic stress.
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Affiliation(s)
- Gerd Seibold
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Stefan Dempf
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Joy Schreiner
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Bernhard J Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
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32
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Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2007; 70:939-1031. [PMID: 17158705 PMCID: PMC1698508 DOI: 10.1128/mmbr.00024-06] [Citation(s) in RCA: 985] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
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Affiliation(s)
- Josef Deutscher
- Microbiologie et Génétique Moléculaire, INRA-CNRS-INA PG UMR 2585, Thiverval-Grignon, France.
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Morán-Zorzano MT, Viale AM, Muñoz FJ, Alonso-Casajús N, Eydallín GG, Zugasti B, Baroja-Fernández E, Pozueta-Romero J. Escherichia coli AspP activity is enhanced by macromolecular crowding and by both glucose-1,6-bisphosphate and nucleotide-sugars. FEBS Lett 2007; 581:1035-40. [PMID: 17306798 DOI: 10.1016/j.febslet.2007.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 01/24/2007] [Accepted: 02/01/2007] [Indexed: 11/25/2022]
Abstract
Escherichia coli ADP-sugar pyrophosphatase (AspP) is a "Nudix" hydrolase that catalyzes the hydrolytic breakdown of ADP-glucose linked to glycogen biosynthesis. Moderate increases of AspP activity in the cell are accompanied by significant reductions of the glycogen content. In vitro analyses showed that AspP activity is strongly enhanced by macromolecular crowding and by both glucose-1,6-bisphosphate and nucleotide-sugars, providing a first set of indicative evidences that AspP is a highly regulated enzyme. To our knowledge, AspP is the sole bacterial enzyme described to date which is activated by both G1,6P(2) and nucleotide-sugars.
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Affiliation(s)
- María Teresa Morán-Zorzano
- Instituto de Agrobiotecnología, Universidad Pública de Navarra/Gobierno de Navarra/Consejo Superior de Investigaciones Científicas, Carretera de Mutilva s/n, 31192 Mutilva Baja, Navarra, Spain
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Yoo SH, Keppel C, Spalding M, Jane JL. Effects of growth condition on the structure of glycogen produced in cyanobacterium Synechocystis sp. PCC6803. Int J Biol Macromol 2006; 40:498-504. [PMID: 17175020 DOI: 10.1016/j.ijbiomac.2006.11.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/11/2006] [Accepted: 11/20/2006] [Indexed: 11/26/2022]
Abstract
Growth and glycogen production were characterized for Synechocystis sp. strain PCC6803 grown under continuous fluorescent light in four variations of BG-11 medium: either with (G+) or without (G-) 5mM glucose, and with a normal (N+, 1.5 g sodium nitrate/L) or a reduced (N-, 0.084 g sodium nitrate/L) nitrogen concentration. Glucose-supplemented BG-11 with a normal nitrogen concentration (N+G+) produced the highest growth rate and the greatest cell density. Although the maximum cell mass production was observed in the N+G+ medium, the highest glycogen yield (19.0mg/g wet cell mass) was achieved under the glucose-supplemented, nitrogen-limiting condition (N-G+). The addition of glucose enhanced cell growth, while nitrogen limitation apparently directed carbon flux into glycogen accumulation rather than cell growth. Transmission electron microscopic analysis showed that, under nitrogen-limiting conditions (N-G+), glycogen particles accumulated in large amounts and filled the cytosol of the cells. Analysis by high-performance size-exclusion chromatography further revealed that the glycogen produced in N-G+ medium had the longest average branch chain-length (DP10.4) among the conditions tested. When the yield and structure of glycogen were examined in different growth phases, the greatest yield (36.6 mg/g wet cell mass) and the longest branch chain-length (DP10.7) were observed 2 days after the fully grown cells in the N+G+ medium were transferred to the growth restricting (N-G+) medium.
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Affiliation(s)
- Sang-Ho Yoo
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50010, USA.
