1
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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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Akinsemolu A, Onyeaka H. Exploring the Role of Green Microbes in Sustainable Bioproduction of Biodegradable Polymers. Polymers (Basel) 2023; 15:4617. [PMID: 38232039 PMCID: PMC10708544 DOI: 10.3390/polym15234617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 12/02/2023] [Indexed: 01/19/2024] Open
Abstract
Research efforts have shifted to creating biodegradable polymers to offset the harmful environmental impacts associated with the accumulation of non-degradable synthetic polymers in the environment. This review presents a comprehensive examination of the role of green microbes in fostering sustainable bioproduction of these environment-friendly polymers. Green microbes, primarily algae and cyanobacteria, have emerged as promising bio-factories due to their ability to capture carbon dioxide and utilize solar energy efficiently. It further discusses the metabolic pathways harnessed for the synthesis of biopolymers such as polyhydroxyalkanoates (PHAs) and the potential for genetic engineering to augment their production yields. Additionally, the techno-economic feasibility of using green microbes, challenges associated with the up-scaling of biopolymer production, and potential solutions are elaborated upon. With the twin goals of environmental protection and economic viability, green microbes pave the way for a sustainable polymer industry.
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Affiliation(s)
- Adenike Akinsemolu
- Institute of Advanced Studies, University of Birmingham, Birmingham B15 2TT, UK
- Department of Integrated Science, Adeyemi Federal University of Education, Ondo 351101, Nigeria
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
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3
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Chen L, Zhao N, McClements DJ, Hamaker BR, Miao M. Advanced dendritic glucan-derived biomaterials: From molecular structure to versatile applications. Compr Rev Food Sci Food Saf 2023; 22:4107-4146. [PMID: 37350042 DOI: 10.1111/1541-4337.13201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023]
Abstract
There is considerable interest in the development of advanced biomaterials with improved or novel functionality for diversified applications. Dendritic glucans, such as phytoglycogen and glycogen, are abundant biomaterials with highly branched three-dimensional globular architectures, which endow them with unique structural and functional attributes, including small size, large specific surface area, high water solubility, low viscosity, high water retention, and the availability of numerous modifiable surface groups. Dendritic glucans can be synthesized by in vivo biocatalysis reactions using glucosyl-1-phosphate as a substrate, which can be obtained from plant, animal, or microbial sources. They can also be synthesized by in vitro methods using sucrose or starch as a substrate, which may be more suitable for large-scale industrial production. The large numbers of hydroxyl groups on the surfaces of dendritic glucan provide a platform for diverse derivatizations, including nonreducing end, hydroxyl functionalization, molecular degradation, and conjugation modifications. Due to their unique physicochemical and functional attributes, dendritic glucans have been widely applied in the food, pharmaceutical, biomedical, cosmetic, and chemical industries. For instance, they have been used as delivery systems, adsorbents, tissue engineering scaffolds, biosensors, and bioelectronic components. This article reviews progress in the design, synthesis, and application of dendritic glucans over the past several decades.
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Affiliation(s)
- Long Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Ningjing Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - David J McClements
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana, USA
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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4
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Patel HP, Martinez‐Ramirez G, Dobrzynski E, Iglesias AA, Liu D, Ballicora MA. A critical inter-subunit interaction for the transmission of the allosteric signal in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci 2023; 32:e4747. [PMID: 37551561 PMCID: PMC10461462 DOI: 10.1002/pro.4747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
ADP-glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter-subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6-phosphate and pyruvate. Three pairs of distinct subunit-subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning mutagenesis showed that a mutation at the Arg11 position disrupted the activation of the enzyme. Considering the distance of these residues from the allosteric and catalytic sites, we hypothesized that the interaction between Arg11 and Asp141 is critical for allosteric signaling rather than effector binding. To prove our hypothesis, we mutated those two sites (D141A, D141E, D141N, D141R, R11D, and R11K) and performed kinetic and binding analysis. Mutations that altered the charge affected the regulation the most. To prove that the interaction per se (rather than the presence of specific residues) is critical, we partially rescued the R11D protein by introducing a second mutation (R11D/D141R). This could not restore the activator effect on kcat , but it did rescue the effect on substrate affinity. Our results indicate the critical functional role of Arg11 and Asp141 to relay the allosteric signal in this subunit interface.
