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Vargas JA, Sculaccio SA, Pinto APA, Pereira HD, Mendes LFS, Flores JF, Cobos M, Castro JC, Garratt RC, Leonardo DA. Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit camu-camu. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2754-2771. [PMID: 38224521 DOI: 10.1093/jxb/erae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
l-Ascorbic acid (AsA, vitamin C) is a pivotal dietary nutrient with multifaceted importance in living organisms. In plants, the Smirnoff-Wheeler pathway is the primary route for AsA biosynthesis, and understanding the mechanistic details behind its component enzymes has implications for plant biology, nutritional science, and biotechnology. As part of an initiative to determine the structures of all six core enzymes of the pathway, the present study focuses on three of them in the model species Myrciaria dubia (camu-camu): GDP-d-mannose 3',5'-epimerase (GME), l-galactose dehydrogenase (l-GalDH), and l-galactono-1,4-lactone dehydrogenase (l-GalLDH). We provide insights into substrate and cofactor binding and the conformational changes they induce. The MdGME structure reveals a distorted substrate in the active site, pertinent to the catalytic mechanism. Mdl-GalDH shows that the way in which NAD+ association affects loop structure over the active site is not conserved when compared with its homologue in spinach. Finally, the structure of Mdl-GalLDH is described for the first time. This allows for the rationalization of previously identified residues which play important roles in the active site or in the formation of the covalent bond with FAD. In conclusion, this study enhances our understanding of AsA biosynthesis in plants, and the information provided should prove useful for biotechnological applications.
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Affiliation(s)
- Jhon A Vargas
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Susana A Sculaccio
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Andressa P A Pinto
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Humberto D'Muniz Pereira
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Luis F S Mendes
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Jhoao F Flores
- Institute of Biology, State University of Campinas, Rua Monteiro Lobato 255, Campinas, SP 13083-862, Brazil
| | - Marianela Cobos
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, 1600, Iquitos, Peru
- Departamento de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Zungarococha, Ciudad Universitaria. Iquitos, Perú
| | - Juan C Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, 1600, Iquitos, Peru
- Departamento de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Zungarococha, Ciudad Universitaria. Iquitos, Perú
| | - Richard C Garratt
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Diego A Leonardo
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
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Smirnoff N, Wheeler GL. The ascorbate biosynthesis pathway in plants is known, but there is a way to go with understanding control and functions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2604-2630. [PMID: 38300237 PMCID: PMC11066809 DOI: 10.1093/jxb/erad505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/29/2024] [Indexed: 02/02/2024]
Abstract
Ascorbate (vitamin C) is one of the most abundant primary metabolites in plants. Its complex chemistry enables it to function as an antioxidant, as a free radical scavenger, and as a reductant for iron and copper. Ascorbate biosynthesis occurs via the mannose/l-galactose pathway in green plants, and the evidence for this pathway being the major route is reviewed. Ascorbate accumulation is leaves is responsive to light, reflecting various roles in photoprotection. GDP-l-galactose phosphorylase (GGP) is the first dedicated step in the pathway and is important in controlling ascorbate synthesis. Its expression is determined by a combination of transcription and translation. Translation is controlled by an upstream open reading frame (uORF) which blocks translation of the main GGP-coding sequence, possibly in an ascorbate-dependent manner. GGP associates with a PAS-LOV protein, inhibiting its activity, and dissociation is induced by blue light. While low ascorbate mutants are susceptible to oxidative stress, they grow nearly normally. In contrast, mutants lacking ascorbate do not grow unless rescued by supplementation. Further research should investigate possible basal functions of ascorbate in severely deficient plants involving prevention of iron overoxidation in 2-oxoglutarate-dependent dioxygenases and iron mobilization during seed development and germination.
