1
|
Crowe S, Liu Y, Zhao X, Scheller HV, Keasling JD. Advances in Engineering Nucleotide Sugar Metabolism for Natural Product Glycosylation in Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1589-1599. [PMID: 38820348 PMCID: PMC11197093 DOI: 10.1021/acssynbio.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024]
Abstract
Glycosylation is a ubiquitous modification present across all of biology, affecting many things such as physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Nucleotide sugars are important precursors needed to study glycosylation and produce glycosylated products. Saccharomyces cerevisiae is a potentially powerful platform for producing glycosylated biomolecules, but it lacks nucleotide sugar diversity. Nucleotide sugar metabolism is complex, and understanding how to engineer it will be necessary to both access and study heterologous glycosylations found across biology. This review overviews the potential challenges with engineering nucleotide sugar metabolism in yeast from the salvage pathways that convert free sugars to their associated UDP-sugars to de novo synthesis where nucleotide sugars are interconverted through a complex metabolic network with governing feedback mechanisms. Finally, recent examples of engineering complex glycosylation of small molecules in S. cerevisiae are explored and assessed.
Collapse
Affiliation(s)
- Samantha
A. Crowe
- Department
of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California
Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
| | - Yuzhong Liu
- California
Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
| | - Xixi Zhao
- California
Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
| | - Henrik V. Scheller
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Plant and Microbial Biology, University
of California, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Department
of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California
Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
- Division
of Biological Systems and Engineering, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Center
for Biosustainability, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
- Center
for Synthetic Biochemistry, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
2
|
Crowe SA, Zhao X, Gan F, Chen X, Hudson GA, Astolfi MCT, Scheller HV, Liu Y, Keasling JD. Engineered Saccharomyces cerevisiae as a Biosynthetic Platform of Nucleotide Sugars. ACS Synth Biol 2024; 13:1215-1224. [PMID: 38467016 DOI: 10.1021/acssynbio.3c00666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Glycosylation of biomolecules can greatly alter their physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Glycosylation reactions rely on the stepwise addition of sugars using nucleotide diphosphate (NDP)-sugars. Making these substrates readily available will greatly accelerate the characterization of new glycosylation reactions, elucidation of their underlying regulation mechanisms, and production of glycosylated molecules. In this work, we engineered Saccharomyces cerevisiae to heterologously express nucleotide sugar synthases to access a wide variety of uridine diphosphate (UDP)-sugars from simple starting materials (i.e., glucose and galactose). Specifically, activated glucose, uridine diphosphate d-glucose (UDP-d-Glc), can be converted to UDP-d-glucuronic acid (UDP-d-GlcA), UDP-d-xylose (UDP-d-Xyl), UDP-d-apiose (UDP-d-Api), UDP-d-fucose (UDP-d-Fuc), UDP-l-rhamnose (UDP-l-Rha), UDP-l-arabinopyranose (UDP-l-Arap), and UDP-l-arabinofuranose (UDP-l-Araf) using the corresponding nucleotide sugar synthases of plant and microbial origins. We also expressed genes encoding the salvage pathway to directly activate free sugars to achieve the biosynthesis of UDP-l-Arap and UDP-l-Araf. We observed strong inhibition of UDP-d-Glc 6-dehydrogenase (UGD) by the downstream product UDP-d-Xyl, which we circumvented using an induction system (Tet-On) to delay the production of UDP-d-Xyl to maintain the upstream UDP-sugar pool. Finally, we performed a time-course study using strains containing the biosynthetic pathways to produce five non-native UDP-sugars to elucidate their time-dependent interconversion and the role of UDP-d-Xyl in regulating UDP-sugar metabolism. These engineered yeast strains are a robust platform to (i) functionally characterize sugar synthases in vivo, (ii) biosynthesize a diverse selection of UDP-sugars, (iii) examine the regulation of intracellular UDP-sugar interconversions, and (iv) produce glycosylated secondary metabolites and proteins.
Collapse
Affiliation(s)
- Samantha A Crowe
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Xixi Zhao
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Fei Gan
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Xiaoyue Chen
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Graham A Hudson
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Maria C T Astolfi
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Yuzhong Liu
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jay D Keasling
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen 518071, China
| |
Collapse
|
3
|
Mojanaga OO, Acharya KR, Lloyd MD. Recombinant protein production for structural and kinetic studies: A case study using M. tuberculosis α-methylacyl-CoA racemase (MCR). Methods Enzymol 2023; 690:1-37. [PMID: 37858526 DOI: 10.1016/bs.mie.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Modern drug discovery is a target-driven approach in which a particular protein such as an enzyme is implicated in the disease process. Commonly, small-molecule drugs are identified using screening, rational design, and structural biology approaches. Drug screening, testing and optimization is typically conducted in vitro, and copious amounts of protein are required. The advent of recombinant DNA technologies has resulted in a rise in proteins purified by affinity techniques, typically by incorporating an "affinity tag" at the N- or C-terminus. Use of these tagged proteins and affinity techniques comes with a host of issues. This chapter describes the production of an untagged enzyme, α-methylacyl-CoA racemase (MCR) from Mycobacterium tuberculosis, using a recombinant E. coli system. Purification of the enzyme on a 100 mg scale using tandem anion-exchange chromatographies (DEAE-sepharose and RESOURCE-Q columns), and size-exclusion chromatographies is described. A modified protocol allowing the purification of cationic proteins is also described, based on tandem cation-exchange chromatographies (using CM-sepharose and RESOURCE-S columns) and size-exclusion chromatographies. The resulting MCR protein is suitable for biochemical and structural biology applications. The described protocols have wide applicability to the purification of other recombinant proteins and enzymes without using affinity chromatography.
Collapse
Affiliation(s)
- Otsile O Mojanaga
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - K Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| | - Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath, United Kingdom.
| |
Collapse
|
4
|
Zhou Y, Cui Y, Qu X. Comparative transcriptome analysis for the biosynthesis of antioxidant exopolysaccharide in Streptococcus thermophilus CS6. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:5321-5332. [PMID: 35318677 DOI: 10.1002/jsfa.11886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Food grade Streptococcus thermophilus produces biological exopolysaccharides (EPSs) with great potential with respect to catering for higher health-promoting demands; however, how S. thermophilus regulates the biosynthesis of EPS is not completely understood, decelerating the application of these polymers. In our previous study, maltose, soy peptone and initial pH were three key factors of enhancing EPS yield in S. thermophilus CS6. Therefore, we aimed to investigate the regulating mechanisms of EPS biosynthesis in S. thermophilus CS6 via the method of comparative transcriptome and differential carbohydrate metabolism. RESULTS Soy peptone addition (58.6 g L-1 ) and a moderate pH (6.5) contributed to a high bacterial biomass and a high EPS yield (407 mg L-1 ). Maltose, soy peptone and initial pH greatly influenced lactose utilization in CS6. Soy peptone addition induced a high accumulation of mannose and arabinose in intracellular CS6, differential monosaccharide composition (mannose, glucose and arabinose) in EPS and high radical [2,2-diphenyl-1-picrylhydrazyl, superoxide and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)] scavenging activities. Carbohydrate transportation, sugar activation and eps cluster-associated genes were differentially expressed to regulate EPS biosynthesis. Correlation analysis indicated high production of EPSs depended on high expression of lacS, galPMKUTE, pgm, gt2-5&4-1 and epsLM. CONCLUSION The production of antioxidant EPS in S. thermophilus CS6 depended on the regulation of galactose metabolism cluster and eps cluster. The present study recommends a new approach for enhancing EPS production by transcriptomic regulation for further food and health application of EPS. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yang Zhou
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin, China
| | - Yanhua Cui
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin, China
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, China
| |
Collapse
|
5
|
Zou G, Ren J, Wu D, Zhang H, Gong M, Li W, Zhang J, Yang Y. Characterization and Heterologous Expression of UDP-Glucose 4-Epimerase From a Hericium erinaceus Mutant with High Polysaccharide Production. Front Bioeng Biotechnol 2021; 9:796278. [PMID: 34900974 PMCID: PMC8655778 DOI: 10.3389/fbioe.2021.796278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/03/2021] [Indexed: 02/02/2023] Open
Abstract
Hericium erinaceus is an important medicinal fungus in traditional Chinese medicine because of its polysaccharides and other natural products. Compared terpenoids and polyketides, the analysis of synthetic pathway of polysaccharides is more difficult because of the many genes involved in central metabolism. In previous studies, A6180, encoding a putative UDP-glucose 4-epimerase (UGE) in an H. erinaceus mutant with high production of active polysaccharides, was significantly upregulated. Since there is no reliable genetic manipulation technology for H. erinaceus, we employed Escherichia coli and Saccharomyces cerevisiae to study the function and activity of A6180. The recombinant overexpression vector pET22b-A6180 was constructed for heterologous expression in E. coli. The enzymatic properties of the recombinant protein were investigated. It showed that the recombinant A6180 could strongly convert UDP-α-D-glucose into UDP-α-D-galactose under optimal conditions (pH 6.0, 30°C). In addition, when A6180 was introduced into S. cerevisiae BY4742, xylose was detected in the polysaccharide composition of the yeast transformant. This suggested that the protein coded by A6180 might be a multifunctional enzyme. The generated polysaccharides with a new composition of sugars showed enhanced macrophage activity in vitro. These results indicate that A6180 plays an important role in the structure and activity of polysaccharides. It is a promising strategy for producing polysaccharides with higher activity by introducing A6180 into polysaccharide-producing mushrooms.