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Affiliation(s)
- Hiral P. Patel
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Emily Dobrzynski
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Dali Liu
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | - Miguel A. Ballicora
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
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5
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Han X, D'Angelo C, Otamendi A, Cifuente JO, de Astigarraga E, Ochoa-Lizarralde B, Grininger M, Routier FH, Guerin ME, Fuehring J, Etxebeste O, Connell SR. CryoEM analysis of the essential native UDP-glucose pyrophosphorylase from Aspergillus nidulans reveals key conformations for activity regulation and function. mBio 2023; 14:e0041423. [PMID: 37409813 PMCID: PMC10470519 DOI: 10.1128/mbio.00414-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Invasive aspergillosis is one of the most serious clinical invasive fungal infections, resulting in a high case fatality rate among immunocompromised patients. The disease is caused by saprophytic molds in the genus Aspergillus, including Aspergillus fumigatus, the most significant pathogenic species. The fungal cell wall, an essential structure mainly composed of glucan, chitin, galactomannan, and galactosaminogalactan, represents an important target for the development of antifungal drugs. UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) is a central enzyme in the metabolism of carbohydrates that catalyzes the biosynthesis of UDP-glucose, a key precursor of fungal cell wall polysaccharides. Here, we demonstrate that the function of UGP is vital for Aspergillus nidulans (AnUGP). To understand the molecular basis of AnUGP function, we describe a cryoEM structure (global resolution of 3.5 Å for the locally refined subunit and 4 Å for the octameric complex) of a native AnUGP. The structure reveals an octameric architecture with each subunit comprising an N-terminal α-helical domain, a central catalytic glycosyltransferase A-like (GT-A-like) domain, and a C-terminal (CT) left-handed β-helix oligomerization domain. AnUGP displays unprecedented conformational variability between the CT oligomerization domain and the central GT-A-like catalytic domain. In combination with activity measurements and bioinformatics analysis, we unveil the molecular mechanism of substrate recognition and specificity for AnUGP. Altogether, our study not only contributes to understanding the molecular mechanism of catalysis/regulation of an important class of enzymes but also provides the genetic, biochemical, and structural groundwork for the future exploitation of UGP as a potential antifungal target. IMPORTANCE Fungi cause diverse diseases in humans, ranging from allergic syndromes to life-threatening invasive diseases, together affecting more than a billion people worldwide. Increasing drug resistance in Aspergillus species represents an emerging global health threat, making the design of antifungals with novel mechanisms of action a worldwide priority. The cryoEM structure of UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) from the filamentous fungus Aspergillus nidulans reveals an octameric architecture displaying unprecedented conformational variability between the C-terminal oligomerization domain and the central glycosyltransferase A-like catalytic domain in the individual protomers. While the active site and oligomerization interfaces are more highly conserved, these dynamic interfaces include motifs restricted to specific clades of filamentous fungi. Functional study of these motifs could lead to the definition of new targets for antifungals inhibiting UGP activity and, thus, the architecture of the cell wall of filamentous fungal pathogens.
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Affiliation(s)
- Xu Han
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Cecilia D'Angelo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Ainara Otamendi
- Laboratory of Biology, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, UPV/EHU, San Sebastian, Spain
| | - Javier O. Cifuente
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Elisa de Astigarraga
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Borja Ochoa-Lizarralde
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Marcelo E. Guerin
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jana Fuehring
- Institute for Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Oier Etxebeste
- Laboratory of Biology, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, UPV/EHU, San Sebastian, Spain
| | - Sean R. Connell
- Structural Biology of Cellular Machines Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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6
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Sahoo S, Khuswaha GS, Misra N, Suar M. Exploiting AGPase genes and encoded proteins to prioritize development of optimum engineered strains in microalgae towards sustainable biofuel production. World J Microbiol Biotechnol 2023; 39:209. [PMID: 37237168 DOI: 10.1007/s11274-023-03654-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Although ADP glucose pyrophosphorylase (AGPase), with two large subunits (ls) and two small subunits (ss), is a promising knockout target for increasing the neutral lipid content, the details regarding the sequence-structure features and their distribution within metabolic system in microalgae is rather limited. Against this backdrop, a comprehensive genome-wide comparative analysis on 14 sequenced microalgal genomes was performed. For the first time the heterotetrameric structure of the enzyme and the interaction of the catalytic unit with the substrate was also studied. Novel findings of the present study includes: (i) at the DNA level, the genes controlling the ss are more conserved than those controlling the ls; the variation in both the gene groups is mainly due to exon number, exon length and exon phase distribution; (ii) at protein level, the ss genes are more conserved relative to those for ls; (III) three putative key consensus sequences 'LGGGAGTRLYPLTKNRAKPAV', 'WFQGTADAV' and 'ASMGIYVFRKD' were ubiquitously conserved in all the AGPases; (iv) molecular dynamics investigations revealed that the modeled AGPase heterotetrameric structure, from oleaginous algae Chlamydomonas reinharditii, was completely stable in real time environment; (v) The binding interfaces of catalytic unit, ssAGPase, from C. reinharditii with α-D-glucose 1-phosphate (αGP) was also analyzed. The results of the present study have provided system-based insights into the structure-function of the genes and encoded proteins, which provided clues for exploitation of variability in these genes that, could be further utilized to design site-specific mutagenic experiments for engineering of microalgal strains towards sustainable development of biofuel.
