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Identification of the galactitol dehydrogenase, LadB, that is part of the oxido-reductive d-galactose catabolic pathway in Aspergillus niger. Fungal Genet Biol 2012; 49:152-9. [DOI: 10.1016/j.fgb.2011.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/11/2011] [Accepted: 11/14/2011] [Indexed: 11/22/2022]
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252
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Siow RS, Teo SS, Ho WY, Shukor MYA, Phang SM, Ho CL. MOLECULAR CLONING AND BIOCHEMICAL CHARACTERIZATION OF GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE FROM GRACILARIA CHANGII (RHODOPHYTA)(1). JOURNAL OF PHYCOLOGY 2012; 48:155-62. [PMID: 27009660 DOI: 10.1111/j.1529-8817.2011.01105.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Galactose-1-phosphate uridylyltransferase (GALT) catalyzes the reversible conversion of glucose-1-phosphate and UDP-galactose to galactose-1-phosphate and UDP-glucose. This enzyme is also responsible for one of the biochemical steps that produce the precursors of agar and agarose. In this study, we report the molecular cloning and sequence analyses of a cDNA encoding GALT, from Gracilaria changii (B. M. Xia et I. A. Abbott) I. A. Abbott, J. Zhang et B. M. Xia, which constitutes a genus of seaweeds that supply more than 60% of the world's agar and agarose. We have subcloned this cDNA into a bacterial expression cloning vector and characterized the enzyme activities of its recombinant proteins in vitro. The GcGALT gene was shown to be up-regulated by salinity stresses. The abundance of transcripts encoding GcGALT was the highest in G. changii, followed by Gracilaria edulis and Gracilaria salicornia in a descending order, corresponding to their respective agar contents. Our findings indicated that GALT could be one of the components that determines the agar yield in Gracilaria species.
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Affiliation(s)
- Rouh-San Siow
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaInstitute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, MalaysiaFaculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
| | - Swee-Sen Teo
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaInstitute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, MalaysiaFaculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
| | - Wan-Yong Ho
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaInstitute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, MalaysiaFaculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
| | - Mohd Yunus Abd Shukor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaInstitute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, MalaysiaFaculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
| | - Siew-Moi Phang
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaInstitute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, MalaysiaFaculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
| | - Chai-Ling Ho
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaInstitute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, MalaysiaFaculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
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253
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Seiboth B, Herold S, Kubicek CP. Metabolic engineering of inducer formation for cellulase and hemicellulase gene expression in Trichoderma reesei. Subcell Biochem 2012; 64:367-90. [PMID: 23080260 DOI: 10.1007/978-94-007-5055-5_18] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The filamentous fungus T. reeseiis today a paradigm for the commercial scale production of different plant cell wall degrading enzymes mainly cellulases and hemicellulases. Its enzymes have a long history of safe use in industry and well established applications are found within the pulp, paper, food, feed or textile processing industries. However, when these enzymes are to be used for the saccharification of cellulosic plant biomass to simple sugars which can be further converted to biofuels or other biorefinery products, and thus compete with chemicals produced from fossil sources, additional efforts are needed to reduce costs and maximize yield and efficiency of the produced enzyme mixtures. One approach to this end is the use of genetic engineering to manipulate the biochemical and regulatory pathways that operate during enzyme production and control enzyme yield. This review aims at a description of the state of art in this area.
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Affiliation(s)
- Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, 166-5, A-1060, Vienna, Austria
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254
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Boutureira O, Bernardes GJL, Fernández-González M, Anthony DC, Davis BG. Selenenylsulfide-Linked Homogeneous Glycopeptides and Glycoproteins: Synthesis of Human “Hepatic Se Metabolite A”. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106658] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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255
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Boutureira O, Bernardes GJL, Fernández-González M, Anthony DC, Davis BG. Selenenylsulfide-Linked Homogeneous Glycopeptides and Glycoproteins: Synthesis of Human “Hepatic Se Metabolite A”. Angew Chem Int Ed Engl 2011; 51:1432-6. [DOI: 10.1002/anie.201106658] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Indexed: 12/22/2022]
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256
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Sen M, Shah B, Rakshit S, Singh V, Padmanabhan B, Ponnusamy M, Pari K, Vishwakarma R, Nandi D, Sadhale PP. UDP-glucose 4, 6-dehydratase activity plays an important role in maintaining cell wall integrity and virulence of Candida albicans. PLoS Pathog 2011; 7:e1002384. [PMID: 22114559 PMCID: PMC3219719 DOI: 10.1371/journal.ppat.1002384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 10/01/2011] [Indexed: 11/18/2022] Open
Abstract
Candida albicans, a human fungal pathogen, undergoes morphogenetic changes that are associated with virulence. We report here that GAL102 in C. albicans encodes a homolog of dTDP-glucose 4,6-dehydratase, an enzyme that affects cell wall properties as well as virulence of many pathogenic bacteria. We found that GAL102 deletion leads to greater sensitivity to antifungal drugs and cell wall destabilizing agents like Calcofluor white and Congo red. The mutant also formed biofilms consisting mainly of hyphal cells that show less turgor. The NMR analysis of cell wall mannans of gal102 deletion strain revealed that a major constituent of mannan is missing and the phosphomannan component known to affect virulence is greatly reduced. We also observed that there was a substantial reduction in the expression of genes involved in biofilm formation but increase in the expression of genes encoding glycosylphosphatidylinositol-anchored proteins in the mutant. These, along with altered mannosylation of cell wall proteins together might be responsible for multiple phenotypes displayed by the mutant. Finally, the mutant was unable to grow in the presence of resident peritoneal macrophages and elicited a weak pro-inflammatory cytokine response in vitro. Similarly, this mutant elicited a poor serum pro-inflammatory cytokine response as judged by IFNγ and TNFα levels and showed reduced virulence in a mouse model of systemic candidiasis. Importantly, an Ala substitution for a conserved Lys residue in the active site motif YXXXK, that abrogates the enzyme activity also showed reduced virulence and increased filamentation similar to the gal102 deletion strain. Since inactivating the enzyme encoded by GAL102 makes the cells sensitive to antifungal drugs and reduces its virulence, it can serve as a potential drug target in combination therapies for C. albicans and related pathogens.
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Affiliation(s)
- Manimala Sen
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Bhavin Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Srabanti Rakshit
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vijender Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Bhavna Padmanabhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | | | | | | | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Parag P. Sadhale
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- * E-mail:
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257
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N-acetylgalactosamine Kinase: A Naturally Promiscuous Small Molecule Kinase. Appl Biochem Biotechnol 2011; 166:57-63. [DOI: 10.1007/s12010-011-9403-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/26/2011] [Indexed: 10/17/2022]
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258
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Inoue K, Nishimoto M, Kitaoka M. One-pot enzymatic production of 2-acetamido-2-deoxy-D-galactose (GalNAc) from 2-acetamido-2-deoxy-D-glucose (GlcNAc). Carbohydr Res 2011; 346:2432-6. [PMID: 21955790 DOI: 10.1016/j.carres.2011.08.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/31/2011] [Accepted: 08/31/2011] [Indexed: 10/17/2022]
Abstract
2-Acetamido-2-deoxy-D-galactose (GalNAc) is a common monosaccharide found in biologically functional sugar chains, but its availability is often limited due to the lack of abundant natural sources. In order to produce GalNAc from abundantly available sugars, 2-acetamido-2-deoxy-D-glucose (GlcNAc) was converted to GalNAc by a one-pot reaction using three enzymes involved in the galacto-N-biose/lacto-N-biose I pathway of bifidobacteria. Starting the reaction with 600 mM GlcNAc, 170 mM GalNAc was produced at equilibrium in the presence of catalytic amounts of ATP and UDP-Glc under optimized conditions. GalNAc was separated from GlcNAc using water-eluting cation-exchange chromatography with a commonly available cation-exchange resin.