Collapse
Affiliation(s)
- Gen Zou
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Juanbao Ren
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China.,College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, China
| | - Di Wu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Henan Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ming Gong
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wen Li
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jingsong Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Yang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
6
|
Banford S, Timson DJ. The structural and molecular biology of type IV galactosemia. Biochimie 2020; 183:13-17. [PMID: 33181226 DOI: 10.1016/j.biochi.2020.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Type IV galactosemia is a recently discovered inherited metabolic disease. It is caused by mutations in the GALM gene which result in reduced activity of the enzyme galactose mutarotase. This enzyme catalyses the interconversion of the α- and β-anomers of d-galactose and some other monosaccharides. Human galactose mutarotase is monomeric and its structure is largely composed of β-sheets. The catalytic mechanism requires a histidine residue acting as an acid, and a glutamate acting as a base. Together, these residues open the pyranose ring of d-galactose enabling free rotation of the bond between the first two carbon atoms in the monosaccharide. This can cause reversal of the configuration of the hydroxyl group attached to carbon 1. Type IV galactosemia manifests with similar symptoms to type II galactosemia (galactokinase deficiency), i.e. early onset cataracts. However, as a recently discovered disease, the longer-term consequences are unknown. The physiological role, if any, of galactose mutarotase's reactions with other monosaccharides are not yet known. The possible associations with other proteins also require further investigation.
Collapse
Affiliation(s)
- Samantha Banford
- South Eastern Health and Social Care Trust, Upper Newtownards Road, Dundonald, Belfast, BT16 1RH, UK
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewis Road, Brighton, BN2 4GJ, UK.
| |
Collapse
|
7
|
Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PFG, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ. Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. Sci Rep 2018; 8:7949. [PMID: 29785040 PMCID: PMC5962585 DOI: 10.1038/s41598-018-26170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/01/2018] [Indexed: 01/30/2023] Open
Abstract
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: 'archetypal' transcriptional blocks that are regulated in a concerted fashion in response to external stimuli.
Collapse
Affiliation(s)
- David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Joseph L Costello
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
| | - William Rowe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, Loughborough University, Loughborough, United Kingdom
| | - Paul F G Sims
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, United Kingdom
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Chris M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
8
|
Saha N, Dutta S, Datta SP, Sarkar S. The minimal ESCRT machinery of Giardia lamblia has altered inter-subunit interactions within the ESCRT-II and ESCRT-III complexes. Eur J Cell Biol 2017; 97:44-62. [PMID: 29224850 DOI: 10.1016/j.ejcb.2017.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022] Open
Abstract
The ESCRT pathway functions at different subcellular membranes to induce their negative curvature, and it has been largely characterized in model eukaryotes belonging to Opisthokonta. But searches of the genomes of many nonopisthokonts belonging to various supergroups indicate that some of them may harbour fewer ESCRT components. Of the genomes explored thus far, one of the most minimal set of ESCRT components was identified in the human pathogen Giardia lamblia, which belongs to Excavata. Here we report that an ESCRT-mediated pathway most likely operates at the peripheral vesicles, which are located at the cell periphery and the bare zone of this protist. Functional comparison of all the identified putative giardial ESCRT components, with the corresponding well-characterized orthologues from Saccharomyces cerevisiae, indicated that only some of the ESCRT components could functionally substitute for the corresponding yeast proteins. While GlVps25, GlVps2, and all three paralogues of GlVps4, tested positive in functional complementation assays, GlVps22, GlVps20, and GlVps24 did not. Binary interactions of either GlVps22 or GlVps25, with other ESCRT-II components from Giardia or yeast indicate that the giardial Vps36 orthologue is either completely missing or highly diverged. Interactions within the giardial ESCRT-III components also differ from those in yeast; while GlVps46a interacts preferentially with Vps24 compared to Vps2, GlVps46b, like the yeast orthologue, interacts with both.
Collapse
Affiliation(s)
- Nabanita Saha
- Department of Biochemistry, Bose Institute, P 1/12 CIT Road Scheme VII M, Kolkata 700054, West Bengal, India.
| | - Somnath Dutta
- Department of Biochemistry, Bose Institute, P 1/12 CIT Road Scheme VII M, Kolkata 700054, West Bengal, India.
| | - Shankari P Datta
- Department of Biochemistry, Bose Institute, P 1/12 CIT Road Scheme VII M, Kolkata 700054, West Bengal, India.
| | - Srimonti Sarkar
- Department of Biochemistry, Bose Institute, P 1/12 CIT Road Scheme VII M, Kolkata 700054, West Bengal, India.
| |
Collapse
|
9
|
Jin FJ, Han P, Zhuang M, Zhang ZM, Jin L, Koyama Y. Comparative proteomic analysis: SclR is importantly involved in carbohydrate metabolism in Aspergillus oryzae. Appl Microbiol Biotechnol 2017; 102:319-332. [PMID: 29098410 DOI: 10.1007/s00253-017-8588-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022]
Abstract
The helix-loop-helix (HLH) family of transcriptional factors is a key player in a wide range of developmental processes in organisms from mammals to microbes. We previously identified the bHLH transcription factor SclR in Aspergillus oryzae and found that the loss of SclR function led to significant phenotypic changes, such as rapid protein degradation and cell lysis in dextrin-polypeptone-yeast extract liquid medium. The result implied that SclR is potentially important in both traditional fermentative manufacturing and commercial enzyme production in A. oryzae because of its effect on growth. Therefore, this study presents a comparative assessment at the proteome level of the intracellular differences between an sclR-disrupted strain and a control strain using isobaric tandem mass tag (TMT) labeling for quantification. A total of 5447 proteins were identified, and 568 were differentially expressed proteins (DEPs). Of the DEPs, 251 proteins were increased by 1.5-fold, and 317 proteins were decreased by 1.5-fold in an sclR-disrupted strain compared to the control. The comparison of the quantitative TMT results revealed that SclR was mainly involved in carbon metabolism, especially carbohydrate metabolism. In addition, an enzyme profile by a semi-quantitative method (API-ZYM) indicated that three enzymes (β-galactosidase, α-glucosidase, and α-mannosidase) were significantly less active in the ∆sclR strain than in the control. Moreover, quantitative RT-PCR showed that the expression of certain genes was changed similarly to their corresponding proteins. These results suggested that a possible function of SclR during growth of A. oryzae is its important involvement in carbohydrate metabolism.