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Affiliation(s)
- Susrita Sahoo
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Gajraj Singh Khuswaha
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, 751024, India
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India.
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, 751024, India.
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India.
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, 751024, India.
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7
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Alghamdi MA, Hussien RA, Zheng Y, Patel HP, Asencion Diez MD, A Iglesias A, Liu D, Ballicora MA. Site-directed mutagenesis of Serine-72 reveals the location of the fructose 6-phosphate regulatory site of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci 2022; 31:e4376. [PMID: 35762722 PMCID: PMC9234290 DOI: 10.1002/pro.4376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/27/2022] [Accepted: 06/05/2022] [Indexed: 11/10/2022]
Abstract
The allosteric regulation of ADP-glucose pyrophosphorylase is critical for the biosynthesis of glycogen in bacteria and starch in plants. The enzyme from Agrobacterium tumefaciens is activated by fructose 6-phosphate (Fru6P) and pyruvate (Pyr). The Pyr site has been recently found, but the site where Fru6P binds has remained unknown. We hypothesize that a sulfate ion previously found in the crystal structure reveals a part of the regulatory site mimicking the presence of the phosphoryl moiety of the activator Fru6P. Ser72 interacts with this sulfate ion and, if the hypothesis is correct, Ser72 would affect the interaction with Fru6P and activation of the enzyme. Here, we report structural, binding, and kinetic analysis of Ser72 mutants of the A. tumefaciens ADP-glucose pyrophosphorylase. By X-ray crystallography, we found that when Ser72 was replaced by Asp or Glu side chain carboxylates protruded into the sulfate-binding pocket. They would present a strong steric and electrostatic hindrance to the phosphoryl moiety of Fru6P, while being remote from the Pyr site. In agreement, we found that Fru6P could not activate or bind to S72E or S72D mutants, whereas Pyr was still an effective activator. These mutants also blocked the binding of the inhibitor AMP. This could potentially have biotechnological importance in obtaining enzyme forms insensitive to inhibition. Other mutations in this position (Ala, Cys, and Trp) confirmed the importance of Ser72 in regulation. We propose that the ADP-glucose pyrophosphorylase from A. tumefaciens have two distinct sites for Fru6P and Pyr working in tandem to regulate glycogen biosynthesis.
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Affiliation(s)
- Mashael A Alghamdi
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.,Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Rania A Hussien
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.,Department of Chemistry, Al Baha University, Al Baha, Saudi Arabia
| | - Yuanzhang Zheng
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
| | - Hiral P Patel
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
| | - Matías D Asencion Diez
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.,Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Paraje "El Pozo", CCT-Santa Fe, Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Paraje "El Pozo", CCT-Santa Fe, Santa Fe, Argentina
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
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8
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Li H, Zhang Z, Liu J, Guo Z, Chen M, Li B, Xue H, Ji S, Li H, Qin L, Zhu L, Wang J, Zhu H. Identification of the Key Enzymes in WL Gum Biosynthesis and Critical Composition in Viscosity Control. Front Bioeng Biotechnol 2022; 10:918687. [PMID: 35711643 PMCID: PMC9197254 DOI: 10.3389/fbioe.2022.918687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
As an important microbial exopolysaccharide, the sphingan WL gum could be widely used in petroleum, food, and many other fields. However, its lower production is still limiting its wider application. Therefore, to gain insights into the bottlenecks of WL gum production by identifying the key enzymes in the WL gum biosynthesis pathway, more than 20 genes were over-expressed in Sphingomonas sp. WG and their effects on WL gum production and structure were investigated. Compared to the control strain, the WL gum production of welB over-expression strain was increased by 19.0 and 21.0% at 36 and 84 h, respectively. The WL gum production of both atrB and atrD over-expression strains reached 47 g/L, which was approximately 34.5% higher than that of the control strain at 36 h. Therefore, WelB, AtrB, and AtrD may be the key enzymes in WL production. Interestingly, the broth viscosity of most over-expression strains decreased, especially the welJ over-expression strain whose viscosity decreased by 99.3% at 84 h. Polysaccharides' structural features were investigated to find the critical components in viscosity control. The uronic acid content and total sugar content was affected by only a few genes, therefore, uronic acid and total sugar content may be not the key composition. In comparison, the acetyl degrees were enhanced by over-expression of most genes, which meant that acetyl content may be the critical factor and negatively correlated with the apparent viscosity of WL gum. This work provides useful information on the understanding of the bottlenecks of WL gum biosynthesis and will be helpful for the construction of high WL gum-yielding strains and rheological property controlling in different industries.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zaimei Zhang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Jianlin Liu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zhongrui Guo