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Affiliation(s)
- Kousuke Inoue
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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259
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Jun H, Kieselbach T, Jönsson LJ. Enzyme production by filamentous fungi: analysis of the secretome of Trichoderma reesei grown on unconventional carbon source. Microb Cell Fact 2011; 10:68. [PMID: 21861877 PMCID: PMC3179704 DOI: 10.1186/1475-2859-10-68] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/23/2011] [Indexed: 12/17/2022] Open
Abstract
Background Spent hydrolysates from bioethanolic fermentation processes based on agricultural residues have potential as an abundant and inexpensive source of pentose sugars and acids that could serve as nutrients for industrial enzyme-producing microorganisms, especially filamentous fungi. However, the enzyme mixtures produced in such media are poorly defined. In this study, the secretome of Trichoderma reesei Rut C-30 grown either on a spent hydrolysate model medium (SHMM) or on a lactose-based standard medium (LBSM) was explored using proteomics. Results Our results show that both the SHMM and LBSM serve as excellent growth media for T. reesei Rut C-30. In total, 52 protein spots on 2-D gels were identified by using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and electrospray ionization liquid chromatography tandem mass spectrometry (ESI-LC MS/MS). As expected, a considerable number of the identified proteins were related to the degradation of lignocellulosic biomass. The enzyme production profiles in the two media were similar, but β-glucosidase and β-galactosidase were only produced in LBSM. The main cellobiohydrolases (Cel7A/Cel6A) and endoglucanases (Cel7B/Cel5A) were identified in both media and the cellobiohydrolases, i.e. Cel7A and Cel6A, were the most abundant cellulolytic enzymes. Moreover, both media can also serve as a potent inducer of xylanolytic enzymes. Several key enzymes involved in sugar assimilation and regulation of cellulase formation were identified, and were found to be differentially expressed in the two growth media. Conclusions This study not only provides a catalogue of the prevalent proteins secreted by T. reesei in the two media, but the results also suggest that production of hydrolytic enzymes using unconventional carbon sources, such as components in spent hydrolysates, deserves further attention in the future.
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Affiliation(s)
- He Jun
- Department of Chemistry, Umeå University, Umeå, Sweden.
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260
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Unique regulatory mechanism for D-galactose utilization in Aspergillus nidulans. Appl Environ Microbiol 2011; 77:7084-7. [PMID: 21821745 DOI: 10.1128/aem.05290-11] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes two novel regulators, GalX and GalR, that control d-galactose utilization in Aspergillus nidulans. This system is unique for A. nidulans since no GalR homologs were found in other ascomycetes. GalR shares significant sequence identity with the arabinanolytic and xylanolytic regulators AraR and XlnR, but GalX is more distantly related.
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261
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Yacoubi R, Job C, Belghazi M, Chaibi W, Job D. Toward Characterizing Seed Vigor in Alfalfa Through Proteomic Analysis of Germination and Priming. J Proteome Res 2011; 10:3891-903. [DOI: 10.1021/pr101274f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Rafika Yacoubi
- Laboratoire de Biologie et Physiologie Cellulaire Végétales, Département de Biologie, Université de Tunis, Tunisie
| | - Claudette Job
- Centre National de la Recherche Scientifique-Université Claude Bernard Lyon 1-Institut National des Sciences Appliquées-Bayer CropScience Joint Laboratory, UMR 5240 Lyon cedex 9, France
| | - Maya Belghazi
- Centre d’Analyses Protéomiques de Marseille (CAPM), IFR Jean Roche, Faculté de médecine, Marseille cedex 20, France
| | - Wided Chaibi
- Laboratoire de Biologie et Physiologie Cellulaire Végétales, Département de Biologie, Université de Tunis, Tunisie
| | - Dominique Job
- Centre National de la Recherche Scientifique-Université Claude Bernard Lyon 1-Institut National des Sciences Appliquées-Bayer CropScience Joint Laboratory, UMR 5240 Lyon cedex 9, France
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262
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Michalska K, Cuff ME, Tesar C, Feldmann B, Joachimiak A. Structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:678-89. [PMID: 21795809 PMCID: PMC3144851 DOI: 10.1107/s0907444911021834] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/06/2011] [Indexed: 11/10/2022]
Abstract
In most organisms, efficient D-galactose utilization requires the highly conserved Leloir pathway that converts D-galactose to D-glucose 1-phosphate. However, in some bacterial and fungal species alternative routes of D-galactose assimilation have been identified. In the so-called De Ley-Doudoroff pathway, D-galactose is metabolized into pyruvate and D-glyceraldehyde 3-phosphate in five consecutive reactions carried out by specific enzymes. The penultimate step in this pathway involves the phosphorylation of 2-oxo-3-deoxygalactonate to 2-oxo-3-deoxygalactonate 6-phosphate catalyzed by 2-oxo-3-deoxygalactonate kinase, with ATP serving as a phosphoryl-group donor. Here, a crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae determined at 2.1 Å resolution is reported, the first structure of an enzyme from the De Ley-Doudoroff pathway. Structural comparison indicates that the enzyme belongs to the ASKHA (acetate and sugar kinases/hsc70/actin) family of phosphotransferases. The protein is composed of two α/β domains, each of which contains a core common to all family members. Additional elements introduced between conserved structural motifs define the unique features of 2-oxo-3-deoxygalactonate kinase and possibly determine the biological function of the protein.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | - Marianne E. Cuff
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Christine Tesar
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | - Brian Feldmann
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, USA
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263
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Li C, Wang Y, Liu L, Hu Y, Zhang F, Mergen S, Wang G, Schläppi MR, Chu C. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency. PLoS Genet 2011; 7:e1002196. [PMID: 21829379 PMCID: PMC3145628 DOI: 10.1371/journal.pgen.1002196] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Accepted: 06/07/2011] [Indexed: 11/18/2022] Open
Abstract
Photosynthesis is the final determinator for crop yield. To gain insight into genes controlling photosynthetic capacity, we selected from our large T-DNA mutant population a rice stunted growth mutant with decreased carbon assimilate and yield production named photoassimilate defective1 (phd1). Molecular and biochemical analyses revealed that PHD1 encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. The chloroplast localization of PHD1 was confirmed by immunoblots, immunocytochemistry, and UGE activity in isolated chloroplasts, which was approximately 50% lower in the phd1-1 mutant than in the wild type. In addition, the amounts of UDP-glucose and UDP-galactose substrates in chloroplasts were significantly higher and lower, respectively, indicating that PHD1 was responsible for a major part of UGE activity in plastids. The relative amount of monogalactosyldiacylglycerol (MGDG), a major chloroplast membrane galactolipid, was decreased in the mutant, while the digalactosyldiacylglycerol (DGDG) amount was not significantly altered, suggesting that PHD1 participates mainly in UDP-galactose supply for MGDG biosynthesis in chloroplasts. The phd1 mutant showed decreased chlorophyll content, photosynthetic activity, and altered chloroplast ultrastructure, suggesting that a correct amount of galactoglycerolipids and the ratio of glycolipids versus phospholipids are necessary for proper chloroplast function. Downregulated expression of starch biosynthesis genes and upregulated expression of sucrose cleavage genes might be a result of reduced photosynthetic activity and account for the decreased starch and sucrose levels seen in phd1 leaves. PHD1 overexpression increased photosynthetic efficiency, biomass, and grain production, suggesting that PHD1 plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity. These findings will be useful for improving crop yields and for bioenergy crop engineering. Photosynthesis is carried out in chloroplast, a plant-specific organelle. Photosynthetic membranes in chloroplasts contain high levels of glycolipids, and UDP-galactose is a dominating donor for glycolipid biosynthesis. Although glycolipid assembly of photosynthetic membranes has been characterized at the genetic and enzymatic level, the mechanism of substrate supply of UDP-galactose for the glycolipid biosynthetic pathway remains obscure. By genetic screening of rice mutants that are impaired in photosynthetic capacity and carbon assimilation, we identified PHD1 as a novel nucleotide sugar epimerase involved in a process of glycolipid biosynthesis and participating in photosynthetic membrane biogenesis. PHD1 was preferentially expressed in green and meristem tissues, and the PHD1 protein was targeted to chloroplasts. We revealed that UDP-galactose for glycolipid biosynthesis catalyzed by the new enzyme was generated inside chloroplasts, and the reduced amounts of glycolipids in the mutant led to decreased chlorophyll content and photosynthetic activity. Overexpression of this gene lead to growth acceleration, enhanced photosynthetic efficiency, and finally improved biomass and grain yield in rice. These results suggest that PHD1 has significant economic implications in both traditional crop improvement and bioenergy crop production.