Collapse
Affiliation(s)
- Feng-Jie Jin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
| | - Pei Han
- Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, 9 Deng Zhuang South Rd, Beijing, 100094, China
| | - Miao Zhuang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Zhi-Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Long Jin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yasuji Koyama
- Noda Institute for Scientific Research, 399 Noda, Noda City, 278-0037, Japan
| |
Collapse
|
10
|
Bereketoglu C, Arga KY, Eraslan S, Mertoglu B. Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure. Physiol Genomics 2017; 49:549-566. [PMID: 28887370 DOI: 10.1152/physiolgenomics.00034.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/17/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023] Open
Abstract
Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a nonionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/l; <15% cell number reduction) and high (5 mg/l; >65% cell number reduction) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/l NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed. Similarly, 678 (168 repressed, 510 induced) and 688 genes (215 repressed, 473 induced) were differentially expressed in cells exposed to 5 mg/l NP for 120 and 180 min, respectively. Only 15 downregulated and 63 upregulated genes were common between low and high NP inhibitory concentration exposure for 120 min, whereas 16 downregulated and 31 upregulated genes were common after the 180-min exposure. Several processes/pathways were prominently affected by either low or high inhibitory concentration exposure, while certain processes were affected by both inhibitory concentrations, including ion transport, response to chemicals, transmembrane transport, cellular amino acids, and carbohydrate metabolism. While minimal expression changes were observed with low inhibitory concentration exposure, 5 mg/l NP treatment induced substantial expression changes in genes involved in oxidative phosphorylation, cell wall biogenesis, ribosomal biogenesis, and RNA processing, and encoding heat shock proteins and ubiquitin-conjugating enzymes. Collectively, these results provide considerable information on effects of NP at the molecular level.
Collapse
Affiliation(s)
- Ceyhun Bereketoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey; .,Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gümüşhane University; Baglarbasi, Gumushane, Turkey; and
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey
| | - Serpil Eraslan
- Department of Chemical Engineering, Boğaziçi University, Bebek, Istanbul, Turkey
| | - Bulent Mertoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey
| |
Collapse
|
11
|
Michel AH, Hatakeyama R, Kimmig P, Arter M, Peter M, Matos J, De Virgilio C, Kornmann B. Functional mapping of yeast genomes by saturated transposition. eLife 2017; 6. [PMID: 28481201 PMCID: PMC5466422 DOI: 10.7554/elife.23570] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/06/2017] [Indexed: 12/17/2022] Open
Abstract
Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput. DOI:http://dx.doi.org/10.7554/eLife.23570.001 Genes are stretches of DNA that carry the instructions to build and maintain cells. Many studies in genetics involve inactivating one or more genes and observing the consequences. If the loss of a gene kills the cell, that gene is likely to be vital for life. If it does not, the gene may not be essential, or a similar gene may be able to take over its role. Baker’s yeast is a simple organism that shares many characteristics with human cells. Many yeast genes have a counterpart among human genes, and so studying baker’s yeast can reveal clues about our own genetics. Michel et al. report an adaptation for baker’s yeast of a technique called “Transposon sequencing”, which had been used in other single-celled organisms to study the effects of interrupting genes. Briefly, a virus-like piece of DNA, called a transposon, inserts randomly into the genetic material and switches off individual genes. The DNA is then sequenced to reveal every gene that can be disrupted without killing the cell, and remaining genes are inferred to be essential for life. The approach, named SATAY (which is short for “saturated transposon analysis in yeast”), uses this strategy to create millions of baker’s yeast cells, each with a different gene switched off. Because the number of cells generated this way vastly exceeds the number of genes, every gene will be switched off by several independent transposons. Therefore the technique allows all yeast genes to be inactivated several times in one single experiment. The cells can be grown in varying conditions during the experiment, revealing the genes needed for survival in different situations. Non-essential genes can also be inactivated beforehand to uncover if any genes might be compensating for their absence. In the future, this technique may be used to better understand human diseases, such as cancer, since many disease-causing genes in humans have counterparts in yeast. DOI:http://dx.doi.org/10.7554/eLife.23570.002
Collapse
Affiliation(s)
- Agnès H Michel
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Philipp Kimmig
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Meret Arter
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Joao Matos
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | | |
Collapse
|
12
|
Georis I, Isabelle G, Tate JJ, Vierendeels F, Cooper TG, Dubois E. Premature termination of GAT1 transcription explains paradoxical negative correlation between nitrogen-responsive mRNA, but constitutive low-level protein production. RNA Biol 2016; 12:824-37. [PMID: 26259534 PMCID: PMC4615157 DOI: 10.1080/15476286.2015.1058476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The first step in executing the genetic program of a cell is production of mRNA. In yeast, almost every gene is transcribed as multiple distinct isoforms, differing at their 5′ and/or 3′ termini. However, the implications and functional significance of the transcriptome-wide diversity of mRNA termini remains largely unexplored. In this paper, we show that the GAT1 gene, encoding a transcriptional activator of nitrogen-responsive catabolic genes, produces a variety of mRNAs differing in their 5′ and 3′ termini. Alternative transcription initiation leads to the constitutive, low level production of 2 full length proteins differing in their N-termini, whereas premature transcriptional termination generates a short, highly nitrogen catabolite repression- (NCR-) sensitive transcript that, as far as we can determine, is not translated under the growth conditions we used, but rather likely protects the cell from excess Gat1.
Collapse
Affiliation(s)
| | - Georis Isabelle
- a Yeast Physiology ; Institut de Recherches Microbiologiques J. M. Wiame ; Laboratoire de Microbiologie Université Libre de Bruxelles ; Brussels , Belgium
| | | | | | | | | |
Collapse
|
13
|
Drozdova PB, Tarasov OV, Matveenko AG, Radchenko EA, Sopova JV, Polev DE, Inge-Vechtomov SG, Dobrynin PV. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PLoS One 2016; 11:e0154722. [PMID: 27152522 PMCID: PMC4859572 DOI: 10.1371/journal.pone.0154722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/18/2016] [Indexed: 01/09/2023] Open
Abstract
The Peterhof genetic collection of Saccharomyces cerevisiae strains (PGC) is a large laboratory stock that has accumulated several thousands of strains for over than half a century. It originated independently of other common laboratory stocks from a distillery lineage (race XII). Several PGC strains have been extensively used in certain fields of yeast research but their genomes have not been thoroughly explored yet. Here we employed whole genome sequencing to characterize five selected PGC strains including one of the closest to the progenitor, 15V-P4, and several strains that have been used to study translation termination and prions in yeast (25-25-2V-P3982, 1B-D1606, 74-D694, and 6P-33G-D373). The genetic distance between the PGC progenitor and S288C is comparable to that between two geographically isolated populations. The PGC seems to be closer to two bakery strains than to S288C-related laboratory stocks or European wine strains. In genomes of the PGC strains, we found several loci which are absent from the S288C genome; 15V-P4 harbors a rare combination of the gene cluster characteristic for wine strains and the RTM1 cluster. We closely examined known and previously uncharacterized gene variants of particular strains and were able to establish the molecular basis for known phenotypes including phenylalanine auxotrophy, clumping behavior and galactose utilization. Finally, we made sequencing data and results of the analysis available for the yeast community. Our data widen the knowledge about genetic variation between Saccharomyces cerevisiae strains and can form the basis for planning future work in PGC-related strains and with PGC-derived alleles.
Collapse
Affiliation(s)
- Polina B. Drozdova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | - Oleg V. Tarasov
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Scientific Center of RAS, St. Petersburg, Russia
| | - Andrew G. Matveenko
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Elina A. Radchenko
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | - Julia V. Sopova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, St. Petersburg, Russia
| | - Dmitrii E. Polev
- Research Resource Center for Molecular and Cell Technologies, Research Park, Saint-Petersburg State University, St. Petersburg, Russia
| | - Sergey G. Inge-Vechtomov
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Pavel V. Dobrynin
- Bioinformatics Institute, St. Petersburg, Russia
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
14
|
Biofuel Production Based on Carbohydrates from Both Brown and Red Macroalgae: Recent Developments in Key Biotechnologies. Int J Mol Sci 2016; 17:145. [PMID: 26861307 PMCID: PMC4783879 DOI: 10.3390/ijms17020145] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/15/2016] [Indexed: 02/06/2023] Open
Abstract
Marine macroalgae (green, red and brown macroalgae) have attracted attention as an alternative source of renewable biomass for producing both fuels and chemicals due to their high content of suitable carbohydrates and to their advantages over terrestrial biomass. However, except for green macroalgae, which contain relatively easily-fermentable glucans as their major carbohydrates, practical utilization of red and brown macroalgae has been regarded as difficult due to the major carbohydrates (alginate and mannitol of brown macroalgae and 3,6-anhydro-L-galactose of red macroalgae) not being easily fermentable. Recently, several key biotechnologies using microbes have been developed enabling utilization of these brown and red macroalgal carbohydrates as carbon sources for the production of fuels (ethanol). In this review, we focus on these recent developments with emphasis on microbiological biotechnologies.