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Affiliation(s)
- Nicholas Smirnoff
- Biosciences, Faculty of Health and Life Sciences, Exeter EX4 4QD, UK
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3
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Ghosh M, Narindoshvili T, Thoden JB, Schumann ME, Holden HM, Raushel FM. Biosynthesis of Cytidine Diphosphate-6-d-Glucitol for the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 2024; 63:699-710. [PMID: 38386885 PMCID: PMC10918830 DOI: 10.1021/acs.biochem.3c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/12/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Campylobacter jejuni is a Gram-negative pathogenic bacterium commonly found in chickens and is the leading cause of human diarrheal disease worldwide. The various serotypes of C. jejuni produce structurally distinct capsular polysaccharides (CPSs) on the exterior surfaces of the cell wall. The capsular polysaccharide from C. jejuni serotype HS:5 is composed of a repeating sequence of d-glycero-d-manno-heptose and d-glucitol-6-phosphate. We previously defined the pathway for the production of d-glycero-d-manno-heptose in C. jejuni. Here, we elucidate the biosynthetic pathway for the assembly of cytidine diphosphate (CDP)-6-d-glucitol by the combined action of two previously uncharacterized enzymes. The first enzyme catalyzes the formation of CDP-6-d-fructose from cytidine triphosphate (CTP) and d-fructose-6-phosphate. The second enzyme reduces CDP-6-d-fructose with NADPH to generate CDP-6-d-glucitol. Using sequence similarity network (SSN) and genome neighborhood network (GNN) analyses, we predict that these pairs of proteins are responsible for the biosynthesis of CDP-6-d-glucitol and/or CDP-d-mannitol in the lipopolysaccharides (LPSs) and capsular polysaccharides in more than 200 other organisms. In addition, high resolution X-ray structures of the second enzyme are reported, which provide novel insight into the manner in which an open-chain nucleotide-linked sugar is harbored in an active site cleft.
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Affiliation(s)
- Manas
K. Ghosh
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Tamari Narindoshvili
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - James B. Thoden
- Department
of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Mitchell E. Schumann
- Department
of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Hazel M. Holden
- Department
of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Frank M. Raushel
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
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4
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Wang Y, Diao S, Li H, Ye L, Suo Y, Zheng Y, Sun P, Han W, Fu J. Comparative Metabolomic and Transcriptomic Analyses Reveal Distinct Ascorbic Acid (AsA) Accumulation Patterns between PCA and PCNA Persimmon Developing Fruit. Int J Mol Sci 2023; 24:15362. [PMID: 37895041 PMCID: PMC10607040 DOI: 10.3390/ijms242015362] [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: 07/21/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Persimmon fruit has a high nutritional value and significantly varies between pollination-constant astringent (PCA) and pollination-constant non-astringent (PCNA) persimmons. The astringency type affects sugar, flavonoids, and tannin accumulation and is well known in persimmon fruit. However, the impact of the fruit astringency type on ascorbic acid (AsA) accumulation is limited. In this study, typical PCA varieties ('Huojing' and 'Zhongshi5') and PCNA varieties ('Yohou' and 'Jiro') of persimmon fruit were sampled at four developing stages (S1-S4) to provide valuable information on AsA content variation in PCA and PCNA persimmon. Persimmon fruit is rich in ascorbic acid; the AsA content of the four varieties 'Zhongshi5', 'Huojing', 'Jiro', and 'Youhou' mature fruit reached 104.49, 48.69, 69.69, and 47.48 mg/100 g. Fruit of the same astringency type persimmon showed a similar AsA accumulation pattern. AsA content was significantly higher in PCA than PCNA fruit at S1-S3. The initial KEGG analysis of metabolites showed that galactose metabolism is the major biosynthetic pathway of AsA in persimmon fruit. There were significant differences in galactose pathway-related metabolite content in developing PCA and PCNA fruit, such as Lactose, D-Tagatose, and D-Sorbitol content in PCA being higher than that of PCNA. Combined gene expression and WGCNA analyses showed that the expression of the GME (evm.TU.contig4144.37) gene was higher in PCA-type than in PCNA-type fruit in S1-S3 and exhibited the highest correlation with AsA content (r = 690 **, p < 0.01). Four hub genes, including the DNA methylation gene, methyltransferase gene, F-box, and Actin-like Protein, were identified as potential regulators of the GME gene. These results provide basic information on how astringency types affect AsA accumulation and will provide valuable information for further investigation on AsA content variation in persimmon fruit.