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Affiliation(s)
- Chunlai Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Yiqin Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Linchuan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Yingchun Hu
- College of Life Sciences, Peking University, Beijing, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Sod Mergen
- College of Life Sciences, Peking University, Beijing, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Michael R. Schläppi
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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264
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Chang KY, Muddiman DC. Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms. BMC Genomics 2011; 12:358. [PMID: 21745387 PMCID: PMC3146456 DOI: 10.1186/1471-2164-12-358] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 07/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Database searching is the most frequently used approach for automated peptide assignment and protein inference of tandem mass spectra. The results, however, depend on the sequences in target databases and on search algorithms. Recently by using an alternative splicing database, we identified more proteins than with the annotated proteins in Aspergillus flavus. In this study, we aimed at finding a greater number of eligible splice variants based on newly available transcript sequences and the latest genome annotation. The improved database was then used to compare four search algorithms: Mascot, OMSSA, X! Tandem, and InsPecT. RESULTS The updated alternative splicing database predicted 15833 putative protein variants, 61% more than the previous results. There was transcript evidence for 50% of the updated genes compared to the previous 35% coverage. Database searches were conducted using the same set of spectral data, search parameters, and protein database but with different algorithms. The false discovery rates of the peptide-spectrum matches were estimated < 2%. The numbers of the total identified proteins varied from 765 to 867 between algorithms. Whereas 42% (1651/3891) of peptide assignments were unanimous, the comparison showed that 51% (568/1114) of the RefSeq proteins and 15% (11/72) of the putative splice variants were inferred by all algorithms. 12 plausible isoforms were discovered by focusing on the consensus peptides which were detected by at least three different algorithms. The analysis found different conserved domains in two putative isoforms of UDP-galactose 4-epimerase. CONCLUSIONS We were able to detect dozens of new peptides using the improved alternative splicing database with the recently updated annotation of the A. flavus genome. Unlike the identifications of the peptides and the RefSeq proteins, large variations existed between the putative splice variants identified by different algorithms. 12 candidates of putative isoforms were reported based on the consensus peptide-spectrum matches. This suggests that applications of multiple search engines effectively reduced the possible false positive results and validated the protein identifications from tandem mass spectra using an alternative splicing database.
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Affiliation(s)
- Kung-Yen Chang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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265
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Sakuraba H, Kawai T, Yoneda K, Ohshima T. Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis. Arch Biochem Biophys 2011; 512:126-34. [PMID: 21645492 DOI: 10.1016/j.abb.2011.05.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 11/25/2022]
Abstract
The crystal structure of a highly thermostable UDP-galactose 4-epimerase (GalE) from the hyperthermophilic archaeon Pyrobaculum calidifontis was determined at a resolution of 1.8Å. The asymmetric unit contained one subunit, and the functional dimer was generated by a crystallographic two-fold axis. Each monomer consisted of a Rossmann-fold domain with NAD bound and a carboxyl terminal domain. The overall structure of P. calidifontis GalE showed significant similarity to the structures of the GalEs from Escherichia coli, human and Trypanosoma brucei. However, the sizes of several surface loops were markedly smaller in P. calidifontis GalE than the corresponding loops in the other enzymes. Structural comparison revealed that the presence of an extensive hydrophobic interaction at the subunit interface is likely the main factor contributing to the hyperthermostability of the P. calidifontis enzyme. Within the NAD-binding site of P. calidifontis GalE, a loop (NAD-binding loop) tightly holds the adenine ribose moiety of NAD. Moreover, a deletion mutant lacking this loop bound NAD in a loose, reversible manner. Thus the presence of the NAD-binding loop in GalE is largely responsible for preventing the release of the cofactor from the holoenzyme.
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Affiliation(s)
- Haruhiko Sakuraba
- Department of Applied Biological Science, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Japan
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266
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Oppenheimer M, Valenciano AL, Sobrado P. Biosynthesis of galactofuranose in kinetoplastids: novel therapeutic targets for treating leishmaniasis and chagas' disease. Enzyme Res 2011; 2011:415976. [PMID: 21687654 PMCID: PMC3112513 DOI: 10.4061/2011/415976] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/02/2011] [Accepted: 03/14/2011] [Indexed: 12/14/2022] Open
Abstract
Cell surface proteins of parasites play a role in pathogenesis by modulating mammalian cell recognition and cell adhesion during infection. β-Galactofuranose (Galf) is an important component of glycoproteins and glycolipids found on the cell surface of Leishmania spp. and Trypanosoma cruzi. β-Galf-containing glycans have been shown to be important in parasite-cell interaction and protection against oxidative stress. Here, we discuss the role of β-Galf in pathogenesis and recent studies on the Galf-biosynthetic enzymes: UDP-galactose 4′ epimerase (GalE), UDP-galactopyranose mutase (UGM), and UDP-galactofuranosyl transferase (GalfT). The central role in Galf formation, its unique chemical mechanism, and the absence of a homologous enzyme in humans identify UGM as the most attractive drug target in the β-Galf-biosynthetic pathway in protozoan parasites.
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267
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Frisch K, Bender D, Hansen SB, Keiding S, Sørensen M. Nucleophilic radiosynthesis of 2-[18F]fluoro-2-deoxy-D-galactose from Talose triflate and biodistribution in a porcine model. Nucl Med Biol 2011; 38:477-83. [PMID: 21531284 PMCID: PMC3131089 DOI: 10.1016/j.nucmedbio.2010.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 10/15/2010] [Accepted: 11/04/2010] [Indexed: 11/21/2022]
Abstract
INTRODUCTION The galactose analogue 2-[(18)F]fluoro-2-deoxy-D-galactose (FDGal) is a promising positron emission tomography (PET) tracer for studies of regional differences in liver metabolic function and for clinical evaluation of patients with liver cirrhosis and patients undergoing treatment of liver diseases. However, there is an unmet need for routine production of FDGal from readily available starting material. In this study, we present the preparation of FDGal with high radiochemical purity and in amounts sufficient for clinical investigations from commercially available Talose triflate (1,3,4,6-tetra-O-acetyl-2-O-trifluoromethanesulfonyl-β-D-talopyranose). In addition, the biodistribution of FDGal in the pig is presented. METHODS FDGal was prepared by nucleophilic fluorination of Talose triflate followed by basic hydrolysis. The entire synthesis was performed using the GE TRACERlab MX 2-[(18)F]fluoro-2-deoxy-D-glucose (FDG) synthesizer and existing methods for quality control of FDG were applied. Biodistribution of FDGal was studied by successive whole-body PET recordings of two anaesthetized 37-kg pigs. RESULTS Up to 3.7 GBq sterile, pyrogen-free and no-carrier-added FDGal was produced with a radiochemical yield of 3.8±1.2% and a radiochemical purity of 98±1% (42 productions; yield is decay corrected). The adopted quality control methods for FDG were directly applicable for FDGal. Biodistribution studies in the pig revealed the liver and the urinary bladder as critical organs in terms of radiation dose. CONCLUSION Commercially available Talose triflate is a suitable starting material for routine productions of FDGal. The presented radiosynthesis and quality control methods allow for the production of pure, no-carrier-added FDGal in sufficient amounts for clinical PET-investigations of the liver.
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Affiliation(s)
- Kim Frisch
- PET Centre, Aarhus University Hospital, DK-8000 Aarhus, Denmark.