Collapse
|
15
|
Ra CH, Kim YJ, Lee SY, Jeong GT, Kim SK. Effects of galactose adaptation in yeast for ethanol fermentation from red seaweed, Gracilaria verrucosa. Bioprocess Biosyst Eng 2015; 38:1715-22. [PMID: 25964182 DOI: 10.1007/s00449-015-1411-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/29/2015] [Indexed: 11/30/2022]
Abstract
A total monosaccharide concentration of 39.6 g/L, representing 74.0 % conversion of 53.5 g/L total carbohydrate from 80 g dw/L (8 % w/v) Gracilaria verrucosa slurry, was obtained by thermal acid hydrolysis and enzymatic saccharification. G. verrucosa hydrolysate was used as a substrate for ethanol production by 'separate hydrolysis and fermentation' (SHF). The ethanol production and yield (Y EtOH) from Saccharomyces cerevisiae KCCM 1129 with and without adaptation to high galactose concentrations were 18.3 g/L with Y EtOH of 0.46 and 13.4 g/L with Y EtOH of 0.34, respectively. Relationship between galactose adaptation effects and mRNA transcriptional levels were evaluated with GAL gene family, regulator genes of the GAL genetic switch and repressor genes in non-adapted and adapted S. cerevisiae. The development of galactose adaptation for ethanol fermentation of G. verrucosa hydrolysates allowed us to enhance the overall ethanol yields and obtain a comprehensive understanding of the gene expression levels and metabolic pathways involved.
Collapse
Affiliation(s)
- Chae Hun Ra
- Department of Biotechnology, Pukyong National University, Busan, 608-737, Korea
| | | | | | | | | |
Collapse
|
16
|
Song L, Liu Z, Tong J, Xiao L, Ma H, Zhang H. Comparative proteomics analysis reveals the mechanism of fertility alternation of thermosensitive genic male sterile rice lines under low temperature inducement. Proteomics 2015; 15:1884-905. [PMID: 25641954 DOI: 10.1002/pmic.201400103] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 12/18/2014] [Accepted: 01/28/2015] [Indexed: 11/10/2022]
Abstract
Thermosensitive genic male sterile (TGMS) rice line has made great economical contributions in rice production. However, the fertility of TGMS rice line during hybrid seed production is frequently influenced by low temperature, thus leading to its fertility/sterility alteration and hybrid seed production failure. To understand the mechanism of fertility alternation under low temperature inducement, the extracted proteins from young panicles of two TGMS rice lines at the fertility alternation sensitivity stage were analyzed by 2DE. Eighty-three protein spots were found to be significantly changed in abundance, and identified by MALDI-TOF-TOF MS. The identified proteins were involved in 16 metabolic pathways and cellular processes. The young panicles of TGMS rice line Zhu 1S possessed the lower ROS-scavenging, indole-3-acetic acid level, soluble protein, and sugar contents as well as the faster anther wall disintegration than those of TGMS rice line Zhun S. All these major differences might result in that the former is more stable in fertility than the latter. Based on the majority of the 83 identified proteins, together with microstructural, physiological, and biochemical results, a possible fertile alteration mechanism in the young panicles of TGMS rice line under low temperature inducement was proposed. Such a result will help us in breeding TGMS rice lines and production of hybrid seed.
Collapse
Affiliation(s)
- Liru Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, P. R. China
| | - Zhongqi Liu
- College of Agronomy, Hunan Agricultural University, Collaborative Innovation Center of Grain and Oil crops in South China, Changsha, P. R. China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, P. R. China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Agricultural University, Changsha, P. R. China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Agricultural University, Changsha, P. R. China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, P. R. China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Collaborative Innovation Center of Grain and Oil crops in South China, Changsha, P. R. China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, P. R. China
| |
Collapse
|
17
|
Sinha A, Datta SP, Ray A, Sarkar S. A reduced VWA domain-containing proteasomal ubiquitin receptor of Giardia lamblia localizes to the flagellar pore regions in microtubule-dependent manner. Parasit Vectors 2015; 8:120. [PMID: 25888841 PMCID: PMC4352536 DOI: 10.1186/s13071-015-0737-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022] Open
Abstract
Background Giardia lamblia switches its lifecycle between trophozoite and cyst forms and the proteasome plays a pivotal role in this switching event. Compared to most model eukaryotes, the proteasome of this parasite has already been documented to have certain variations. This study was undertaken to characterize the ubiquitin receptor, GlRpn10, of the 19S regulatory particle of the Giardia proteasome and determine its cellular localization in trophozoites, encysting trophozoites and cysts. Method Sequence alignment and domain architecture analyses were performed to characterize GlRpn10. In vitro ubiquitin binding assay, functional complementation and biochemical studies verified the protein’s ability to function as ubiquitin receptor in the context of the yeast proteasome. Immunofluorescence localization was performed with antibody against GlRpn10 to determine its distribution in trophozoites, encysting trophozoites and cysts. Real-time PCR and Western blotting were performed to monitor the expression pattern of GlRpn10 during encystation. Result GlRpn10 contained a functional ubiquitin interacting motif, which was capable of binding to ubiquitin. Although it contained a truncated VWA domain, it was still capable of partially complementing the function of the yeast Rpn10 orthologue. Apart from localizing to the nucleus and cytosol, GlRpn10 was also present at flagellar pores of trophozoites and this localization was microtubule-dependent. Although there was no change in the cellular levels of GlRpn10 during encystation, its selective distribution at the flagellar pores was absent. Conclusion GlRpn10 contains a noncanonical VWA domain that is partially functional in yeast. Besides the expected nuclear and cytosolic distribution, the protein displays microtubule-dependent flagellar pore localization in trophozoites. While the protein remained in the nucleus and cytosol in encysting trophozoites, it could no longer be detected at the flagellar pores. This absence at the flagellar pore regions in encysting trophozoites is likely to involve redistribution of the protein, rather than decreased gene expression or selective protein degradation. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0737-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Abhishek Sinha
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Shankari Prasad Datta
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Atrayee Ray
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| | - Srimonti Sarkar
- Department of Biochemistry, Bose Institute, P 1/12, C. I. T. Road, Scheme - VII M, Kolkata, 700054, West Bengal, India.
| |
Collapse
|
18
|
Li S, Ha SJ, Kim HJ, Galazka JM, Cate JHD, Jin YS, Zhao H. Investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization. J Biotechnol 2013; 168:1-6. [PMID: 23954547 DOI: 10.1016/j.jbiotec.2013.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
Functional expression of a cellodextrin transporter and an intracellular β-glucosidase from Neurospora crassa in Saccharomyces cerevisiae enables simultaneous co-fermentation of cellobiose and non-glucose sugars such as xylose. Here we investigate the functional role of aldose 1-epimerase (AEP) in engineered cellobiose utilization. One AEP (Gal10) and two putative AEPs (Yhr210c and Ynr071c sharing 50.6% and 51.0% amino acid identity with Gal10, respectively) were selected. Deletion of GAL10 led to complete loss of both AEP activity and cell growth on cellobiose, while GAL10 complementation restored the AEP activity and cell growth. In addition, deletion of YHR210C or YNR071C resulted in improved cellobiose utilization. These results suggest that the intracellular mutarotation of β-glucose to α-glucose might be a rate controlling step and Gal10 play a crucial role in cellobiose fermentation by engineered S. cerevisiae.