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Affiliation(s)
- Yiru Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Songfeng Diao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Huawei Li
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Lingshuai Ye
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
- Research Institute of Fast-Growing Trees, Chinese Academy of Forestry, Zhanjiang 524022, China
| | - Yujing Suo
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Yanhao Zheng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Peng Sun
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Weijuan Han
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Jianmin Fu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
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5
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Wang L, Patena W, Van Baalen KA, Xie Y, Singer ER, Gavrilenko S, Warren-Williams M, Han L, Harrigan HR, Hartz LD, Chen V, Ton VTNP, Kyin S, Shwe HH, Cahn MH, Wilson AT, Onishi M, Hu J, Schnell DJ, McWhite CD, Jonikas MC. A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways. Cell 2023; 186:3499-3518.e14. [PMID: 37437571 DOI: 10.1016/j.cell.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kelly A Van Baalen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihua Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emily R Singer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Linqu Han
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Henry R Harrigan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Linnea D Hartz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vivian Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vinh T N P Ton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Saw Kyin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henry H Shwe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Matthew H Cahn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jianping Hu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Claire D McWhite
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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6
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Castro JC, Castro CG, Cobos M. Genetic and biochemical strategies for regulation of L-ascorbic acid biosynthesis in plants through the L-galactose pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1099829. [PMID: 37021310 PMCID: PMC10069634 DOI: 10.3389/fpls.2023.1099829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Vitamin C (L-ascorbic acid, AsA) is an essential compound with pleiotropic functions in many organisms. Since its isolation in the last century, AsA has attracted the attention of the scientific community, allowing the discovery of the L-galactose pathway, which is the main pathway for AsA biosynthesis in plants. Thus, the aim of this review is to analyze the genetic and biochemical strategies employed by plant cells for regulating AsA biosynthesis through the L-galactose pathway. In this pathway, participates eight enzymes encoded by the genes PMI, PMM, GMP, GME, GGP, GPP, GDH, and GLDH. All these genes and their encoded enzymes have been well characterized, demonstrating their participation in AsA biosynthesis. Also, have described some genetic and biochemical strategies that allow its regulation. The genetic strategy includes regulation at transcriptional and post-transcriptional levels. In the first one, it was demonstrated that the expression levels of the genes correlate directly with AsA content in the tissues/organs of the plants. Also, it was proved that these genes are light-induced because they have light-responsive promoter motifs (e.g., ATC, I-box, GT1 motif, etc.). In addition, were identified some transcription factors that function as activators (e.g., SlICE1, AtERF98, SlHZ24, etc.) or inactivators (e.g., SlL1L4, ABI4, SlNYYA10) regulate the transcription of these genes. In the second one, it was proved that some genes have alternative splicing events and could be a mechanism to control AsA biosynthesis. Also, it was demonstrated that a conserved cis-acting upstream open reading frame (5'-uORF) located in the 5'-untranslated region of the GGP gene induces its post-transcriptional repression. Among the biochemical strategies discovered is the control of the enzyme levels (usually by decreasing their quantities), control of the enzyme catalytic activity (by increasing or decreasing its activity), feedback inhibition of some enzymes (GME and GGP), subcellular compartmentation of AsA, the metabolon assembly of the enzymes, and control of AsA biosynthesis by electron flow. Together, the construction of this basic knowledge has been establishing the foundations for generating genetically improved varieties of fruits and vegetables enriched with AsA, commonly used in animal and human feed.