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Mengqi Chen
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Benchao Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Han Xue
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Sixue Ji
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Hang Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Lijian Qin
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Ling Zhu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Hu Zhu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, China.,Engineering Research Center of Industrial Biocatalysis, Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, China.,College of Chemical Engineering and Materials Science, Quanzhou Normal University, Quanzhou, China
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9
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Figueroa CM, Asencion Diez MD, Ballicora MA, Iglesias AA. Structure, function, and evolution of plant ADP-glucose pyrophosphorylase. PLANT MOLECULAR BIOLOGY 2022; 108:307-323. [PMID: 35006475 DOI: 10.1007/s11103-021-01235-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023]
Abstract
This review outlines research performed in the last two decades on the structural, kinetic, regulatory and evolutionary aspects of ADP-glucose pyrophosphorylase, the regulatory enzyme for starch biosynthesis. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the pathway of glycogen and starch synthesis in bacteria and plants, respectively. Plant ADP-Glc PPase is a heterotetramer allosterically regulated by metabolites and post-translational modifications. In this review, we focus on the three-dimensional structure of the plant enzyme, the amino acids that bind the regulatory molecules, and the regions involved in transmitting the allosteric signal to the catalytic site. We provide a model for the evolution of the small and large subunits, which produce heterotetramers with distinct catalytic and regulatory properties. Additionally, we review the various post-translational modifications observed in ADP-Glc PPases from different species and tissues. Finally, we discuss the subcellular localization of the enzyme found in grain endosperm from grasses, such as maize and rice. Overall, this work brings together research performed in the last two decades to better understand the multiple mechanisms involved in the regulation of ADP-Glc PPase. The rational modification of this enzyme could improve the yield and resilience of economically important crops, which is particularly important in the current scenario of climate change and food shortage.
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Affiliation(s)
- Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA.
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina.
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10
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Joosten RP, Nicholls RA, Agirre J. Towards consistency in geometry restraints for carbohydrates in the pyranose form: modern dictionary generators reviewed. Curr Med Chem 2021; 29:1193-1207. [PMID: 34477506 PMCID: PMC7612510 DOI: 10.2174/0929867328666210902140754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/03/2021] [Accepted: 08/07/2021] [Indexed: 11/23/2022]
Abstract
Macromolecular restrained refinement is nowadays the most used method for improving the agreement between an atomic structural model and experimental data. Restraint dictionaries, a key tool behind the success of the method, allow fine-tuning geometric properties such as distances and angles between atoms beyond simplistic expectations. Dictionary generators can provide restraint target estimates derived from different sources, from fully theoretical to experimental and any combination in between. Carbohydrates are stereochemically complex biomolecules and, in their pyranose form, have clear conformational preferences. As such, they pose unique problems to dictionary generators and in the course of this study, require special attention from software developers. Functional differences between restraint generators will be discussed, as well as the process of achieving consistent results with different software designs. The study will conclude a set of practical considerations, as well as recommendations for the generation of new restraint dictionaries, using the improved software alternatives discussed.
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Affiliation(s)
- Robbie P Joosten
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam. Netherlands
| | - Robert A Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH. United Kingdom
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD. United Kingdom
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11
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Sueda R, Yoshida K, Onodera M, Fukui T, Yatsunami R, Nakamura S. Characterization of a GlgC homolog from extremely halophilic archaeon Haloarcula japonica. Biosci Biotechnol Biochem 2021; 85:1441-1447. [PMID: 33749776 DOI: 10.1093/bbb/zbab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/16/2021] [Indexed: 11/12/2022]
Abstract
Glycogen synthesis in bacteria is mainly organized by the products of glgB, glgC, and glgA genes comprising the widely known glg operon. On the genome of extremely halophilic archaeon Haloarcula japonica, there was a gene cluster analogous to the bacterial glg operon. In this study, we focused on a GlgC homolog of Ha. japonica, and its recombinant enzyme was prepared and characterized. The enzyme showed highest activity toward GTP and glucose-1-phosphate as substrates in the presence of 2.6 m KCl and predicted to be work as "GDP-glucose pyrophosphorylase" in Ha. japonica.