Collapse
Affiliation(s)
- Sijin Li
- Energy Biosciences Institute, Institute for Genomic Biology, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | | | | | | | | | | | | |
Collapse
|
19
|
Pelechano V, Wei W, Steinmetz LM. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 2013; 497:127-31. [PMID: 23615609 PMCID: PMC3705217 DOI: 10.1038/nature12121] [Citation(s) in RCA: 306] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/26/2013] [Indexed: 12/20/2022]
Abstract
Transcript function is determined by sequence elements arranged on an individual RNA molecule. Variation in transcripts can affect messenger RNA stability, localization and translation, or produce truncated proteins that differ in localization or function. Given the existence of overlapping, variable transcript isoforms, determining the functional impact of the transcriptome requires identification of full-length transcripts, rather than just the genomic regions that are transcribed. Here, by jointly determining both transcript ends for millions of RNA molecules, we reveal an extensive layer of isoform diversity previously hidden among overlapping RNA molecules. Variation in transcript boundaries seems to be the rule rather than the exception, even within a single population of yeast cells. Over 26 major transcript isoforms per protein-coding gene were expressed in yeast. Hundreds of short coding RNAs and truncated versions of proteins are concomitantly encoded by alternative transcript isoforms, increasing protein diversity. In addition, approximately 70% of genes express alternative isoforms that vary in post-transcriptional regulatory elements, and tandem genes frequently produce overlapping or even bicistronic transcripts. This extensive transcript diversity is generated by a relatively simple eukaryotic genome with limited splicing, and within a genetically homogeneous population of cells. Our findings have implications for genome compaction, evolution and phenotypic diversity between single cells. These data also indicate that isoform diversity as well as RNA abundance should be considered when assessing the functional repertoire of genomes.
Collapse
Affiliation(s)
- Vicent Pelechano
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | |
Collapse
|
20
|
Matsuzawa T, Hara F, Tanaka N, Tohda H, Takegawa K. Ght2⁺ is required for UDP-galactose synthesis from extracellular galactose by Schizosaccharomyces pombe. Appl Microbiol Biotechnol 2012; 97:4957-64. [PMID: 23254763 DOI: 10.1007/s00253-012-4637-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 12/01/2012] [Accepted: 12/04/2012] [Indexed: 10/27/2022]
Abstract
Schizosaccharomyces pombe has eight hexose transporter genes, ght1 (+) to ght8 (+). Here we report that ght2 (+), which is highly expressed in the presence of glucose, is essential for UDP-galactose synthesis from extracellular galactose when cells grow on glucose. The galactosylation defect of a uge1Δ mutant defective in synthesis of UDP-galactose from glucose was suppressed in galactose-containing medium, but disruption of ght2 (+) in the uge1Δ mutant reversed suppression of the galactosylation defect. Expression of Saccharomyces cerevisiae GAL2 in uge1Δght2Δ cells suppressed the defective galactosylation phenotype in galactose-containing medium. These results indicate that galactose is transported from the medium to the cytosol in a Ght2-dependent manner, and is then converted into UDP-galactose.
Collapse
Affiliation(s)
- Tomohiko Matsuzawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | | | | | | | | |
Collapse
|
21
|
Huang EL, Lefsrud MG. Temporal analysis of xylose fermentation by Scheffersomyces stipitis using shotgun proteomics. ACTA ACUST UNITED AC 2012; 39:1507-14. [DOI: 10.1007/s10295-012-1147-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 05/03/2012] [Indexed: 01/31/2023]
Abstract
Abstract
Proteomics and fermentation technology have begun to integrate to investigate fermentation organisms in bioprocess development. This is the first shotgun proteomics study employed to monitor the proteomes of Scheffersomyces stipitis during xylose fermentation under oxygen limitation. We identified 958 nonredundant proteins and observed highly similar proteomes from exponential to early stationary phases. In analyzing the temporal proteome, we identified unique expression patterns in biological processes and metabolic pathways, including alternative respiration salicylhydroxamic acid (SHAM) pathway, activation of glyoxylate cycle, expression of galactose enzymes, and secondary zinc-containing alcohol dehydrogenase and O-glycosyl hydrolases. We identified the expression of a putative, high-affinity xylose sugar transporter Xut1p, but low-affinity xylose transporters were absent. Throughout cell growth, housekeeping processes included oxidative phosphorylation, glycolysis, nonoxidative branch of the pentose phosphate pathway, gluconeogenesis, biosynthesis of amino acids and aminoacyl total RNA (tRNA), protein synthesis and proteolysis, fatty acid metabolism, and cell division. This study emphasized qualitative analysis and demonstrated that shotgun proteomics is capable of monitoring S. stipitis fermentation and identifying physiological states, such as nutrient deficiency.
Collapse
Affiliation(s)
- Eric L Huang
- grid.14709.3b 0000000419368649 Bioresource Engineering McGill University 21111 Lakeshore Road H9X 3V9 Ste-Anne-de-Bellevue QC Canada
| | - Mark G Lefsrud
- grid.14709.3b 0000000419368649 Bioresource Engineering McGill University 21111 Lakeshore Road H9X 3V9 Ste-Anne-de-Bellevue QC Canada
| |
Collapse
|
22
|
Matsuzawa T, Ohashi T, Nakase M, Yoritsune KI, Takegawa K. Galactose-Specific Recognition System in the Fission Yeast Schizosaccharomyces pombe. TRENDS GLYCOSCI GLYC 2012. [DOI: 10.4052/tigg.24.24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Tomohiko Matsuzawa
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Takao Ohashi
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Mai Nakase
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Ken-ichi Yoritsune
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Kaoru Takegawa
- Department of Bioscience & Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| |
Collapse
|
23
|
Sharma A, Malakar P. Structure modeling and comparative genomics for epimerase enzyme (Gal10p). Bioinformation 2010; 5:266-70. [PMID: 21364830 PMCID: PMC3055706 DOI: 10.6026/97320630005266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 10/20/2010] [Indexed: 11/23/2022] Open
Abstract
The Gal10p (UDP-Galactose 4-epimerase) protein is known for regulation of D-galactose metabolism. It catalyzes the inter-conversion between UDPgalactose and UDP-glucose. Knowledge of protein structure, neighboring interacting partners as well as functional residues of the Gal10p is crucial for carry out its function. These problems are still uncovered in case of the Epimerase enzyme. Structure of Epimerase enzyme has already been determined in S.cerevisiae and E.coli, however, no structural information for this protein is available for K.lactis. We used the homology modeling approach to model the structure of Gal10p in K.lactis. Furthermore, functional residues were predicted for modeled Gal10 protein and the strength of interaction between Gal10p and other Gal proteins was carried out by protein -protein interaction studies. The interaction studies revealed that the affinity of Gal10p for other Gal proteins vary in different organisms. Sequence and structure comparison of Epimerase enzyme showed that the orthologs in K.lactis and S.cervisiae are more similar to each other as compared to the ortholog in E.coli .The studies carried by us will help in better understanding of the galactose metabolism. The above studies may be applied to Human Gal10p, where it can help in gaining useful insight into Galactosemia disease.