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Bejar CM, Jin X, Ballicora MA, Preiss J. Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases. J Biol Chem 2006; 281:40473-84. [PMID: 17079236 DOI: 10.1074/jbc.m607088200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ADP-Glc pyrophosphorylase (PPase), a key regulatory enzyme in the biosynthetic pathway of starch and bacterial glycogen, catalyzes the synthesis of ADP-Glc from Glc-1-P and ATP. A homology model of the three-dimensional structure of the Escherichia coli enzyme complexed with ADP-Glc has been generated to study the substrate-binding site in detail. A set of amino acids in the model has been identified to be in close proximity to the glucose moiety of the ADP-Glc ligand. The role of these amino acids (Glu(194), Ser(212), Tyr(216), Asp(239), Phe(240), Trp(274), and Asp(276)) was studied by site-directed mutagenesis through the characterization of the kinetic properties and thermal stability of the designed mutants. All purified alanine mutants had 1 or 2 orders of magnitude lower apparent affinity for Glc-1-P compared with the wild type, indicating that the selected set of amino acids plays an important role in their interaction with the substrate. These amino acids, which are conserved within the ADP-Glc PPase family, were replaced with other residues to investigate the effect of size, hydrophobicity, polarity, aromaticity, or charge on the affinity for Glc-1-P. In this study, the architecture of the Glc-1-P-binding site is characterized. The model overlaps with the Glc-1-P site of other PPases such as Pseudomonas aeruginosa dTDP-Glc PPase and Salmonella typhi CDP-Glc PPase. Therefore, the data reported here may have implications for other members of the nucleotide-diphosphoglucose PPase family.
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Affiliation(s)
- Clarisa Maria Bejar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Bhagwat AA, Tan J, Sharma M, Kothary M, Low S, Tall BD, Bhagwat M. Functional heterogeneity of RpoS in stress tolerance of enterohemorrhagic Escherichia coli strains. Appl Environ Microbiol 2006; 72:4978-86. [PMID: 16820496 PMCID: PMC1489321 DOI: 10.1128/aem.02842-05] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stationary-phase sigma factor (RpoS) regulates many cellular responses to environmental stress conditions such as heat, acid, and alkali shocks. On the other hand, mutations at the rpoS locus have frequently been detected among pathogenic as well as commensal strains of Escherichia coli. The objective of this study was to perform a functional analysis of the RpoS-mediated stress responses of enterohemorrhagic E. coli strains from food-borne outbreaks. E. coli strains belonging to serotypes O157:H7, O111:H11, and O26:H11 exhibited polymorphisms for two phenotypes widely used to monitor rpoS mutations, heat tolerance and glycogen synthesis, as well as for two others, alkali tolerance and adherence to Caco-2 cells. However, these strains synthesized the oxidative acid resistance system through an rpoS-dependent pathway. During the transition from mildly acidic growth conditions (pH 5.5) to alkaline stress (pH 10.2), cell survival was dependent on rpoS functionality. Some strains were able to overcome negative regulation by RpoS and induced higher beta-galactosidase activity without compromising their acid resistance. There were no major differences in the DNA sequences in the rpoS coding regions among the tested strains. The heterogeneity of rpoS-dependent phenotypes observed for stress-related phenotypes was also evident in the Caco-2 cell adherence assay. Wild-type O157:H7 strains with native rpoS were less adherent than rpoS-complemented counterpart strains, suggesting that rpoS functionality is needed. These results show that some pathogenic E. coli strains can maintain their acid tolerance capability while compromising other RpoS-dependent stress responses. Such adaptation processes may have significant impact on a pathogen's survival in food processing environments, as well in the host's stomach and intestine.
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Affiliation(s)
- Arvind A Bhagwat
- Produce Quality and Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Bldg. 002, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA.