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Affiliation(s)
- Rin Sueda
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Kento Yoshida
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Masahiko Onodera
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Rie Yatsunami
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.,National Institute of Technology, Numazu College, Numazu, Shizuoka, Japan
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12
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Liu Z, Mukherjee M, Wu Y, Huang Q, Cai P. Increased particle size of goethite enhances the antibacterial effect on human pathogen Escherichia coli O157:H7: A Raman spectroscopic study. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124174. [PMID: 33144022 DOI: 10.1016/j.jhazmat.2020.124174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
The persistence of Escherichia coli O157:H7 in soil is one of the most common causes of the food-borne outbreaks. Nano-sized iron oxide minerals in soil, especially goethite, have been found to reduce bacterial viability, which helps to control the spread of human pathogens. However, little is known about the antibacterial effects of iron oxides with different particle sizes. Our result revealed that the micro-sized goethite exhibited a more effective antibacterial activity against E. coli O157:H7 than the nano-sized goethite. The underlying antibacterial mechanisms were further investigated via single-cell Raman microspectroscopy. The exposure to nano-sized goethite increased the levels of ribonucleoside-related substances, phenylalanine and adenosine 5'-triphosphate, while decreased those of glycogen, protein and lipopolysaccharide & outer membrane porins (LPS & OMPs). Meanwhile, micro-sized goethite triggered less variation in ribonucleoside-related substances and induced more reduction in LPS & OMPs. Therefore, the antibacterial effects of nano-sized goethite were mediated by both ROS-dependent RNA damage and cell membrane destruction, whereas micro-sized goethite induced severer membrane damage and less ROS-dependent oxidative stress. This work demonstrates the role of particle sizes in antibacterial effects of iron oxides and provides implications for the pathogen control in soil.
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Affiliation(s)
- Zhourui Liu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate School and School of Civil and Environmental Engineering, Nanyang Technological University, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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13
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Cifuente JO, Comino N, D'Angelo C, Marina A, Gil-Carton D, Albesa-Jové D, Guerin ME. The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM. Curr Res Struct Biol 2020; 2:89-103. [PMID: 34235472 PMCID: PMC8244506 DOI: 10.1016/j.crstbi.2020.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 11/10/2022] Open
Abstract
Glycogen and starch are the major carbon and energy reserve polysaccharides in nature, providing living organisms with a survival advantage. The evolution of the enzymatic machinery responsible for the biosynthesis and degradation of such polysaccharides, led the development of mechanisms to control the assembly and disassembly rate, to store and recover glucose according to cell energy demands. The tetrameric enzyme ADP-glucose pyrophosphorylase (AGPase) catalyzes and regulates the initial step in the biosynthesis of both α-polyglucans. AGPase displays cooperativity and allosteric regulation by sensing metabolites from the cell energy flux. The understanding of the allosteric signal transduction mechanisms in AGPase arises as a long-standing challenge. In this work, we disclose the cryoEM structures of the paradigmatic homotetrameric AGPase from Escherichia coli (EcAGPase), in complex with either positive or negative physiological allosteric regulators, fructose-1,6-bisphosphate (FBP) and AMP respectively, both at 3.0 Å resolution. Strikingly, the structures reveal that FBP binds deeply into the allosteric cleft and overlaps the AMP site. As a consequence, FBP promotes a concerted conformational switch of a regulatory loop, RL2, from a "locked" to a "free" state, modulating ATP binding and activating the enzyme. This notion is strongly supported by our complementary biophysical and bioinformatics evidence, and a careful analysis of vast enzyme kinetics data on single-point mutants of EcAGPase. The cryoEM structures uncover the residue interaction networks (RIN) between the allosteric and the catalytic components of the enzyme, providing unique details on how the signaling information is transmitted across the tetramer, from which cooperativity emerges. Altogether, the conformational states visualized by cryoEM reveal the regulatory mechanism of EcAGPase, laying the foundations to understand the allosteric control of bacterial glycogen biosynthesis at the molecular level of detail.