Collapse
Affiliation(s)
- Ashwani Sharma
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai-400076, Maharashtra, India
| | - Pushkar Malakar
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai-400076, Maharashtra, India
| |
Collapse
|
24
|
Matsuzawa T, Fujita Y, Tanaka N, Tohda H, Itadani A, Takegawa K. New insights into galactose metabolism by Schizosaccharomyces pombe: isolation and characterization of a galactose-assimilating mutant. J Biosci Bioeng 2010; 111:158-66. [PMID: 21075050 DOI: 10.1016/j.jbiosc.2010.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/07/2010] [Accepted: 10/11/2010] [Indexed: 10/18/2022]
Abstract
The fission yeast Schizosaccharomyces pombe cannot use galactose as a carbon or energy source, and little is known about galactose metabolism in this species. Here we report isolation of a galactose-assimilating mutant that grows on a medium containing galactose as a sole carbon source through use of a proofreading-deficient DNA polymerase δ variant encoded by cdc6-1. Based on comparative analysis of gene expression profiles in the wild-type and the mutant (FG2-8), we found that SPBPB2B2.10c (gal7+), SPBPB2B2.12c (gal10+) and SPBPB2B2.13 (gal1+), homologous to Saccharomyces cerevisiae GAL7, GAL10 and GAL1, respectively, and SPBPB2B2.08, SPBPB2B2.09c, and SPBPB2B2.11 that localize close to the gal genes, were highly expressed and dramatically induced by addition of galactose. The gal7Δ strain, carrying an integrated ura4+ marker at the gal7+ locus, grew on 5-fluoroorotic acid (5-FOA)-containing medium. In contrast, the FG2-8 gal7Δ strain could not grow on 5-FOA medium. In addition, expression of gal7+, SPBPB2B2.13, gal10+ and gal1+ genes increased in the wild-type strain when carried on a vector, and these transformants grew on galactose medium. We suggest that gal7+, gal10+, and gal1+ are localized close to a chromosomal terminal repressed by gene silencing in S. pombe. In contrast, gene silencing was defective in the FG2-8 strain making galactose assimilation possible.
Collapse
Affiliation(s)
- Tomohiko Matsuzawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | | | | | | | | | | |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Brahma A, Banerjee N, Bhattacharyya D. UDP-galactose 4-epimerase from Kluyveromyces fragilis--catalytic sites of the homodimeric enzyme are functional and regulated. FEBS J 2009; 276:6725-40. [PMID: 19843183 DOI: 10.1111/j.1742-4658.2009.07386.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-galactose 4-epimerase from Kluyveromyces fragilis is a homodimer containing one catalytic site and one NAD(+) as cofactor per subunit. One 5'-UMP, a competitive inhibitor, binds per dimer of epimerase as isolated and causes inactivation. Addition of 0.2 mm inhibitor to the enzyme in vitro leads to three sequential steps: first, the inhibitor binds to the unoccupied site; second, the inhibitor bound ex vivo is displaced allosterically; and finally, both sites are occupied by the inhibitor. These reactions have been monitored by kinetic lag in substrate conversion, coenzyme fluorescence, protection against trypsin digestion, and reductive inhibition. The transition profiles indicate the existence of a stable intermediate with one inhibitor-binding site remaining unoccupied. Reductive inhibition of this intermediate reduced the activity to 58% +/- 2%, with modification of one catalytic site. A change of conformation of the epimerase upon binding with substrate or inhibitor was evident from fluorescence emission spectra. The epimerase demonstrated a biphasic Michaelis-Menten dependency. The epimerase devoid of 5'-UMP showed a Michaelis-Menten dependency that can be explained by assuming simultaneous operation of two catalytic sites. A monomeric form of the epimerase was devoid of such regulation. The inhibitory profile of 5'-UMP also suggested negative cooperativity. Incubation of the epimerase with combinations of substrate analogs rendered one of the sites inactive, supporting the presence of two functional and regulated catalytic sites. Dissimilar kinetic patterns of the reconstituted enzyme after treatment with p-chloromercuribenzoate indicated stability of the dimeric enzyme against fast association-dissociation, which could otherwise generate multiple forms of the enzyme with functional heterogeneity.
Collapse
Affiliation(s)
- Amrita Brahma
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR), Jadavpur, Kolkata, India
| | | | | |
Collapse
|
27
|
van den Brink J, Akeroyd M, van der Hoeven R, Pronk JT, de Winde JH, Daran-Lapujade P. Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions. MICROBIOLOGY-SGM 2009; 155:1340-1350. [PMID: 19332835 DOI: 10.1099/mic.0.025775-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Glucose is the favoured carbon source for Saccharomyces cerevisiae, and the Leloir pathway for galactose utilization is only induced in the presence of galactose during glucose-derepressed conditions. The goal of this study was to investigate the dynamics of glucose-galactose transitions. To this end, well-controlled, glucose-limited chemostat cultures were switched to galactose-excess conditions. Surprisingly, galactose was not consumed upon a switch to galactose excess under anaerobic conditions. However, the transcripts of the Leloir pathway were highly increased upon galactose excess under both aerobic and anaerobic conditions. Protein and enzyme-activity assays showed that impaired galactose consumption under anaerobiosis coincided with the absence of the Leloir-pathway proteins. Further results showed that absence of protein synthesis was not caused by glucose-mediated translation inhibition. Analysis of adenosine nucleotide pools revealed a fast decrease of the energy charge after the switch from glucose to galactose under anaerobic conditions. Similar results were obtained when glucose-galactose transitions were analysed under aerobic conditions with a respiratory-deficient strain. It is concluded that under fermentative conditions, the energy charge was too low to allow synthesis of the Leloir proteins. Hence, this study conclusively shows that the intracellular energy status is an important factor in the metabolic flexibility of S. cerevisiae upon changes in its environment.
Collapse
Affiliation(s)
- J van den Brink
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - M Akeroyd
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - J T Pronk
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J H de Winde
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - P Daran-Lapujade
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| |
Collapse
|
28
|
Qian Z, Meng B, Wang Q, Wang Z, Zhou C, Wang Q, Tu S, Lin L, Ma Y, Liu S. Systematic characterization of a novel gal operon in Thermoanaerobacter tengcongensis. MICROBIOLOGY-SGM 2009; 155:1717-1725. [PMID: 19372161 DOI: 10.1099/mic.0.025536-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
On the basis of the Thermoanaerobacter tengcongensis genome, a novel type of gal operon was deduced. The gene expression and biochemical properties of this operon were further characterized. RT-PCR analysis of the intergenic regions suggested that the transcription of the gal operon was continuous. With gene cloning and enzyme activity assays, TTE1929, TTE1928 and TTE1927 were identified to be GalT, GalK and GalE, respectively. Results elicited from polarimetry assays revealed that TTE1925, a hypothetical protein, was a novel mutarotase, termed MR-Tt. TTE1926 was identified as a regulator that could bind to two operators in the operon promoter. The transcriptional start sites were mapped, and this suggested that there are two promoters in this operon. Expression of the gal genes was significantly induced by galactose, whereas only MR-Tt expression was detected in glucose-cultured T. tengcongensis at both the mRNA and the protein level. In addition, the abundance of gal proteins was examined at different temperatures. At temperatures ranging from 60 to 80 degrees C, the level of MR-Tt protein was relatively stable, but that of the other gal proteins was dramatically decreased. The operator-binding complexes were isolated and identified by electrophoretic mobility shift assay-liquid chromatography (EMSA-LC) MS-MS, which suggested that several regulatory proteins, such as GalR and a sensory histidine kinase, participate in the regulation of the gal operon.
Collapse
Affiliation(s)
- Zhong Qian
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Bo Meng
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Quanhui Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhuowei Wang
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Chuanqi Zhou
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Qian Wang
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Shuyang Tu
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Liang Lin
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| | - Yanhe Ma
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Siqi Liu
- Beijing Proteomics Institute, Beijing 101318, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, PR China
| |
Collapse
|
29
|
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.