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Alonso-Casajús N, Dauvillée D, Viale AM, Muñoz FJ, Baroja-Fernández E, Morán-Zorzano MT, Eydallin G, Ball S, Pozueta-Romero J. Glycogen phosphorylase, the product of the glgP Gene, catalyzes glycogen breakdown by removing glucose units from the nonreducing ends in Escherichia coli. J Bacteriol 2006; 188:5266-72. [PMID: 16816199 PMCID: PMC1539952 DOI: 10.1128/jb.01566-05] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To understand the biological function of bacterial glycogen phosphorylase (GlgP), we have produced and characterized Escherichia coli cells with null or altered glgP expression. glgP deletion mutants (DeltaglgP) totally lacked glycogen phosphorylase activity, indicating that all the enzymatic activity is dependent upon the glgP product. Moderate increases of glycogen phosphorylase activity were accompanied by marked reductions of the intracellular glycogen levels in cells cultured in the presence of glucose. In turn, both glycogen content and rates of glycogen accumulation in DeltaglgP cells were severalfold higher than those of wild-type cells. These defects correlated with the presence of longer external chains in the polysaccharide accumulated by DeltaglgP cells. The overall results thus show that GlgP catalyzes glycogen breakdown and affects glycogen structure by removing glucose units from the polysaccharide outer chains in E. coli.
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Affiliation(s)
- Nora Alonso-Casajús
- Agrobioteknologiako Instituta, Nafarroako Unibertsitate Publikoa and Consejo Superior de Investigaciones Científicas, Mutiloako etorbidea zenbaki gabe, 31192 Mutiloabeti, Nafarroa, Spain
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Abranches J, Candella MM, Wen ZT, Baker HV, Burne RA. Different roles of EIIABMan and EIIGlc in regulation of energy metabolism, biofilm development, and competence in Streptococcus mutans. J Bacteriol 2006; 188:3748-56. [PMID: 16707667 PMCID: PMC1482907 DOI: 10.1128/jb.00169-06] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Accepted: 03/21/2006] [Indexed: 11/20/2022] Open
Abstract
The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is the major carbohydrate transport system in oral streptococci. The mannose-PTS of Streptococcus mutans, which transports mannose and glucose, is involved in carbon catabolite repression (CCR) and regulates the expression of known virulence genes. In this study, we investigated the role of EII(Glc) and EIIAB(Man) in sugar metabolism, gene regulation, biofilm formation, and competence. The results demonstrate that the inactivation of ptsG, encoding a putative EII(Glc), did not lead to major changes in sugar metabolism or affect the phenotypes of interest. However, the loss of EII(Glc) was shown to have a significant impact on the proteome and to affect the expression of a known virulence factor, fructan hydrolase (fruA). JAM1, a mutant strain lacking EIIAB(Man), had an impaired capacity to form biofilms in the presence of glucose and displayed a decreased ability to be transformed with exogenous DNA. Also, the lactose- and cellobiose-PTSs were positively and negatively regulated by EIIAB(Man), respectively. Microarrays were used to investigate the profound phenotypic changes displayed by JAM1, revealing that EIIAB(Man) of S. mutans has a key regulatory role in energy metabolism, possibly by sensing the energy levels of the cells or the carbohydrate availability and, in response, regulating the activity of transcription factors and carbohydrate transporters.
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Affiliation(s)
- Jacqueline Abranches
- Department of Oral Biology, University of Florida College of Dentistry, P.O. Box 100424, Gainesville, FL 32610, USA
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Linebarger CRL, Boehlein SK, Sewell AK, Shaw J, Hannah LC. Heat stability of maize endosperm ADP-glucose pyrophosphorylase is enhanced by insertion of a cysteine in the N terminus of the small subunit. PLANT PHYSIOLOGY 2005; 139:1625-34. [PMID: 16299180 PMCID: PMC1310547 DOI: 10.1104/pp.105.067637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 09/11/2005] [Accepted: 09/13/2005] [Indexed: 05/05/2023]
Abstract
ADP-glucose pyrophosphorylase (AGPase) is a key regulatory enzyme in starch biosynthesis. However, plant AGPases differ in several parameters, including spatial and temporal expression, allosteric regulation, and heat stability. AGPases of cereal endosperms are heat labile, while those in other tissues, such as the potato (Solanum tuberosum) tuber, are heat stable. Sequence comparisons of heat-stable and heat-labile AGPases identified an N-terminal motif unique to heat-stable enzymes. Insertion of this motif into recombinant maize (Zea mays) endosperm AGPase increased the half-life at 58 degrees C more than 70-fold. Km values for physiological substrates were unaffected, although Kcat was doubled. A cysteine within the inserted motif gives rise to small subunit homodimers not found in the wild-type maize enzyme. Placement of this N-terminal motif into a mosaic small subunit containing the N terminus from maize endosperm and the C terminus from potato tuber AGPase increases heat stability more than 300-fold.