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Affiliation(s)
- Juan C. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Carlos G. Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Marianela Cobos
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
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7
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Chen M, Guo Z, Sun J, Tang W, Wang M, Tang Y, Li P, Wu B, Chen Y. Insights into the biosynthesis of septacidin l-heptosamine moiety unveils a VOC family sugar epimerase. Acta Pharm Sin B 2023; 13:765-774. [PMID: 36873169 PMCID: PMC9978623 DOI: 10.1016/j.apsb.2022.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/10/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
l-Heptopyranoses are important components of bacterial polysaccharides and biological active secondary metabolites like septacidin (SEP), which represents a group of nucleoside antibiotics with antitumor, antifungal, and pain-relief activities. However, little is known about the formation mechanisms of those l-heptose moieties. In this study, we deciphered the biosynthetic pathway of the l,l-gluco-heptosamine moiety in SEPs by functional characterizing four genes and proposed that SepI initiates the process by oxidizing the 4'-hydroxyl of l-glycero-α-d-manno-heptose moiety of SEP-328 (2) to a keto group. Subsequently, SepJ (C5 epimerase) and SepA (C3 epimerase) shape the 4'-keto-l-heptopyranose moiety by sequential epimerization reactions. At the last step, an aminotransferase SepG installs the 4'-amino group of the l,l-gluco-heptosamine moiety to generate SEP-327 (3). An interesting phenomenon is that the SEP intermediates with 4'-keto-l-heptopyranose moieties exist as special bicyclic sugars with hemiacetal-hemiketal structures. Notably, l-pyranose is usually converted from d-pyranose by bifunctional C3/C5 epimerase. SepA is an unprecedented monofunctional l-pyranose C3 epimerase. Further in silico and experimental studies revealed that it represents an overlooked metal dependent-sugar epimerase family bearing vicinal oxygen chelate (VOC) architecture.
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Affiliation(s)
- Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Laboratory of Microbial Metabolic Engineering, Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Jinyuan Sun
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatische C4-Epimerisierung von UDP-Glucuronsäure: präzise gesteuerte Rotation eines transienten 4-Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202211937. [PMID: 38515538 PMCID: PMC10952283 DOI: 10.1002/ange.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Indexed: 03/23/2024]
Abstract
AbstractUDP‐Glucuronsäure(UDP‐GlcA)‐4‐Epimerase repräsentiert eine wichtige Fragestellung in der Enzymkatalyse: die Balance zwischen konformativer Flexibilität und genauer Positionierung. Das Enzym koordiniert die C4‐Oxidation des Substrats durch NAD+ mit der Rotation eines leicht decarboxylierbaren β‐Ketosäure‐Intermediats im aktiven Zentrum zur Ermöglichung der stereoinvertierenden Reduktion der Ketogruppe durch NADH. Wir zeigen hier die nur schwer erfassbare Rotationskoordinate des 4‐Ketointermediats. Distorsion des Zuckerrings in eine Boot‐Konformation erzeugt torsionale Mobilität in der Bindungstasche des Enzyms. Die Endpunkte der Rotation zeigen den 4‐Ketozucker in einer unverformten 4C1‐Sesselkonformation. Die äquatorial positionierte Carboxylatgruppe ist ungünstig für die 4‐Ketozucker‐Decarboxylierung. Varianten der Epimerase zeigen Decarboxylierung, wenn sie die Bindung mit der Carboxylatgruppe im entgegengesetzten Rotationsisomer des Substrats entfernen. R185A/D‐Substitutionen wandeln die Epimerase in UDP‐Xylose‐Synthasen um, welche UDP‐GlcA in stereospezifischen, konfigurationserhaltenden Reaktionen decarboxylieren.