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268
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Bhatt VS, Guo CY, Guan W, Zhao G, Yi W, Liu ZJ, Wang PG. Altered architecture of substrate binding region defines the unique specificity of UDP-GalNAc 4-epimerases. Protein Sci 2011; 20:856-66. [PMID: 21384454 DOI: 10.1002/pro.611] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/21/2011] [Indexed: 11/07/2022]
Abstract
UDP-hexose 4-epimerases play a pivotal role in lipopolysaccharide (LPS) biosynthesis and Leloir pathway. These epimerases are classified into three groups based on whether they recognize nonacetylated UDP-hexoses (Group 1), both N-acetylated and nonacetylated UDP-hexoses (Group 2) or only N-acetylated UDP-hexoses (Group 3). Although the catalysis has been investigated extensively, yet a definitive model rationalizing the substrate specificity of all the three groups on a common platform is largely lacking. In this work, we present the crystal structure of WbgU, a novel UDP-hexose 4-epimerase that belongs to the Group 3. WbgU is involved in biosynthetic pathway of the unusual glycan 2-deoxy-L-altruronic acid that is found in the LPS of the pathogen Pleisomonas shigelloides. A model that defines its substrate specificity is proposed on the basis of the active site architecture. Representatives from all the three groups are then compared to rationalize their substrate specificity. This investigation reveals that the Group 3 active site architecture is markedly different from the "conserved scaffold" of the Group 1 and the Group 2 epimerases and highlights the interactions potentially responsible for the origin of specificity of the Group 3 epimerases toward N-acetylated hexoses. This study provides a platform for further engineering of the UDP-hexose 4-epimerases, leads to a deeper understanding of the LPS biosynthesis and carbohydrate recognition by proteins. It may also have implications in development of novel antibiotics and more economic synthesis of UDP-GalNAc and downstream products such as carbohydrate based vaccines.
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Affiliation(s)
- Veer S Bhatt
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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269
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The role of the active site residues in human galactokinase: implications for the mechanisms of GHMP kinases. Bioorg Chem 2011; 39:120-6. [PMID: 21474160 DOI: 10.1016/j.bioorg.2011.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 11/20/2022]
Abstract
Galactokinase catalyses the phosphorylation of galactose at the expense of ATP. Like other members of the GHMP family of kinases it is postulated to function through an active site base mechanism in which Asp-186 abstracts a proton from galactose. This asparate residue was altered to alanine and to asparagine by site-directed mutagenesis of the corresponding gene. This resulted in variant enzyme with no detectable galactokinase activity. Alteration of Arg-37, which lies adjacent to Asp-186 and is postulated to assist the catalytic base, to lysine resulted in an active enzyme. However, alteration of this residue to glutamate abolished activity. All the variant enzymes, except the arginine to lysine substitution, were structurally unstable (as judged by native gel electrophoresis in the presence of urea) compared to the wild type. This suggests that the lack of activity results from this structural instability, in addition to any direct effects on the catalytic mechanism. Computational estimations of the pK(a) values of the arginine and aspartate residues, suggest that Arg-37 remains protonated throughout the catalytic cycle whereas Asp-186 has an abnormally high pK(a) value (7.18). Quantum mechanics/molecular mechanics (QM/MM) calculations suggest that Asp-186 moves closer to the galactose molecule during catalysis. The experimental and theoretical studies presented here argue for a mechanism in which the C(1)-OH bond in the sugar is weakened by the presence of Asp-186 thus facilitating nucleophilic attack by the oxygen atom on the γ-phosphorus of ATP.
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270
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Goldstein N, Cohen Y, Pode-Shakked B, Sigalov E, Vilensky B, Peleg L, Anikster Y. The GALT rush: high carrier frequency of an unusual deletion mutation of the GALT gene in the Ashkenazi population. Mol Genet Metab 2011; 102:157-60. [PMID: 21059483 DOI: 10.1016/j.ymgme.2010.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/11/2010] [Accepted: 10/11/2010] [Indexed: 11/29/2022]
Abstract
Classic galactosemia is an autosomal recessive disorder of galactose metabolism manifesting in the first weeks of life following exposure to a milk-based diet. Despite the benefit of avoidance of lactose, many patients suffer from long-term complications including neurological deficits and ovarian failure. To date, over 230 mutations have been described in the GALT gene resulting in galactosemia. Recently, an unusual mutation was characterized causing a 5.5 kb deletion, with a relatively high carrier rate in subjects of Ashkenazi Jewish (AJ) descent. The aim of this study was to estimate the carrier frequency of this mutation in the AJ population in Israel. For this purpose we developed a high-throughput methodology to genotype both normal and deleted alleles using a chip-based matrix-assisted laser desorption-time-of-flight (MALDI-TOF) mass spectrometer and Multiplex PCR. DNA samples of 760 anonymous AJ subjects were submitted for analysis, subsequently detecting six individuals heterozygous for the GALT deletion mutation, giving a carrier frequency of 1 in 127 (0.79%). Based on these results, we suggest that the method described here provides a basis for genetic screening and prenatal counseling and can potentially reduce the morbidity and mortality associated with delayed diagnosis of galactosemia in this patient population.
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Affiliation(s)
- Nurit Goldstein
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
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271
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Descroix K, Wagner GK. The first C-glycosidic analogue of a novel galactosyltransferase inhibitor. Org Biomol Chem 2011; 9:1855-63. [PMID: 21267505 DOI: 10.1039/c0ob00630k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural analogues and mimics of the natural sugar-nucleotide UDP-galactose (UDP-Gal) are sought after as chemical tools for glycobiology and drug discovery. We have recently developed a novel class of galactosyltransferase (GalT) inhibitors derived from UDP-Gal, bearing an additional substituent at the 5-position of the uracil base. Herein we report the first C-glycosidic derivative of this new class of GalT inhibitors. We describe a practical convergent synthesis of the new UDP-C-Gal derivative, including a systematic study into the use of radical chemistry for the preparation of galactosyl ethylphosphonate, a key synthetic intermediate. The new inhibitor showed activity against a bacterial UDP-Gal 4'-epimerase at micromolar concentrations. This is the first example of a base-modified UDP-sugar as an inhibitor of a UDP-sugar-dependent enzyme which is not a glycosyltransferase, and these results may therefore have implications for the design of inhibitors of these enzymes in the future.
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Affiliation(s)
- Karine Descroix
- School of Pharmacy, University of East Anglia, Norwich, UK NR4 7TJ
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272
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Madhavan A, Srivastava A, Kondo A, Bisaria VS. Bioconversion of lignocellulose-derived sugars to ethanol by engineered Saccharomyces cerevisiae. Crit Rev Biotechnol 2011; 32:22-48. [PMID: 21204601 DOI: 10.3109/07388551.2010.539551] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Lignocellulosic biomass from agricultural and agro-industrial residues represents one of the most important renewable resources that can be utilized for the biological production of ethanol. The yeast Saccharomyces cerevisiae is widely used for the commercial production of bioethanol from sucrose or starch-derived glucose. While glucose and other hexose sugars like galactose and mannose can be fermented to ethanol by S. cerevisiae, the major pentose sugars D-xylose and L-arabinose remain unutilized. Nevertheless, D-xylulose, the keto isomer of xylose, can be fermented slowly by the yeast and thus, the incorporation of functional routes for the conversion of xylose and arabinose to xylulose or xylulose-5-phosphate in Saccharomyces cerevisiae can help to improve the ethanol productivity and make the fermentation process more cost-effective. Other crucial bottlenecks in pentose fermentation include low activity of the pentose phosphate pathway enzymes and competitive inhibition of xylose and arabinose transport into the cell cytoplasm by glucose and other hexose sugars. Along with a brief introduction of the pretreatment of lignocellulose and detoxification of the hydrolysate, this review provides an updated overview of (a) the key steps involved in the uptake and metabolism of the hexose sugars: glucose, galactose, and mannose, together with the pentose sugars: xylose and arabinose, (b) various factors that play a major role in the efficient fermentation of pentose sugars along with hexose sugars, and (c) the approaches used to overcome the metabolic constraints in the production of bioethanol from lignocellulose-derived sugars by developing recombinant S. cerevisiae strains.