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Affiliation(s)
- Carla R Lyerly Linebarger
- Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32610-0245, USA
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Abstract
Escherichia coli and Salmonella enterica serovar Typhimurium exhibit a remarkable versatility in the usage of different sugars as the sole source of carbon and energy, reflecting their ability to make use of the digested meals of mammalia and of the ample offerings in the wild. Degradation of sugars starts with their energy-dependent uptake through the cytoplasmic membrane and is carried on further by specific enzymes in the cytoplasm, destined finally for degradation in central metabolic pathways. As variant as the different sugars are, the biochemical strategies to act on them are few. They include phosphorylation, keto-enol isomerization, oxido/reductions, and aldol cleavage. The catabolic repertoire for using carbohydrate sources is largely the same in E. coli and in serovar Typhimurium. Nonetheless, significant differences are found, even among the strains and substrains of each species. We have grouped the sugars to be discussed according to their first step in metabolism, which is their active transport, and follow their path to glycolysis, catalyzed by the sugar-specific enzymes. We will first discuss the phosphotransferase system (PTS) sugars, then the sugars transported by ATP-binding cassette (ABC) transporters, followed by those that are taken up via proton motive force (PMF)-dependent transporters. We have focused on the catabolism and pathway regulation of hexose and pentose monosaccharides as well as the corresponding sugar alcohols but have also included disaccharides and simple glycosides while excluding polysaccharide catabolism, except for maltodextrins.
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Affiliation(s)
- Christoph Mayer
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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Stubbe J, Tian J, He A, Sinskey AJ, Lawrence AG, Liu P. NONTEMPLATE-DEPENDENT POLYMERIZATION PROCESSES: Polyhydroxyalkanoate Synthases as a Paradigm. Annu Rev Biochem 2005; 74:433-80. [PMID: 15952894 DOI: 10.1146/annurev.biochem.74.082803.133013] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review focuses on nontemplate-dependent polymerases that use water-soluble substrates and convert them into water-insoluble polymers that form granules or inclusions within the cell. The initial part of the review summarizes briefly the current knowledge of polymer formation catalyzed by starch and glycogen synthases, polyphosphate kinase (a polymerase), cyanophycin synthetases, and rubber synthases. Specifically, our current understanding of their mechanisms of initiation, elongation (including granule formation), termination, remodeling, and polymer reutilization will be presented. General underlying principles that govern these types of polymerization reactions will be enumerated as a paradigm for all nontemplate-dependent polymerizations. The bulk of the review then focuses on polyhydroxyalkanoate (PHA) synthases that generate polyoxoesters. These enzymes are of interest as they generate biodegradable polymers. Our current knowledge of PHA production and utilization in vitro and in vivo as well as the contribution of many proteins to these processes will be reviewed.
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Affiliation(s)
- Joanne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Dauvillée D, Kinderf IS, Li Z, Kosar-Hashemi B, Samuel MS, Rampling L, Ball S, Morell MK. Role of the Escherichia coli glgX gene in glycogen metabolism. J Bacteriol 2005; 187:1465-73. [PMID: 15687211 PMCID: PMC545640 DOI: 10.1128/jb.187.4.1465-1473.2005] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A role for the Escherichia coli glgX gene in bacterial glycogen synthesis and/or degradation has been inferred from the sequence homology between the glgX gene and the genes encoding isoamylase-type debranching enzymes; however, experimental evidence or definition of the role of the gene has been lacking. Construction of E. coli strains with defined deletions in the glgX gene is reported here. The results show that the GlgX gene encodes an isoamylase-type debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues. This specificity ensures that GlgX does not generate an extensive futile cycle during glycogen synthesis in which chains with more than four glucose residues are transferred by the branching enzyme. Disruption of glgX leads to overproduction of glycogen containing short external chains. These results suggest that the GlgX protein is predominantly involved in glycogen catabolism by selectively debranching the polysaccharide outer chains that were previously recessed by glycogen phosphorylase.