Collapse
Affiliation(s)
- Frédérique Moyrand
- Unité de Mycologie Moléculaire, Institut Pasteur, CNRS, URA3012, 75724 Paris Cedex 15, France
| | | | | | | |
Collapse
|
30
|
Fekete E, Seiboth B, Kubicek CP, Szentirmai A, Karaffa L. Lack of aldose 1-epimerase in Hypocrea jecorina (anamorph Trichoderma reesei): a key to cellulase gene expression on lactose. Proc Natl Acad Sci U S A 2008; 105:7141-6. [PMID: 18480250 PMCID: PMC2438218 DOI: 10.1073/pnas.0802789105] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Indexed: 11/18/2022] Open
Abstract
The heterodisaccharide lactose (1,4-O-beta-D-galactopyranosyl-D-glucose) induces cellulase formation in the ascomycete Hypocrea jecorina (= Trichoderma reesei). Lactose assimilation is slow, and the assimilation of its beta-D-galactose moiety depends mainly on the operation of a recently described reductive pathway and depends less on the Leloir pathway, which accepts only alpha-D-galactose. We therefore reasoned whether galactomutarotase [aldose 1-epimerase (AEP)] activity might limit lactose assimilation and thus influence cellulase formation. We identified three putative AEP-encoding genes (aep1, aep2, aep3) in H. jecorina, of which two encoded intracellular protein (AEP1 and AEP2) and one encoded an extracellular protein (AEP3). Although all three were transcribed, only the aep3 transcript was detected on lactose. However, no mutarotase activity was detected in the mycelia, their cell walls, or the extracellular medium during growth on lactose. Therefore, the effect of galactomutarotase activity on lactose assimilation was studied with H. jecorina strains expressing the C-terminal galactose mutarotase part of the Saccharomyces cerevisiae Gal10. These strains showed increased growth on lactose in a gene copy number-dependent manner, although their formation of extracellular beta-galactosidase activity and transcription of the genes encoding the first steps in the Leloir and the reductive pathway was similar to the parental strain QM9414. Cellulase gene transcription on lactose dramatically decreased in these strains, but remained unaffected during growth on cellulose. Our data show that cellulase induction in H. jecorina by lactose requires the beta-anomer of D-galactose and reveal the lack of mutarotase activity during growth on lactose as an important key for cellulase formation on this sugar.
Collapse
Affiliation(s)
- Erzsébet Fekete
- *Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 56, H-4010, Debrecen, Hungary; and
| | - Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/1665, A-1060 Vienna, Austria
| | - Christian P. Kubicek
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/1665, A-1060 Vienna, Austria
| | - Attila Szentirmai
- *Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 56, H-4010, Debrecen, Hungary; and
| | - Levente Karaffa
- *Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 56, H-4010, Debrecen, Hungary; and
| |
Collapse
|
31
|
Sellick CA, Campbell RN, Reece RJ. Galactose metabolism in yeast-structure and regulation of the leloir pathway enzymes and the genes encoding them. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 269:111-50. [PMID: 18779058 DOI: 10.1016/s1937-6448(08)01003-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The enzymes of the Leloir pathway catalyze the conversion of galactose to a more metabolically useful version, glucose-6-phosphate. This pathway is required as galactose itself cannot be used for glycolysis directly. In most organisms, including the yeast Saccharomyces cerevisiae, five enzymes are required to catalyze this conversion: a galactose mutarotase, a galactokinase, a galactose-1-phosphate uridyltransferase, a UDP-galactose-4-epimerase, and a phosphoglucomutase. In yeast, the genes encoding these enzymes are tightly controlled at the level of transcription and are only transcribed under specific sets of conditions. In the presence of glucose, the genes encoding the Leloir pathway enzymes (often called the GAL genes) are repressed through the action of a transcriptional repressor Mig1p. In the presence of galactose, but in the absence of glucose, the concerted actions of three other proteins Gal4p, Gal80p, and Gal3p, and two small molecules (galactose and ATP) enable the rapid and high-level activation of the GAL genes. The precise molecular mechanism of the GAL genetic switch is controversial. Recent work on solving the three-dimensional structures of the various GAL enzymes proteins and the GAL transcriptional switch proteins affords a unique opportunity to delve into the precise, and potentially unambiguous, molecular mechanism of a highly exploited transcriptional circuit. Understanding the details of the transcriptional and metabolic events that occur in this pathway can be used as a paradigm for understanding the integration of metabolism and transcriptional control more generally, and will assist our understanding of fundamental biochemical processes and how these might be exploited.
Collapse
|
32
|
Roodt Y, Bragg R, Albertyn J. The cloning and sequencing of the UDP-galactose 4-epimerase gene (galE) from Avibacterium paragallinarum. ACTA ACUST UNITED AC 2007; 18:265-8. [PMID: 17541831 DOI: 10.1080/10425170701207067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The putative uridine diphosphate (UDP)-galactose 4-epimerase encoding gene, galE, was isolated from Avibacterium paragallinarum with the use of degenerate primers, colony hybridization and inverse PCR. The data revealed an open reading frame of 1017 bp encoding a protein of 338 amino acids with a molecular weight of 37 kDa and an isoelectric point of 5.5. High sequence homology was obtained with an 87, 91 and 89% sequence identity on protein level towards the galE genes from Actinobacillus pleuropneumoniae, Haemophilus influenza and Pasteurella multocida, respectively. To verify that the cloned galE gene encodes for a UDP-galactose 4-epimeras, this gene was cloned into the pYES-2 expression vector, followed by transformation in a Saccharomyces cerevisiae gal10 deletion strain. Complementation of the gal10 deletion mutant with the galE gene confirmed that this gene encodes a UDP-galactose 4-epimerase.
Collapse
Affiliation(s)
- Yolande Roodt
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | | | | |
Collapse
|
33
|
Agarwal S, Gopal K, Upadhyaya T, Dixit A. Biochemical and functional characterization of UDP-galactose 4-epimerase from Aeromonas hydrophila. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:828-37. [PMID: 17553760 DOI: 10.1016/j.bbapap.2007.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 04/08/2007] [Accepted: 04/17/2007] [Indexed: 11/21/2022]
Abstract
Bacteria of genus Aeromonas, responsible for a variety of pathological conditions in humans and fish, are ubiquitous waterborne bacteria. Aeromonas produces several virulent factors including a complex of lipopolysaccharide and surface array protein, involved in colonization. UDP-galactose 4-epimerase (GalE) catalyzes the production of UDP-galactose, a precursor for lipopolysaccharide biosynthesis, and thus is an important drug target. GalE exhibits interspecies variation and heterogeneity at its structural and functional level and therefore, the differences between the GalE of the host and the pathogen can be exploited for drug designing. In the present study, we report biochemical and functional characterization of the recombinant GalE of Aeromonas hydrophila. Unlike GalE reported from all other species, the purified recombinant GalE of A. hydrophila was found to exist as a monomer. This is the first report of UDP-galactose 4-epimerase from any species being a monomer. The molecular mass of the 6xHis-rGalE was determined to be 38271.477 (m/z). The 6xHis-rGalE with a K(m) of 0.5 mM for UDP-galactose exhibited optimum activity at 37 degrees C and pH 8-9. Spectrofluorimetric and CD analysis confirmed that the thermal inactivation was due to structural changes and not due to the NAD-dissociation. A relatively more ordered structure of the enzyme at pH 8 and 9 as compared to that at pH 6 or 7 suggests a key role of the electrostatic interactions in maintaining its native tertiary structure.
Collapse
Affiliation(s)
- Shivani Agarwal
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | | | | | | |
Collapse
|
34
|
Namdjou DJ, Sauerzapfe B, Schmiedel J, Dräger G, Bernatchez S, Wakarchuk WW, Elling L. Combination of UDP-Glc(NAc) 4′-Epimerase and Galactose Oxidase in a One-Pot Synthesis of Biotinylated Nucleotide Sugars. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200606169] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
35
|
Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ. Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr Biol 2006; 16:1857-64. [PMID: 16979565 DOI: 10.1016/j.cub.2006.07.052] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 07/04/2006] [Accepted: 07/18/2006] [Indexed: 11/17/2022]
Abstract
Filamentous fungi and oomycetes are eukaryotic microorganisms that grow by producing networks of thread-like hyphae, which secrete enzymes to break down complex nutrients, such as wood and plant material, and recover the resulting simple sugars and amino acids by osmotrophy. These organisms are extremely similar in both appearance and lifestyle and include some of the most economically important plant pathogens . However, the morphological similarity of fungi and oomycetes is misleading because they represent some of the most distantly related eukaryote evolutionary groupings, and their shared osmotrophic growth habit is interpreted as being the result of convergent evolution . The fungi branch with the animals, whereas the oomycetes branch with photosynthetic algae as part of the Chromalveolata . In this report, we provide strong phylogenetic evidence that multiple horizontal gene transfers (HGT) have occurred from filamentous ascomycete fungi to the distantly related oomycetes. We also present evidence that a subset of the associated gene families was initially the product of prokaryote-to-fungi HGT. The predicted functions of the gene products associated with fungi-to-oomycete HGT suggest that this process has played a significant role in the evolution of the osmotrophic, filamentous lifestyle on two separate branches of the eukaryote tree.