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Affiliation(s)
- Anjali Madhavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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273
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Development and application of a method for counterselectable in-frame deletion in Clostridium perfringens. Appl Environ Microbiol 2010; 77:1375-82. [PMID: 21183644 DOI: 10.1128/aem.01572-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many pathogenic clostridial species produce toxins and enzymes. To facilitate genome-wide identification of virulence factors and biotechnological application of their useful products, we have developed a markerless in-frame deletion method for Clostridium perfringens which allows efficient counterselection and multiple-gene disruption. The system comprises a galKT gene disruptant and a suicide galK plasmid into which two fragments of a target gene for in-frame deletion are cloned. The system was shown to be accurate and simple by using it to disrupt the alpha-toxin gene of the organism. It was also used to construct of two different virulence-attenuated strains, ΗΝ1303 and HN1314: the former is a disruptant of the virRS operon, which regulates the expression of virulence factors, and the latter is a disruptant of the six genes encoding the α, θ, and κ toxins; a clostripain-like protease; a 190-kDa secretory protein; and a putative cell wall lytic endopeptidase. Comparison of the two disruptants in terms of growth ability and the background levels of secreted proteins showed that HN1314 is more useful than ΗΝ1303 as a host for the large-scale production of recombinant proteins.
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274
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Agarwal S, Mishra N, Agarwal S, Dixit A. Characterization of the active site and coenzyme binding pocket of the monomeric UDP- galactose 4'- epimerase of Aeromonas hydrophila. BMB Rep 2010; 43:419-26. [PMID: 20587332 DOI: 10.5483/bmbrep.2010.43.6.419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aeromonas hydrophila is a bacterial pathogen that infects a large number of eukaryotes, including humans. The UDP-galactose 4'-epimerase (GalE) catalyzes interconversion of UDPgalactose to UDP-glucose and plays a key role in lipopolysaccharide biosynthesis. This makes it an important virulence determinant, and therefore a potential drug target. Our earlier studies revealed that unlike other GalEs, GalE of A. hydrophila exists as a monomer. This uniqueness necessitated elucidation of its structure and active site. Chemical modification of the 6xHis-rGalE demonstrated the role of histidine residue in catalysis and that it did not constitute the substrate binding pocket. Loss of the 6xHis-rGalE activity and coenzyme fluorescence with thiol modifying reagents established the role of two distinct vicinal thiols in catalysis. Chemical modification studies revealed arginine to be essential for catalysis. Site-directed mutagenesis indicated Tyr149 and Lys153 to be involved in catalysis. Use of glycerol as a cosolvent enhanced the GalE thermostability significantly.
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275
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Yap YW, Chen MJ, Choy MS, Peng ZF, Whiteman M, Manikandan J, Melendez AJ, Cheung NS. Temporal transcriptomic profiling reveals cellular targets that govern survival in HOCl-mediated neuronal apoptosis. Life Sci 2010; 87:457-67. [DOI: 10.1016/j.lfs.2010.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 08/02/2010] [Accepted: 08/19/2010] [Indexed: 12/19/2022]
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276
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You W, Qiu X, Zhang Y, Ma J, Gao Y, Zhang X, Niu L, Teng M. Crystallization and preliminary X-ray diffraction analysis of the putative aldose 1-epimerase YeaD from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:951-3. [PMID: 20693678 PMCID: PMC2917301 DOI: 10.1107/s1744309110024140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/21/2010] [Indexed: 11/11/2022]
Abstract
Escherichia coli YeaD (ecYeaD) is suggested to be a member of the galactose mutarotase-like superfamily. Galactose mutarotase is an enzyme that converts alpha-galactose to beta-galactose. The known structures of these galactose mutarotase-like proteins are similar to those of galactose mutarotases, with the catalytic residues being conserved, but there are some differences between them in the substrate-binding pocket. In order to reveal the specificity of ecYeaD, a three-dimensional structure is essential. Full-length ecYeaD with an additional 6xHis tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 4000 as a precipitant at 283 K. An X-ray diffraction data set was collected to a resolution of 1.9 A from a single flash-cooled crystal that belonged to space group P2(1)2(1)2(1).
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Affiliation(s)
- Weijie You
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Xiaoting Qiu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Yujie Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Jinming Ma
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Yongxiang Gao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Xiao Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
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277
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Durrant JD, Urbaniak MD, Ferguson MAJ, McCammon JA. Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness. J Med Chem 2010; 53:5025-32. [PMID: 20527952 PMCID: PMC2895357 DOI: 10.1021/jm100456a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Trypanosoma brucei, the causative agent of human African trypanosomiasis, affects tens of thousands of sub-Saharan Africans. As current therapeutics are inadequate due to toxic side effects, drug resistance, and limited effectiveness, novel therapies are urgently needed. UDP-galactose 4′-epimerase (TbGalE), an enzyme of the Leloir pathway of galactose metabolism, is one promising T. brucei drug target. We here use the relaxed complex scheme, an advanced computer-docking methodology that accounts for full protein flexibility, to identify inhibitors of TbGalE. An initial hit rate of 62% was obtained at 100 μM, ultimately leading to the identification of 14 low-micromolar inhibitors. Thirteen of these inhibitors belong to a distinct series with a conserved binding motif that may prove useful in future drug design and optimization.
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Affiliation(s)
- Jacob D Durrant
- Biomedical Sciences Program, University of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, USA.
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278
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Kushner RF, Ryan EL, Sefton JMI, Sanders RD, Lucioni PJ, Moberg KH, Fridovich-Keil JL. A Drosophila melanogaster model of classic galactosemia. Dis Model Mech 2010; 3:618-27. [PMID: 20519569 DOI: 10.1242/dmm.005041] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Classic galactosemia is a potentially lethal disorder that results from profound impairment of galactose-1-phosphate uridylyltransferase (GALT). Despite decades of research, the underlying pathophysiology of classic galactosemia remains unclear, in part owing to the lack of an appropriate animal model. Here, we report the establishment of a Drosophila melanogaster model of classic galactosemia; this is the first whole-animal genetic model to mimic aspects of the patient phenotype. Analogous to humans, GALT-deficient D. melanogaster survive under conditions of galactose restriction, but accumulate elevated levels of galactose-1-phosphate and succumb during larval development following galactose exposure. As in patients, the potentially lethal damage is reversible if dietary galactose restriction is initiated early in life. GALT-deficient Drosophila also exhibit locomotor complications despite dietary galactose restriction, and both the acute and long-term complications can be rescued by transgenic expression of human GALT. Using this new Drosophila model, we have begun to dissect the timing, extent and mechanism(s) of galactose sensitivity in the absence of GALT activity.
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Affiliation(s)
- Rebekah F Kushner
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, USA
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279
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Sanders RD, Sefton JMI, Moberg KH, Fridovich-Keil JL. UDP-galactose 4' epimerase (GALE) is essential for development of Drosophila melanogaster. Dis Model Mech 2010; 3:628-38. [PMID: 20519568 DOI: 10.1242/dmm.005058] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
UDP-galactose 4' epimerase (GALE) catalyzes the interconversion of UDP-galactose and UDP-glucose in the final step of the Leloir pathway; human GALE (hGALE) also interconverts UDP-N-acetylgalactosamine and UDP-N-acetylglucosamine. GALE therefore plays key roles in the metabolism of dietary galactose, in the production of endogenous galactose, and in maintaining the ratios of key substrates for glycoprotein and glycolipid biosynthesis. Partial impairment of hGALE results in the potentially lethal disorder epimerase-deficiency galactosemia. We report here the generation and initial characterization of a first whole-animal model of GALE deficiency using the fruit fly Drosophila melanogaster. Our results confirm that GALE function is essential in developing animals; Drosophila lacking GALE die as embryos but are rescued by the expression of a human GALE transgene. Larvae in which GALE has been conditionally knocked down die within days of GALE loss. Conditional knockdown and transgene expression studies further demonstrate that GALE expression in the gut primordium and Malpighian tubules is both necessary and sufficient for survival. Finally, like patients with generalized epimerase deficiency galactosemia, Drosophila with partial GALE loss survive in the absence of galactose but succumb in development if exposed to dietary galactose. These data establish the utility of the fly model of GALE deficiency and set the stage for future studies to define the mechanism(s) and modifiers of outcome in epimerase deficiency galactosemia.