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Cupp-Vickery JR, Igarashi RY, Meyer CR. Preliminary crystallographic analysis of ADP-glucose pyrophosphorylase from Agrobacterium tumefaciens. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:266-8. [PMID: 16511013 PMCID: PMC1952281 DOI: 10.1107/s1744309105002265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Accepted: 01/20/2005] [Indexed: 11/11/2022]
Abstract
ADP-glucose pyrophosphorylase catalyzes the conversion of glucose-1-phosphate and ATP to ADP-glucose and pyrophosphate, a key regulated step in both bacterial glycogen and plant starch biosynthesis. Crystals of ADP-glucose pyrophosphorylase from Agrobacterium tumefaciens (420 amino acids, 47 kDa) have been obtained by the sitting-drop vapor-diffusion method using lithium sulfate as a precipitant. A complete native X-ray diffraction data set was collected to a resolution of 2.0 A from a single crystal at 100 K. The crystals belong to space group I222, with unit-cell parameters a = 92.03, b = 141.251, c = 423.64 A. To solve the phase problem, a complete anomalous data set was collected from a selenomethionyl derivative. These crystals display one-fifth of the unit-cell volume of the wild-type crystals, with unit-cell parameters a = 85.38, b = 93.79, c = 140.29 A and space group I222.
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Affiliation(s)
- Jill R Cupp-Vickery
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
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Siebers B, Tjaden B, Michalke K, Dörr C, Ahmed H, Zaparty M, Gordon P, Sensen CW, Zibat A, Klenk HP, Schuster SC, Hensel R. Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data. J Bacteriol 2004; 186:2179-94. [PMID: 15028704 PMCID: PMC374391 DOI: 10.1128/jb.186.7.2179-2194.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2003] [Accepted: 11/13/2003] [Indexed: 11/20/2022] Open
Abstract
The hyperthermophilic, facultatively heterotrophic crenarchaeum Thermoproteus tenax was analyzed using a low-coverage shotgun-sequencing approach. A total of 1.81 Mbp (representing 98.5% of the total genome), with an average gap size of 100 bp and 5.3-fold coverage, are reported, giving insights into the genome of T. tenax. Genome analysis and biochemical studies enabled us to reconstruct its central carbohydrate metabolism. T. tenax uses a variant of the reversible Embden-Meyerhof-Parnas (EMP) pathway and two different variants of the Entner-Doudoroff (ED) pathway (a nonphosphorylative variant and a semiphosphorylative variant) for carbohydrate catabolism. For the EMP pathway some new, unexpected enzymes were identified. The semiphosphorylative ED pathway, hitherto supposed to be active only in halophiles, is found in T. tenax. No evidence for a functional pentose phosphate pathway, which is essential for the generation of pentoses and NADPH for anabolic purposes in bacteria and eucarya, is found in T. tenax. Most genes involved in the reversible citric acid cycle were identified, suggesting the presence of a functional oxidative cycle under heterotrophic growth conditions and a reductive cycle for CO2 fixation under autotrophic growth conditions. Almost all genes necessary for glycogen and trehalose metabolism were identified in the T. tenax genome.
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Affiliation(s)
- Bettina Siebers
- Department of Microbiology, Universität Duisburg-Essen, 45117 Essen, Germany.