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Affiliation(s)
- Annika J. E. Borg
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Derzeitige Adresse: Nostrum BiodiscoveryAv. De Josep Tarradellas, 8–1008029BarcelonaSpanien
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys, 2308010BarcelonaSpanien
| | - Bernd Nidetzky
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
- Austrian Center of Industrial Biotechnology (acib)Krenngasse 378010GrazÖsterreich
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9
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatic C4-Epimerization of UDP-Glucuronic Acid: Precisely Steered Rotation of a Transient 4-Keto Intermediate for an Inverted Reaction without Decarboxylation. Angew Chem Int Ed Engl 2023; 62:e202211937. [PMID: 36308301 PMCID: PMC10107529 DOI: 10.1002/anie.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) 4-epimerase illustrates an important problem regarding enzyme catalysis: balancing conformational flexibility with precise positioning. The enzyme coordinates the C4-oxidation of the substrate by NAD+ and rotation of a decarboxylation-prone β-keto acid intermediate in the active site, enabling stereoinverting reduction of the keto group by NADH. We reveal the elusive rotational landscape of the 4-keto intermediate. Distortion of the sugar ring into boat conformations induces torsional mobility in the enzyme's binding pocket. The rotational endpoints show that the 4-keto sugar has an undistorted 4 C1 chair conformation. The equatorially placed carboxylate group disfavors decarboxylation of the 4-keto sugar. Epimerase variants lead to decarboxylation upon removal of the binding interactions with the carboxylate group in the opposite rotational isomer of the substrate. Substitutions R185A/D convert the epimerase into UDP-xylose synthases that decarboxylate UDP-GlcA in stereospecific, configuration-retaining reactions.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Present address: Nostrum Biodiscovery, Av. De Josep Tarradellas, 8-10, 08029, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria.,Austrian Center of Industrial Biotechnology (acib), Krenngasse 37, 8010, Graz, Austria
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10
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Advances in Novel Animal Vitamin C Biosynthesis Pathways and the Role of Prokaryote-Based Inferences to Understand Their Origin. Genes (Basel) 2022; 13:genes13101917. [PMID: 36292802 PMCID: PMC9602106 DOI: 10.3390/genes13101917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022] Open
Abstract
Vitamin C (VC) is an essential nutrient required for the optimal function and development of many organisms. VC has been studied for many decades, and still today, the characterization of its functions is a dynamic scientific field, mainly because of its commercial and therapeutic applications. In this review, we discuss, in a comparative way, the increasing evidence for alternative VC synthesis pathways in insects and nematodes, and the potential of myo-inositol as a possible substrate for this metabolic process in metazoans. Methodological approaches that may be useful for the future characterization of the VC synthesis pathways of Caenorhabditis elegans and Drosophila melanogaster are here discussed. We also summarize the current distribution of the eukaryote aldonolactone oxidoreductases gene lineages, while highlighting the added value of studies on prokaryote species that are likely able to synthesize VC for both the characterization of novel VC synthesis pathways and inferences on the complex evolutionary history of such pathways. Such work may help improve the industrial production of VC.
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11
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Vargas JA, Leonardo DA, D’Muniz Pereira H, Lopes AR, Rodriguez HN, Cobos M, Marapara JL, Castro JC, Garratt RC. Structural Characterization of L-Galactose Dehydrogenase: An Essential Enzyme for Vitamin C Biosynthesis. PLANT & CELL PHYSIOLOGY 2022; 63:1140-1155. [PMID: 35765894 PMCID: PMC9381564 DOI: 10.1093/pcp/pcac090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
In plants, it is well-known that ascorbic acid (vitamin C) can be synthesized via multiple metabolic pathways but there is still much to be learned concerning their integration and control mechanisms. Furthermore, the structural biology of the component enzymes has been poorly exploited. Here we describe the first crystal structure for an L-galactose dehydrogenase [Spinacia oleracea GDH (SoGDH) from spinach], from the D-mannose/L-galactose (Smirnoff-Wheeler) pathway which converts L-galactose into L-galactono-1,4-lactone. The kinetic parameters for the enzyme are similar to those from its homolog from camu camu, a super-accumulator of vitamin C found in the Peruvian Amazon. Both enzymes are monomers in solution and have a pH optimum of 7, and their activity is largely unaffected by high concentrations of ascorbic acid, suggesting the absence of a feedback mechanism acting via GDH. Previous reports may have been influenced by changes of the pH of the reaction medium as a function of ascorbic acid concentration. The structure of SoGDH is dominated by a (β/α)8 barrel closely related to aldehyde-keto reductases (AKRs). The structure bound to NAD+ shows that the lack of Arg279 justifies its preference for NAD+ over NADP+, as employed by many AKRs. This favors the oxidation reaction that ultimately leads to ascorbic acid accumulation. When compared with other AKRs, residue substitutions at the C-terminal end of the barrel (Tyr185, Tyr61, Ser59 and Asp128) can be identified to be likely determinants of substrate specificity. The present work contributes toward a more comprehensive understanding of structure-function relationships in the enzymes involved in vitamin C synthesis.