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Affiliation(s)
- Rebecca D Sanders
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, USA
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280
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Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc Natl Acad Sci U S A 2010; 107:10136-41. [PMID: 20479238 PMCID: PMC2890473 DOI: 10.1073/pnas.0914418107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A notable characteristic of fungal genomes is that genes involved in successive steps of a metabolic pathway are often physically linked or clustered. To investigate how such clusters of functionally related genes are assembled and maintained, we examined the evolution of gene sequences and order in the galactose utilization (GAL) pathway in whole-genome data from 80 diverse fungi. We found that GAL gene clusters originated independently and by different mechanisms in three unrelated yeast lineages. Specifically, the GAL cluster found in Saccharomyces and Candida yeasts originated through the relocation of native unclustered genes, whereas the GAL cluster of Schizosaccharomyces yeasts was acquired through horizontal gene transfer from a Candida yeast. In contrast, the GAL cluster of Cryptococcus yeasts was assembled independently from the Saccharomyces/Candida and Schizosaccharomyces GAL clusters and coexists in the Cryptococcus genome with unclustered GAL paralogs. These independently evolved GAL clusters represent a striking example of analogy at the genomic level. We also found that species with GAL clusters exhibited significantly higher rates of GAL pathway loss than species with unclustered GAL genes. These results suggest that clustering of metabolic genes might facilitate fungal adaptation to changing environments both through the acquisition and loss of metabolic capacities.
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281
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El-Ganiny AM, Sheoran I, Sanders DAR, Kaminskyj SGW. Aspergillus nidulans UDP-glucose-4-epimerase UgeA has multiple roles in wall architecture, hyphal morphogenesis, and asexual development. Fungal Genet Biol 2010; 47:629-35. [PMID: 20211750 DOI: 10.1016/j.fgb.2010.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 02/28/2010] [Accepted: 03/02/2010] [Indexed: 11/16/2022]
Abstract
Aspergillus nidulans UDP-glucose-4-epimerase UgeA interconverts UDP-glucose and UDP-galactose and participates in galactose metabolism. The sugar moiety of UDP-galactose is predominantly found as galactopyranose (Galp, the six-membered ring form), which is the substrate for UDP-galactopyranose mutase (encoded by ugmA) to generate UDP-galactofuranose (Galf, the five-membered ring form) that is found in fungal walls. In A. fumigatus, Galf residues appear to be important for virulence. The A. nidulans ugeA Delta strain is viable, and has defects including wide, slow growing, highly branched hyphae and reduced conidiation that resemble the ugmA Delta strain. As for the ugmA Delta strain, ugeA Delta colonies had substantially reduced sporulation but normal spore viability. Conidia of the ugeA Delta strain could not form colonies on galactose as a sole carbon source, however they produced short, multinucleate germlings suggesting they ceased to grow from starvation. UgeA purified from an expression plasmid had a relative molecular weight of 40.6 kDa, and showed in vitro UDP-glucose-4-epimerase activity. Transmission electron microscope cross-sections of wildtype, ugeA Delta, and ugmA Delta hyphae showed they had similar cytoplasmic contents but the walls of each strain were different in appearance and thickness. Both deletion strains showed increased substrate adhesion. Localization of UgeA-GFP and UgmA-GFP was cytoplasmic, and was similar on glucose and galactose. Neither gene product had a longitudinal polarized distribution. Localization of a UgmA-mRFP in a strain that resembled the ugmA Delta strain was cytoplasmic and lacked a longitudinal polarized distribution. The roles of UgeA in A. nidulans growth and morphogenesis are consistent with the importance of Galf, and are related but not identical to the roles of UgmA.
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Affiliation(s)
- Amira M El-Ganiny
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon SK, Canada
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282
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Optimization of the enzymatic one pot reaction for the synthesis of uridine 5'-diphosphogalactose. Bioprocess Biosyst Eng 2010; 33:71-8. [PMID: 19714366 DOI: 10.1007/s00449-009-0365-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 07/28/2009] [Indexed: 10/20/2022]
Abstract
Five recombinant Escherichia coli extracts harboring overexpressed galactokinase, galactose-1-phosphate uridyltransferase, UDP-glucose pyrophophorylase, UMP kinase, and acetate kinase (AK) were utilized for the production of UDP-galactose (UDP-Gal). We analyzed the parameters which limit the yield of UDP-Gal in the reaction, and the reaction was optimized by increasing the concentration of AK. AK was used for the ATP regeneration as well as the conversion of UDP to UTP. The activities of four overexpressed enzymes were identically fixed, and then we increased the activity of AK to 20 times higher than others. The extracts catalyzed the production of UDP-Gal from UMP (10 mM), galactose (12 mM), ATP (1 mM), and acetyl phosphate (40 mM). As the result of the reaction, the conversion yield of UDP-Gal reached to 95% from 10 mMUMP.
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283
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Abstract
In most organisms, productive utilization of galactose requires the highly conserved Leloir pathway of galactose metabolism. Yet, if this metabolic pathway is perturbed due to congenital deficiencies of the three associated enzymes, or an overwhelming presence of galactose, this monosaccharide which is abundantly present in milk and many non-dairy foodstuffs, will become highly toxic to humans and animals. Despite more than four decades of intense research, little is known about the molecular mechanisms of galactose toxicity in human patients and animal models. In this contemporary review, we take a unique approach to present an overview of galactose toxicity resulting from the three known congenital disorders of galactose metabolism and from experimental hypergalactosemia. Additionally, we update the reader about research progress on animal models, as well as advances in clinical management and therapies of these disorders.
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Affiliation(s)
- Kent Lai
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
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284
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Targeted metabolic labeling of yeast N-glycans with unnatural sugars. Proc Natl Acad Sci U S A 2010; 107:3988-93. [PMID: 20142501 DOI: 10.1073/pnas.0911247107] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Metabolic labeling of glycans with synthetic sugar analogs has emerged as an attractive means for introducing nonnatural chemical functionality into glycoproteins. However, the complexities of glycan biosynthesis prevent the installation of nonnatural moieties at defined, predictable locations within glycoproteins at high levels of incorporation. Here, we demonstrate that the conserved N-acetyglucosamine (GlcNAc) residues within chitobiose cores of N-glycans in the model organism Saccharomyces cerevisiae can be specifically targeted for metabolic replacement by unnatural sugars. We introduced an exogenous GlcNAc salvage pathway into yeast, allowing cells to metabolize GlcNAc provided as a supplement to the culture medium. We then rendered the yeast auxotrophic for production of the donor nucleotide-sugar uridine-diphosphate-GlcNAc (UDP-GlcNAc) by deletion of the essential gene GNA1. We demonstrate that gna1Delta strains require a GlcNAc supplement and that expression plasmids containing both exogenous components of the salvage pathway, GlcNAc transporter NGT1 from Candida albicans and GlcNAc kinase NAGK from Homo sapiens, are required for rescue in this context. Further, we show that cells successfully incorporate synthetic GlcNAc analogs N-azidoacetyglucosamine (GlcNAz) and N-(4-pentynoyl)-glucosamine (GlcNAl) into cell-surface glycans and secreted glycoproteins. To verify incorporation of the nonnatural sugars at N-glycan core positions, endoglycosidase H (endoH)-digested peptides from a purified secretory glycoprotein, Ygp1, were analyzed by mass spectrometry. Multiple Ygp1 N-glycosylation sites bearing GlcNAc, isotopically labeled GlcNAc, or GlcNAz were identified; these modifications were dependent on the supplement added to the culture medium. This system enables the production of glycoproteins that are functionalized for specific chemical modifications at their glycosylation sites.