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Ballicora MA, Iglesias AA, Preiss J. ADP-glucose pyrophosphorylase, a regulatory enzyme for bacterial glycogen synthesis. Microbiol Mol Biol Rev 2003; 67:213-25, table of contents. [PMID: 12794190 PMCID: PMC156471 DOI: 10.1128/mmbr.67.2.213-225.2003] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The accumulation of alpha-1,4-polyglucans is an important strategy to cope with transient starvation conditions in the environment. In bacteria and plants, the synthesis of glycogen and starch occurs by utilizing ADP-glucose as the glucosyl donor for elongation of the alpha-1,4-glucosidic chain. The main regulatory step takes place at the level of ADP-glucose synthesis, a reaction catalyzed by ADP-Glc pyrophosphorylase (PPase). Most of the ADP-Glc PPases are allosterically regulated by intermediates of the major carbon assimilatory pathway in the organism. Based on specificity for activator and inhibitor, classification of ADP-Glc PPases has been expanded into nine distinctive classes. According to predictions of the secondary structure of the ADP-Glc PPases, they seem to have a folding pattern common to other sugar nucleotide pyrophosphorylases. All the ADP-Glc PPases as well as other sugar nucleotide pyrophosphorylases appear to have evolved from a common ancestor, and later, ADP-Glc PPases developed specific regulatory properties, probably by addition of extra domains. Studies of different domains by construction of chimeric ADP-Glc PPases support this hypothesis. In addition to previous chemical modification experiments, the latest random and site-directed mutagenesis experiments with conserved amino acids revealed residues important for catalysis and regulation.
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Affiliation(s)
- Miguel A Ballicora
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Lim WJ, Park SR, Kim MK, An CL, Yun HJ, Hong SY, Kim EJ, Shin EC, Lee SW, Lim YP, Yun HD. Cloning and characterization of the glycogen branching enzyme gene existing in tandem with the glycogen debranching enzyme from Pectobacterium chrysanthemi PY35. Biochem Biophys Res Commun 2003; 300:93-101. [PMID: 12480526 DOI: 10.1016/s0006-291x(02)02763-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The glycogen branching enzyme gene (glgB) from Pectobacterium chrysanthemi PY35 was cloned, sequenced, and expressed in Escherichia coli. The glgB gene consisted of an open reading frame of 2196bp encoding a protein of 731 amino acids (calculated molecular weight of 83,859Da). The glgB gene is upstream of glgX and the ORF starts the ATG initiation codon and ends with the TGA stop codon at 2bp upstream of glgX. The enzyme was 43-69% sequence identical with other glycogen branching enzymes. The enzyme is the most similar to GlgB of E. coli and contained the four regions conserved among the alpha-amylase family. The glycogen branching enzyme (GlgB) was purified and the molecular weight of the enzyme was estimated to be 84kDa by SDS-PAGE. The glycogen branching enzyme was optimally active at pH 7 and 30 degrees C.
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Affiliation(s)
- Woo Jin Lim
- Division of Applied Life Science, Gyeongsang National University, Chinju 660-701, Republic of Korea
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Ball SG, Morell MK. From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. ANNUAL REVIEW OF PLANT BIOLOGY 2003; 54:207-33. [PMID: 14502990 DOI: 10.1146/annurev.arplant.54.031902.134927] [Citation(s) in RCA: 441] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants, green algae, and cyanobacteria synthesize storage polysaccharides by a similar ADPglucose-based pathway. Plant starch metabolism can be distinguished from that of bacterial glycogen by the presence of multiple forms of enzyme activities for each step of the pathway. This multiplicity does not coincide with any functional redundancy, as each form has seemingly acquired a distinctive and conserved role in starch metabolism. Comparisons of phenotypes generated by debranching enzyme-defective mutants in Escherichia coli and plants suggest that enzymes previously thought to be involved in polysaccharide degradation have been recruited during evolution to serve a particular purpose in starch biosynthesis. Speculations have been made that link this recruitment to the appearance of semicrystalline starch in photosynthetic eukaryotes. Besides the common core pathway, other enzymes of malto-oligosaccharide metabolism are required for normal starch metabolism. However, according to the genetic and physiological system under study, these enzymes may have acquired distinctive roles.
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Affiliation(s)
- Steven G Ball
- Laboratoire de Chimie Biologique, UMR 8576 du CNRS, Université des Sciences et Technologies de Lille, Bâtiment C9-Cité Scientifique, France.