Collapse
Affiliation(s)
- Thomas A Richards
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, United Kingdom
| | | | | | | | | |
Collapse
|
36
|
Graille M, Baltaze JP, Leulliot N, Liger D, Quevillon-Cheruel S, van Tilbeurgh H. Structure-based Functional Annotation. J Biol Chem 2006; 281:30175-85. [PMID: 16857670 DOI: 10.1074/jbc.m604443200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite the generation of a large amount of sequence information over the last decade, more than 40% of well characterized enzymatic functions still lack associated protein sequences. Assigning protein sequences to documented biochemical functions is an interesting challenge. We illustrate here that structural genomics may be a reasonable approach in addressing these questions. We present the crystal structure of the Saccharomyces cerevisiae YMR099cp, a protein of unknown function. YMR099cp adopts the same fold as galactose mutarotase and shares the same catalytic machinery necessary for the interconversion of the alpha and beta anomers of galactose. The structure revealed the presence in the active site of a sulfate ion attached by an arginine clamp made by the side chain from two strictly conserved arginine residues. This sulfate is ideally positioned to mimic the phosphate group of hexose 6-phosphate. We have subsequently successfully demonstrated that YMR099cp is a hexose-6-phosphate mutarotase with broad substrate specificity. We solved high resolution structures of some substrate enzyme complexes, further confirming our functional hypothesis. The metabolic role of a hexose-6-phosphate mutarotase is discussed. This work illustrates that structural information has been crucial to assign YMR099cp to the orphan EC activity: hexose-phosphate mutarotase.
Collapse
Affiliation(s)
- Marc Graille
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, CNRS UMR8619, F-91405 Orsay Cedex, France
| | | | | | | | | | | |
Collapse
|
37
|
Demir O, Aksan Kurnaz I. An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch. Comput Biol Chem 2006; 30:179-92. [PMID: 16679066 DOI: 10.1016/j.compbiolchem.2006.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 02/28/2006] [Accepted: 02/28/2006] [Indexed: 11/26/2022]
Abstract
Glucose and galactose are two alternative carbon sources in yeast for energy production, producing CO2 and alcohol. The yeast needs to switch from glucose to galactose metabolism as required, by transcriptional regulation of the respective metabolic enzymes. This regulation is achieved mainly through the GAL genetic switch, in addition to glucose repression mechanism. This study integrates the two metabolic pathways with the genetic regulatory circuit using the GEPASI 3.30 simulation environment, and investigates the model behavior under various nutrient conditions. Our system is successful in achieving transcriptional upregulation of the galactose metabolizing enzymes as required. Under high glucose and high galactose concentrations, the in silico yeast chooses to metabolize glucose first, after which it resorts to using the galactose available. We also show what the preferred storage macromolecules are in different metabolic pathways.
Collapse
Affiliation(s)
- Ozlem Demir
- Bogazici University, Department of Molecular Biology and Genetics, 34342 Bebek, Istanbul, Turkey
| | | |
Collapse
|
38
|
Wasilenko J, Fridovich-Keil JL. Relationship between UDP-Galactose 4′-Epimerase Activity and Galactose Sensitivity in Yeast. J Biol Chem 2006; 281:8443-9. [PMID: 16452467 DOI: 10.1074/jbc.m600778200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
UDP-galactose 4'-epimerase (GALE) catalyzes the final step of the highly conserved Leloir pathway of galactose metabolism. Loss of GALE in humans results in a variant form of the metabolic disorder, galactosemia. Loss of GALE in yeast results in galactose-dependent growth arrest. Although the role of GALE in galactose metabolism has been recognized for decades, the precise relationship between GALE activity and galactose sensitivity has remained unclear. Here we have explored this relationship by asking the following. 1) Is GALE rate-limiting for galactose metabolism in yeast? 2) What is the relationship between GALE activity and galactose-dependent growth arrest in yeast? 3) What is the relationship between GALE activity and the abnormal accumulation of galactose metabolites in yeast? To answer these questions we engineered a strain of yeast in which GALE was doxycycline-repressible and studied these cells under conditions of intermediate GALE expression. Our results demonstrated a smooth linear relationship between galactose metabolism and GALE activity over a range from 0 to approximately 5% but a steep threshold relationship between growth rate in galactose and GALE activity over the same range. The relationship between abnormal accumulation of metabolites and GALE activity was also linear over the range from 0 to approximately 5%, suggesting that if the abnormal accumulation of metabolites underlies galactose-dependent growth-arrest in GALE-impaired yeast, either the impact of individual metabolites must be synergistic and/or the threshold of sensitivity must be very steep. Together these data reveal important points of similarity and contrast between the roles of GALE and galactose-1-phosphate uridylyltransferase in galactose metabolism in yeast and provide a framework for future studies in mammalian systems.
Collapse
Affiliation(s)
- Jamie Wasilenko
- Graduate Program in Genetics and Molecular Biology, Emory University and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | |
Collapse
|
39
|
de Atauri P, Orrell D, Ramsey S, Bolouri H. Is the regulation of galactose 1-phosphate tuned against gene expression noise? Biochem J 2005; 387:77-84. [PMID: 15506917 PMCID: PMC1134934 DOI: 10.1042/bj20041001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The average number of mRNA molecules per active gene in yeast can be remarkably low. Consequently, the relative number of copies of each transcript per cell can vary greatly from moment to moment. When these transcripts are encoding metabolic enzymes, how do the resulting variations in enzyme concentrations affect the regulation of metabolic intermediates? Using a kinetic model of galactose utilization in yeast, we analysed the transmission of noise from transcription and translation on metabolic intermediate regulation. In particular, the effect of the kinetic properties of the galactose-1-phosphate uridylyltransferase reaction on the transmission of noise was analysed.
Collapse
Affiliation(s)
- Pedro de Atauri
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, U.S.A
| | - David Orrell
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, U.S.A
| | - Stephen Ramsey
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, U.S.A
| | - Hamid Bolouri
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, U.S.A
- To whom correspondence should be addressed (email )
| |
Collapse
|
40
|
Thoden JB, Holden HM. The molecular architecture of galactose mutarotase/UDP-galactose 4-epimerase from Saccharomyces cerevisiae. J Biol Chem 2005; 280:21900-7. [PMID: 15795221 DOI: 10.1074/jbc.m502411200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The metabolic pathway by which beta-D-galactose is converted to glucose 1-phosphate is known as the Leloir pathway and consists of four enzymes. In most organisms, these enzymes appear to exist as soluble entities in the cytoplasm. In yeast such as Saccharomyces cerevisiae, however, the first and last enzymes of the pathway, galactose mutarotase and UDP-galactose 4-epimerase, are contained within a single polypeptide chain referred to as Gal10p. Here we report the three-dimensional structure of Gal10p in complex with NAD(+), UDP-glucose, and beta-D-galactose determined to 1.85-A resolution. The enzyme is dimeric with dimensions of approximately 91 A x 135 A x 108 A and assumes an almost V-shaped appearance. The overall architecture of the individual subunits can be described in terms of two separate N- and C-terminal domains connected by a Type II turn formed by Leu-357 to Val-360. The first 356 residues of Gal10p fold into the classical bilobal topology observed for all other UDP-galactose 4-epimerases studied thus far. This N-terminal domain contains the binding sites for NAD(+) and UDP-glucose. The polypeptide chain extending from Glu-361 to Ser-699 adopts a beta-sandwich motif and harbors the binding site for beta-D-galactose. The two active sites of Gal10p are separated by over 50 A. This investigation represents the first structural analysis of a dual function enzyme in the Leloir pathway.
Collapse
Affiliation(s)
- James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | | |
Collapse
|