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285
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Miarelli M, Signorelli F. Differential expression of liver proteins in Chianina and Holstein young bulls1. J Anim Sci 2010; 88:593-8. [DOI: 10.2527/jas.2009-2193] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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286
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Niou YK, Wu WL, Lin LC, Yu MS, Shu HY, Yang HH, Lin GH. Role of galE on biofilm formation by Thermus spp. Biochem Biophys Res Commun 2009; 390:313-8. [DOI: 10.1016/j.bbrc.2009.09.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 09/28/2009] [Indexed: 11/30/2022]
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287
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Suzuki S, Matsuzawa T, Nukigi Y, Takegawa K, Tanaka N. Characterization of two different types of UDP-glucose/-galactose 4-epimerase involved in galactosylation in fission yeast. MICROBIOLOGY-SGM 2009; 156:708-718. [PMID: 19942659 DOI: 10.1099/mic.0.035279-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Schizosaccharomyces species are currently the only known organisms with two types of genes encoding UDP-glucose/-galactose 4-epimerase, uge1(+) and gal10(+). A strain deleted for uge1(+) exhibited a severe galactosylation defect and a decrease in activity and in UDP-galactose content when grown in glucose-rich medium (2 % glucose), indicating that Uge1p is a major UDP-glucose/-galactose 4-epimerase under these growth conditions. In contrast, gal10(+) was efficiently expressed and involved in galactosylation of cell-surface proteins in low-glucose medium (0.1 % glucose and 2 % glycerol), but not in galactose-containing medium. In a uge1Deltagal10Delta strain, the galactosylation defect was suppressed and UDP-galactose content restored to wild-type levels in galactose-containing medium. Disruption of gal7(+), encoding galactose-1-phosphate uridylyltransferase, in the uge1Deltagal10Delta strain reversed suppression of the galactosylation defect and reduced levels of UDP-galactose, indicating that galactose is transported from the medium to the cytosol and is converted into UDP-galactose via galactose 1-phosphate by Gal7p in Sch. pombe.
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Affiliation(s)
- Shotaro Suzuki
- Department of Applied Biological Sciences, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Tomohiko Matsuzawa
- Department of Applied Biological Sciences, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Yayoi Nukigi
- Department of Applied Biological Sciences, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Naotaka Tanaka
- Department of Applied Biological Sciences, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
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288
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Agarwal S, Gopal K, Chhabra G, Dixit A. Molecular cloning, sequence analysis and homology modeling of galE encoding UDP-galactose 4-epimerase of Aeromonas hydrophila. Bioinformation 2009; 4:216-22. [PMID: 20461162 PMCID: PMC2859578 DOI: 10.6026/97320630004216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Accepted: 11/15/2009] [Indexed: 11/30/2022] Open
Abstract
A. hydrophila, a ubiquitous gram-negative bacterium present in aquatic environments, has been implicated in illness in humans, fish and amphibians.
Lipopolysaccharides (LPS), a surface component of the outer membrane, are one of the main virulent factors of gram-negative bacteria.
UDP-galactose 4-epimerase (GalE) catalyses the last step in the Leloir pathway of galactose metabolism and provides precursor for the biosynthesis
of extracellular LPS and capsule. Due to its key role in LPS biosynthesis, it is a potential drug target. The present study describes cloning, sequence
analysis and prediction of three dimensional structure of the deduced amino acid sequence of the galE of A. hydrophila AH17. The cloned galE
consists of the putative promoter-operator region, and an open reading frame of 338 amino acid residues. Sequence alignment and predicted 3Dstructure
revealed that the GalE of A. hydrophila consists of the signature sequences of the epimerase super family. The present study reports the
molecular modeling / 3D-structure prediction of GalE of A. hydrophila. Further, the potential regions of the enzyme that can be targeted for drug
design are identified.
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Affiliation(s)
- Shivani Agarwal
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi - 110067, India
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289
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Duez C, Zervosen A, Teller N, Melkonian RÃ, Banzubazé E, Bouillenne F, Luxen A, Frère JM. Characterization of the proteins encoded by theBacillus subtilis yoxA-dacCâ operon. FEMS Microbiol Lett 2009; 300:42-7. [DOI: 10.1111/j.1574-6968.2009.01761.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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290
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Kubicek CP, Mikus M, Schuster A, Schmoll M, Seiboth B. Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina. BIOTECHNOLOGY FOR BIOFUELS 2009; 2:19. [PMID: 19723296 PMCID: PMC2749017 DOI: 10.1186/1754-6834-2-19] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 09/01/2009] [Indexed: 05/05/2023]
Abstract
Hypocrea jecorina (= Trichoderma reesei) is the main industrial source of cellulases and hemicellulases used to depolymerise plant biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. Cellulases are formed adaptively, and several positive (XYR1, ACE2, HAP2/3/5) and negative (ACE1, CRE1) components involved in this regulation are now known. In addition, its complete genome sequence has been recently published, thus making the organism susceptible to targeted improvement by metabolic engineering. In this review, we summarise current knowledge about how cellulase biosynthesis is regulated, and outline recent approaches and suitable strategies for facilitating the targeted improvement of cellulase production by genetic engineering.
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Affiliation(s)
- Christian P Kubicek
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - Marianna Mikus
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - André Schuster
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - Monika Schmoll
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, TU Vienna, Getreidemarkt, A-1060 Vienna, Austria
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291
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Prodan-Zitnik I, Karas-Kuzelicki N, Lukac-Bajalo J. Positive correlation between galactose-1-phosphate uridyltransferase (GALT) and UDP-galactose-4'-epimerase (GALE) activities. Clin Biochem 2009; 42:1561-4. [PMID: 19616531 DOI: 10.1016/j.clinbiochem.2009.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 06/09/2009] [Accepted: 07/05/2009] [Indexed: 10/20/2022]
Abstract
OBJECTIVES The aim of our study was to determine whether the activities of galactose-1-phosphate uridyltransferase and UDP-galactose-4'-epimerase are correlated, and in what way they may influence one another. DESIGN AND METHODS Enzyme activities were measured in red blood cells from 214 individuals. RESULTS A statistically significant (p<0.001) positive correlation was observed between GALT and GALE activities. CONCLUSIONS Our results suggest that GALT and GALE activities are correlated and that GALE activity has a greater impact on GALT activity than vice versa.
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Affiliation(s)
- Irena Prodan-Zitnik
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.
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292
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Werner SR, Morgan JA. Expression of a Dianthus flavonoid glucosyltransferase in Saccharomyces cerevisiae for whole-cell biocatalysis. J Biotechnol 2009; 142:233-41. [DOI: 10.1016/j.jbiotec.2009.05.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 03/30/2009] [Accepted: 05/11/2009] [Indexed: 11/29/2022]
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293
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Wang W, Li S, Dong HP, Lv S, Tang YY. Differential impairment of spatial and nonspatial cognition in a mouse model of brain aging. Life Sci 2009; 85:127-35. [DOI: 10.1016/j.lfs.2009.05.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 04/24/2009] [Accepted: 05/03/2009] [Indexed: 02/04/2023]
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294
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Remy E, Meyer M, Blaise F, Simon UK, Kuhn D, Balesdent MH, Rouxel T. A key enzyme of the Leloir pathway is involved in pathogenicity of Leptosphaeria maculans toward oilseed rape. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:725-36. [PMID: 19445597 DOI: 10.1094/mpmi-22-6-0725] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Agrobacterium tumefaciens-mediated random insertional mutagenesis was used to investigate pathogenicity determinants in Leptosphaeria maculans. One tagged nonpathogenic mutant, termed m186, is analyzed in detail here. Microscopic analyses of infected plant tissues revealed that m186 is specifically blocked at the invasive growth phase after an unaffected initial penetration stage and is unable to switch to the necrotrophic lifestyle. In addition, m186 exhibits an altered cell wall and seems to be affected in its ability to produce cell-wall-degrading enzymes. The T-DNA insertion occurs in the intergenic region between two head-to-tail genes, leading to a constitutive upregulation of their expression. Complementation experiments showed that only one of these two genes, Lmepi, fully accounts for the mutant phenotype. Bioinformatics and expression analyses along with functional studies suggested that the Lmepi gene encodes for the highly conserved UDP-glucose-4-epimerase, a key enzyme of the Leloir pathway involved in galactose metabolism. For the third time, this study highlights the intimate connection between primary metabolism and pathogenicity in L. maculans. This finding, along with similar data obtained from the related species Stagonospora nodorum, indicates the importance of in planta nutrition for the success of infection of plants by fungi belonging to class Dothideomycete.