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Henrissat B, Deleury E, Coutinho PM. Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria? Trends Genet 2002; 18:437-40. [PMID: 12175798 DOI: 10.1016/s0168-9525(02)02734-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We searched 55 completely sequenced bacterial genomes for glycogen synthesis and degradation enzymes. A significant proportion of these bacteria appears to lack glycogen metabolism capability. Interestingly, these bacteria are parasitic, symbiotic or fastidious (i.e. difficult to culture outside their normal environment). It is suggested that the lack of bacterial glycogen metabolism is a trait associated with parasitic behaviour in bacteria.
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Affiliation(s)
- Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités de Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France.
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Smidansky ED, Clancy M, Meyer FD, Lanning SP, Blake NK, Talbert LE, Giroux MJ. Enhanced ADP-glucose pyrophosphorylase activity in wheat endosperm increases seed yield. Proc Natl Acad Sci U S A 2002; 99:1724-9. [PMID: 11830676 PMCID: PMC122258 DOI: 10.1073/pnas.022635299] [Citation(s) in RCA: 238] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2000] [Accepted: 11/29/2001] [Indexed: 11/18/2022] Open
Abstract
Yield in cereals is a function of seed number and weight; both parameters are largely controlled by seed sink strength. The allosteric enzyme ADP-glucose pyrophosphorylase (AGP) plays a key role in regulating starch biosynthesis in cereal seeds and is likely the most important determinant of seed sink strength. Plant AGPs are heterotetrameric, consisting of two large and two small subunits. We transformed wheat (Triticum aestivum L.) with a modified form of the maize (Zea mays L.) Shrunken2 gene (Sh2r6hs), which encodes an altered AGP large subunit. The altered large subunit gives rise to a maize AGP heterotetramer with decreased sensitivity to its negative allosteric effector, orthophosphate, and more stable interactions between large and small subunits. The Sh2r6hs transgene was still functional after five generations in wheat. Developing seeds from Sh2r6hs transgenic wheat exhibited increased AGP activity in the presence of a range of orthophosphate concentrations in vitro. Transgenic Sh2r6hs wheat lines produced on average 38% more seed weight per plant. Total plant biomass was increased by 31% in Sh2r6hs plants. Results indicate increased availability and utilization of resources in response to enhanced seed sink strength, increasing seed yield, and total plant biomass.
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Affiliation(s)
- Eric D Smidansky
- Department of Plant Sciences, Montana State University, Bozeman, MT 59717, USA
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Jackson DW, Suzuki K, Oakford L, Simecka JW, Hart ME, Romeo T. Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli. J Bacteriol 2002; 184:290-301. [PMID: 11741870 PMCID: PMC134780 DOI: 10.1128/jb.184.1.290-301.2002] [Citation(s) in RCA: 320] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The predominant mode of growth of bacteria in the environment is within sessile, matrix-enclosed communities known as biofilms. Biofilms often complicate chronic and difficult-to-treat infections by protecting bacteria from the immune system, decreasing antibiotic efficacy, and dispersing planktonic cells to distant body sites. While the biology of bacterial biofilms has become a major focus of microbial research, the regulatory mechanisms of biofilm development remain poorly defined and those of dispersal are unknown. Here we establish that the RNA binding global regulatory protein CsrA (carbon storage regulator) of Escherichia coli K-12 serves as both a repressor of biofilm formation and an activator of biofilm dispersal under a variety of culture conditions. Ectopic expression of the E. coli K-12 csrA gene repressed biofilm formation by related bacterial pathogens. A csrA knockout mutation enhanced biofilm formation in E. coli strains that were defective for extracellular, surface, or regulatory factors previously implicated in biofilm formation. In contrast, this csrA mutation did not affect biofilm formation by a glgA (glycogen synthase) knockout mutant. Complementation studies with glg genes provided further genetic evidence that the effects of CsrA on biofilm formation are mediated largely through the regulation of intracellular glycogen biosynthesis and catabolism. Finally, the expression of a chromosomally encoded csrA'-'lacZ translational fusion was dynamically regulated during biofilm formation in a pattern consistent with its role as a repressor. We propose that global regulation of central carbon flux by CsrA is an extremely important feature of E. coli biofilm development.
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Affiliation(s)
- Debra W Jackson
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center at Fort Worth, Fort Worth, Texas 76107-2699, USA
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