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Key Words
- AGPase, ADP-glucose pyrophosphorylase
- AMP, adenosine 5′-monophosphate
- ATP, adenosine 5′-triphosphate
- EcAGPase, AGPase from E. coli
- Enzyme allosterism
- FBP, fructose 1,6-bisphosphate
- G1P, α-d-glucose-1-phosphate
- GBE, glycogen branching enzyme
- GDE, glycogen debranching enzyme
- GP, glycogen phosphorylase
- GS, glycogen synthase
- GTA-like, glycosyltransferase-A like domain
- Glycogen biosynthesis
- Glycogen regulation
- LβH, left-handed β-helix domain
- Nucleotide sugar biosynthesis
- PPi, pyrophosphate
- RIN, residue interaction network
- SM, sensory motif
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Affiliation(s)
- Javier O. Cifuente
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Cecilia D'Angelo
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Alberto Marina
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Gil-Carton
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Albesa-Jové
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Marcelo E. Guerin
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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14
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Bhayani JA, Hill BL, Sharma A, Iglesias AA, Olsen KW, Ballicora MA. Mapping of a Regulatory Site of the Escherichia coli ADP-Glucose Pyrophosphorylase. Front Mol Biosci 2019; 6:89. [PMID: 31608288 PMCID: PMC6773804 DOI: 10.3389/fmolb.2019.00089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/06/2019] [Indexed: 11/13/2022] Open
Abstract
The enzyme ADP-glucose pyrophosphorylase (ADP-Glc PPase) controls the biosynthesis of glycogen in bacteria and starch in plants. It is regulated by various activators in different organisms according to their metabolic characteristics. In Escherichia coli, the major allosteric activator is fructose 1,6-bisphosphate (FBP). Other potent activator analogs include 1,6-hexanediol bisphosphate (HBP) and pyridoxal 5'-phosphate (PLP). Recently, a crystal structure with FBP bound was reported (PDB ID: 5L6S). However, it is possible that the FBP site found is not directly responsible for the activation of the enzyme. We hypothesized FBP activates by binding one of its phosphate groups to another site ("P1") in which a sulfate molecule was observed. In the E. coli enzyme, Arg40, Arg52, and Arg386 are part of this "P1" pocket and tightly complex this sulfate, which is also present in the crystal structures of ADP-Glc PPases from Agrobacterium tumefaciens and Solanum tuberosum. To test this hypothesis, we modeled alternative binding conformations of FBP, HBP, and PLP into "P1." In addition, we performed a scanning mutagenesis of Arg residues near potential phosphate binding sites ("P1," "P2," "P3"). We found that Arg40 and Arg52 are essential for FBP and PLP binding and activation. In addition, mutation of Arg386 to Ala decreased the apparent affinity for the activators more than 35-fold. We propose that the activator binds at this "P1" pocket, as well as "P2." Arg40 and Arg52 are highly conserved residues and they may be a common feature to complex the phosphate moiety of different sugar phosphate activators in the ADP-Glc PPase family.
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Affiliation(s)
- Jaina A. Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Benjamin L. Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Anisha Sharma
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICET, Santa Fe, Argentina
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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15
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Mir DA, Balamurugan K. In vitro and in vivo efficacy of Caenorhabditis elegans recombinant antimicrobial protein against Gram-negative bacteria. BIOFOULING 2019; 35:900-921. [PMID: 31617758 DOI: 10.1080/08927014.2019.1675048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Antimicrobial peptides (AMPs) are short, positively charged host defense peptides, found in various life forms from microorganisms to humans. AMPs are gaining more attention as substitutes for antibiotics in order to combat the risk posed by multi-drug- resistant pathogens. The nematode Caenorhabditis elegans relies solely on its innate immune defense to cope with its challenging life-style. Bacterial infection in C. elegans leads to induction of antimicrobial proteins, defensins, nemapores, cecropins, and neuropeptide-like proteins, which act to limit bacterial proliferation. This study reports how the C. elegans recombinant antibacterial factor (ABF-1) rapidly inhibited bacterial growth (Salmonella Typhi, Klebsiella pneumonia, Shigella sonnei and Vibrio alginolyticus). The ABF-1 exposure on S. Typhi, showed differential regulation in cell-cycle, DNA repair mechanism, membrane stability, and stress related proteins. The exogenous supply of ABF-1 protein has extended C. elegans survival by reducing the bacterial colony forming units on the nematode intestine. Together, these findings indicate the valuable and potential therapeutic applications of ABF-1 protein as antimicrobial agents against intracellular pathogens.