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Affiliation(s)
- E Remy
- INRA, UMR 1290 BIOGER, F-78026 Versailles cedex, France
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295
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Chu X, Li N, Liu X, Li D. Functional studies of rat galactokinase. J Biotechnol 2009; 141:142-6. [PMID: 19433218 DOI: 10.1016/j.jbiotec.2009.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 03/05/2009] [Accepted: 03/16/2009] [Indexed: 11/18/2022]
Abstract
Galactokinase is an ATP-dependent enzyme that catalyzes the phosphorylation of galactose to form galactose-1-phosphate. The defect in human galactokinase can result in the disease of galactosemia. On the other hand, the control of galactose-1-phosphate production by inhibiting galactokinase is a potential therapy for another disease referred to as classic galactosemia. Many pharmaceutically important compounds derive from carbohydrate-containing natural products, and glycorandomization is one of the most efficient approaches for complex secondary metabolites. Therefore, it is important to further understand the interaction between galactokinase and its substrate or substrate analogs. In the present study, we cloned and purified both N- and C-terminal His-tagged rat galactokinase. We then constructed and purified a variety of variant enzymes, which were studied using kinetics with galactose and its analogs as substrates. We found that the binding of the ATP may induce conformational change to the enzyme so that the enzyme can bind galactose specifically. Asp186 was found to be a possible catalytic residue. The mutants were incubated with fluorescent trinitrophenyl-ATP for the characterization of their ATP binding sites. Various other substrate analogs, aminoglycosides and flavanoids were also tested and found to be competitive inhibitors of rat galactokinase.
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Affiliation(s)
- Xiusheng Chu
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
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296
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Bang YL, Nguyen TTT, Trinh TTB, Kim YJ, Song J, Song YH. Functional analysis of mutations in UDP-galactose-4-epimerase (GALE) associated with galactosemia in Korean patients using mammalian GALE-null cells. FEBS J 2009; 276:1952-61. [DOI: 10.1111/j.1742-4658.2009.06922.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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297
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Bosco M, Machtey M, Iglesias A, Aleanzi M. UDPglucose pyrophosphorylase from Xanthomonas spp. Characterization of the enzyme kinetics, structure and inactivation related to oligomeric dissociation. Biochimie 2009; 91:204-13. [DOI: 10.1016/j.biochi.2008.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 09/03/2008] [Indexed: 11/26/2022]
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298
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Moyrand F, Lafontaine I, Fontaine T, Janbon G. UGE1 and UGE2 regulate the UDP-glucose/UDP-galactose equilibrium in Cryptococcus neoformans. EUKARYOTIC CELL 2008; 7:2069-77. [PMID: 18820075 PMCID: PMC2593187 DOI: 10.1128/ec.00189-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 09/19/2008] [Indexed: 11/20/2022]
Abstract
The genome of the basidiomycete pathogenic yeast Cryptococcus neoformans carries two UDP-glucose epimerase genes (UGE1 and UGE2). UGE2 maps within a galactose cluster composed of a galactokinase homologue gene and a galactose-1-phosphate uridylyltransferase. This clustered organization of the GAL genes is similar to that in most of the hemiascomycete yeast genomes and in Schizosaccharomyces pombe but is otherwise not generally conserved in the fungal kingdom. UGE1 has been identified as necessary for galactoxylomannan biosynthesis and virulence. Here, we show that UGE2 is necessary for C. neoformans cells to utilize galactose as a carbon source at 30 degrees C but is not required for virulence. In contrast, deletion of UGE1 does not affect cell growth on galactose at this temperature. At 37 degrees C, a uge2Delta mutant grows on galactose in a UGE1-dependent manner. This compensation by UGE1 of UGE2 mutation for growth on galactose at 37 degrees C was not associated with upregulation of UGE1 transcription or with an increase of the affinity of the enzyme for UDP-galactose at this temperature. We studied the subcellular localization of the two enzymes. Whereas at 30 degrees C, Uge1p is at least partially associated with intracellular vesicles and Uge2p is on the plasma membrane, in cells growing on galactose at 37 degrees C, Uge1p colocalizes with Uge2p to the plasma membrane, suggesting that its activity is regulated through subcellular localization.
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Affiliation(s)
- Frédérique Moyrand
- Unité de Mycologie Moléculaire, Institut Pasteur, CNRS, URA3012, 75724 Paris Cedex 15, France
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299
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Localization and interaction of the proteins constituting the GAL genetic switch in Saccharomyces cerevisiae. EUKARYOTIC CELL 2008; 7:2061-8. [PMID: 18952899 DOI: 10.1128/ec.00261-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, the GAL genes encode the enzymes required for galactose metabolism. Regulation of these genes has served as the paradigm for eukaryotic transcriptional control over the last 50 years. The switch between inert and active gene expression is dependent upon three proteins--the transcriptional activator Gal4p, the inhibitor Gal80p, and the ligand sensor Gal3p. Here, we present a detailed spatial analysis of the three GAL regulatory proteins produced from their native genomic loci. Using a novel application of photobleaching, we demonstrate, for the first time, that the Gal3p ligand sensor enters the nucleus of yeast cells in the presence of galactose. Additionally, using Förster resonance energy transfer, we show that the interaction between Gal3p and Gal80p occurs throughout the yeast cell. Taken together, these data challenge existing models for the cellular localization of the regulatory proteins during the induction of GAL gene expression by galactose and suggest a mechanism for the induction of the GAL genes in which galactose-bound Gal3p moves from the cytoplasm to the nucleus to interact with the transcriptional inhibitor Gal80p.
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300
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Induction of the galactose enzymes in Escherichia coli is independent of the C-1-hydroxyl optical configuration of the inducer D-galactose. J Bacteriol 2008; 190:7932-8. [PMID: 18931131 DOI: 10.1128/jb.01008-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two optical forms of aldohexose galactose differing at the C-1 position, alpha-D-galactose and beta-D-galactose, are widespread in nature. The two anomers also occur in di- and polysaccharides, as well as in glycoconjugates. The anomeric form of D-galactose, when present in complex carbohydrates, e.g., cell wall, glycoproteins, and glycolipids, is specific. Their interconversion occurs as monomers and is effected by the enzyme mutarotase (aldose-1-epimerase). Mutarotase and other D-galactose-metabolizing enzymes are coded by genes that constitute an operon in Escherichia coli. The operon is repressed by the repressor GalR and induced by D-galactose. Since, depending on the carbon source during growth, the cell can make only one of the two anomers of D-galactose, the cell must also convert one anomer to the other for use in specific biosynthetic pathways. Thus, it is imperative that induction of the gal operon, specifically the mutarotase, be achievable by either anomer of D-galactose. Here we report in vivo and in vitro experiments showing that both alpha-D-galactose and beta-D-galactose are capable of inducing transcription of the gal operon with equal efficiency and kinetics. Whereas all substitutions at the C-1 position in the alpha configuration inactivate the induction capacity of the sugar, the effect of substitutions in the beta configuration varies depending upon the nature of the substitution; methyl and phenyl derivatives induce weakly, but the glucosyl derivative does not.
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