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16
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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: 18] [Impact Index Per Article: 3.6] [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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17
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The Mycobacterium tuberculosis capsule: a cell structure with key implications in pathogenesis. Biochem J 2019; 476:1995-2016. [PMID: 31320388 PMCID: PMC6698057 DOI: 10.1042/bcj20190324] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/17/2023]
Abstract
Bacterial capsules have evolved to be at the forefront of the cell envelope, making them an essential element of bacterial biology. Efforts to understand the Mycobacterium tuberculosis (Mtb) capsule began more than 60 years ago, but the relatively recent development of mycobacterial genetics combined with improved chemical and immunological tools have revealed a more refined view of capsule molecular composition. A glycogen-like α-glucan is the major constituent of the capsule, with lower amounts of arabinomannan and mannan, proteins and lipids. The major Mtb capsular components mediate interactions with phagocytes that favor bacterial survival. Vaccination approaches targeting the mycobacterial capsule have proven successful in controlling bacterial replication. Although the Mtb capsule is composed of polysaccharides of relatively low complexity, the concept of antigenic variability associated with this structure has been suggested by some studies. Understanding how Mtb shapes its envelope during its life cycle is key to developing anti-infective strategies targeting this structure at the host-pathogen interface.
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18
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Liu Q, Liu HC, Zhou YG, Xin YH. Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers. Front Microbiol 2019; 10:1069. [PMID: 31178833 PMCID: PMC6538692 DOI: 10.3389/fmicb.2019.01069] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Numerous mountain glaciers located on the Tibetan Plateau are inhabited by abundant microorganisms. The microorganisms on the glacier surface are exposed to the cold, barren, and high-ultraviolet radiation environments. Although the microbial community composition on glaciers has been revealed by high-throughput sequencing, little is known about the microevolution and adaptive strategy of certain bacterial populations. In this study, we used a polyphasic approach to determine the taxonomic status of 11 psychrophilic Flavobacterium strains isolated from glaciers on the Tibetan Plateau and performed a comparative genomic analysis. The phylogenetic tree based on the concatenated single-copy gene sequences showed the 11 strains clustered together, forming a distinct and novel clade in the genus Flavobacterium. The average nucleotide identity (ANI) values among these strains were higher than 96%. However, the values much lower than 90% between them and related species indicated that they represent a novel species and the name Flavobacterium bomense sp. nov. is proposed. The core and accessory genomes of strains in this new Flavobacterium species showed diverse distinct patterns of gene content and metabolism pathway. In order to infer the driving evolutionary forces of the core genomes, homologous recombination was found to contribute twice as much to nucleotide substitutions as mutations. A series of genes encoding proteins with known or predicted roles in cold adaptation were found in their genomes, for example, cold-shock protein, proteorhodopsin, osmoprotection, and membrane-related proteins. A comparative analysis of the group with optimal growth temperature (OGT) ≤ 20°C and the group with OGT > 20°C of the 32 Flavobacterium type strains and 11 new strains revealed multiple amino acid substitutions, including the decrease of the proline and glutamine content and the increase of the methionine and isoleucine content in the group with OGT ≤ 20°C, which may contribute to increased protein flexibility at low temperatures. Thus, this study discovered a novel Flavobacterium species in glaciers, which has high intraspecific diversity and multiple adaptation mechanisms that enable them to cope and thrive in extreme habitats.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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19
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Hill BL, Mascarenhas R, Patel HP, Asencion Diez MD, Wu R, Iglesias AA, Liu D, Ballicora MA. Structural analysis reveals a pyruvate-binding activator site in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. J Biol Chem 2019; 294:1338-1348. [PMID: 30401744 DOI: 10.1074/jbc.ra118.004246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/21/2018] [Indexed: 11/06/2022] Open
Abstract
The pathways for biosynthesis of glycogen in bacteria and starch in plants are evolutionarily and biochemically related. They are regulated primarily by ADP-glucose pyrophosphorylase, which evolved to satisfy metabolic requirements of a particular organism. Despite the importance of these two pathways, little is known about the mechanism that controls pyrophosphorylase activity or the location of its allosteric sites. Here, we report pyruvate-bound crystal structures of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens, identifying a previously elusive activator site for the enzyme. We found that the tetrameric enzyme binds two molecules of pyruvate in a planar conformation. Each binding site is located in a crevice between the C-terminal domains of two subunits where they stack via a distinct β-helix region. Pyruvate interacts with the side chain of Lys-43 and with the peptide backbone of Ser-328 and Gly-329 from both subunits. These structural insights led to the design of two variants with altered regulatory properties. In one variant (K43A), the allosteric effect was absent, whereas in the other (G329D), the introduced Asp mimicked the presence of pyruvate. The latter generated an enzyme that was preactivated and insensitive to further activation by pyruvate. Our study furnishes a deeper understanding of how glycogen biosynthesis is regulated in bacteria and the mechanism by which transgenic plants increased their starch production. These insights will facilitate rational approaches to enzyme engineering for starch production in crops of agricultural interest and will promote further study of allosteric signal transmission and molecular evolution in this important enzyme family.
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Affiliation(s)
- Benjamin L Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Romila Mascarenhas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Hiral P Patel
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Matías D Asencion Diez
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660; Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral-Consejo Nacional de Investigaciones Científicas y Técnicas (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB) Paraje "El Pozo," Centro Científico Tecnológico (CCT)-Santa Fe, Colectora Ruta Nacional, 168 km 0, 3000 Santa Fe, Argentina
| | - Rui Wu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral-Consejo Nacional de Investigaciones Científicas y Técnicas (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB) Paraje "El Pozo," Centro Científico Tecnológico (CCT)-Santa Fe, Colectora Ruta Nacional, 168 km 0, 3000 Santa Fe, Argentina
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660.
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20
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Ebrecht AC, Solamen L, Hill BL, Iglesias AA, Olsen KW, Ballicora MA. Allosteric Control of Substrate Specificity of the Escherichia coli ADP-Glucose Pyrophosphorylase. Front Chem 2017; 5:41. [PMID: 28674689 PMCID: PMC5474683 DOI: 10.3389/fchem.2017.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/07/2017] [Indexed: 11/29/2022] Open
Abstract
The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism toward the synthesis of reserve polysaccharides. Here, we show that the allosteric activator fructose-1,6-bisphosphate plays a role in such selection by increasing the catalytic efficiency of the enzyme toward the use of ATP rather than other nucleotides. In the presence of fructose-1,6-bisphosphate, the kcat/S0.5 for ATP was near ~600-fold higher that other nucleotides, whereas in the absence of activator was only ~3-fold higher. We propose that the allosteric regulation of certain enzymes is an evolutionary mechanism of adaptation for the selection of specific substrates.
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Affiliation(s)
- Ana C Ebrecht
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States.,Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICETSanta Fe, Argentina
| | - Ligin Solamen
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| | - Benjamin L Hill
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICETSanta Fe, Argentina
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
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21
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Comino N, Cifuente JO, Marina A, Orrantia A, Eguskiza A, Guerin ME. Mechanistic insights into the allosteric regulation of bacterial ADP-glucose pyrophosphorylases. J Biol Chem 2017; 292:6255-6268. [PMID: 28223362 DOI: 10.1074/jbc.m116.773408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Indexed: 11/06/2022] Open
Abstract
ADP-glucose pyrophosphorylase (AGPase) controls bacterial glycogen and plant starch biosynthetic pathways, the most common carbon storage polysaccharides in nature. AGPase activity is allosterically regulated by a series of metabolites in the energetic flux within the cell. Very recently, we reported the first crystal structures of the paradigmatic AGPase from Escherichia coli (EcAGPase) in complex with its preferred physiological negative and positive allosteric regulators, adenosine 5'-monophosphate (AMP) and fructose 1,6-bisphosphate (FBP), respectively. However, understanding the molecular mechanism by which AMP and FBP allosterically modulates EcAGPase enzymatic activity still remains enigmatic. Here we found that single point mutations of key residues in the AMP-binding site decrease its inhibitory effect but also clearly abolish the overall AMP-mediated stabilization effect in wild-type EcAGPase. Single point mutations of key residues for FBP binding did not revert the AMP-mediated stabilization. Strikingly, an EcAGPase-R130A mutant displayed a dramatic increase in activity when compared with wild-type EcAGPase, and this increase correlated with a significant increment of glycogen content in vivo The crystal structure of EcAGPase-R130A revealed unprecedented conformational changes in structural elements involved in the allosteric signal transmission. Altogether, we propose a model in which the positive and negative energy reporters regulate AGPase catalytic activity via intra- and interprotomer cross-talk, with a "sensory motif" and two loops, RL1 and RL2, flanking the ATP-binding site playing a significant role. The information reported herein provides exciting possibilities for industrial/biotechnological applications.
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Affiliation(s)
- Natalia Comino
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Javier O Cifuente
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alberto Marina
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Ane Orrantia
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Ander Eguskiza
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Marcelo E Guerin
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain, .,Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, 48940 Bizkaia, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Leioa, 48940 Bizkaia, Spain, and.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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