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Affiliation(s)
| | | | - Humberto D’Muniz Pereira
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Adriana R Lopes
- Laboratory of Biochemistry, Instituto Butantan, Av. Vital Brasil, São Paulo 1500, Brazil
| | - Hicler N Rodriguez
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, Iquitos 1600, Peru
| | - Marianela Cobos
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, Iquitos 1600, Peru
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú, Av. Abelardo Quiñones km 2.5, Iquitos 16006, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria - Zungarococha, San Juan Bautista 16000, Peru
| | - Jorge L Marapara
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, Iquitos 1600, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria - Zungarococha, San Juan Bautista 16000, Peru
| | - Juan C Castro
- Unidad Especializada del Laboratorio de Investigación en Biotecnología (UELIB), Centro de Investigaciones de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, Iquitos 1600, Peru
- Departamento Académico de Ciencias Biomédicas y Biotecnología (DACBB), Facultad de Ciencias Biológicas (FCB), Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria - Zungarococha, San Juan Bautista 16000, Peru
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12
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Rapp C, Nidetzky B. Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate. ACS Catal 2022; 12:6816-6830. [PMID: 35747200 PMCID: PMC9207888 DOI: 10.1021/acscatal.2c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/12/2022] [Indexed: 11/29/2022]
Abstract
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Transient oxidation–reduction
through hydride transfer with
tightly bound NAD coenzyme is used by a large class of sugar nucleotide
epimerases to promote configurational inversion of carbon stereocenters
in carbohydrate substrates. A requirement for the epimerases to coordinate
hydride abstraction and re-addition with substrate rotation in the
binding pocket poses a challenge for dynamical protein conformational
selection linked to enzyme catalysis. Here, we studied the thermophilic
C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose
substrate (kcat ≈ 1.0 min–1; 60 °C) to explore the sensitivity of the enzymatic hydride
transfer toward environmental fluctuations affected by temperature
(20–80 °C). We determined noncompetitive primary kinetic
isotope effects (KIE) due to 2H at the glucose C2 and showed
that a normal KIE on the kcat (Dkcat) reflects isotope sensitivity of
the hydrogen abstraction to enzyme-NAD+ in a rate-limiting
transient oxidation. The Dkcat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C)
and 3.3 at high temperature (80 °C). The temperature profiles
for kcat with the 1H and 2H substrate showed a decrease in the rate below a dynamically
important breakpoint (∼40 °C), suggesting an equilibrium
shift to an impaired conformational landscape relevant for catalysis
in the low-temperature region. Full Marcus-like model fits of the
rate and KIE profiles provided evidence for a high-temperature reaction
via low-frequency conformational sampling associated with a broad
distribution of hydride donor–acceptor distances (long-distance
population centered at 3.31 ± 0.02 Å), only poorly suitable
for quantum mechanical tunneling. Collectively, dynamical characteristics
of TaCPa2E-catalyzed hydride transfer during transient
oxidation of CDP-glucose reveal important analogies to mechanistically
simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase.
A loose-fit substrate (in TaCPa2E) resembles structural
variants of these enzymes by extensive dynamical sampling to balance
conformational flexibility and catalytic efficiency.
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Affiliation(s)
- Christian Rapp
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
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13
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Structural basis of catalysis and substrate recognition by the NAD(H)-dependent α-d-glucuronidase from the glycoside hydrolase family 4. Biochem J 2021; 478:943-959. [PMID: 33565573 DOI: 10.1042/bcj20200824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022]
Abstract
Members of the glycoside hydrolase family 4 (GH4) employ an unusual glycosidic bond cleavage mechanism utilizing NAD(H) and a divalent metal ion, under reducing conditions. These enzymes act upon a diverse range of glycosides, and unlike most other GH families, homologs here are known to accommodate both α- and β-anomeric specificities within the same active site. Here, we report the catalytic properties and the crystal structures of TmAgu4B, an α-d-glucuronidase from the hyperthermophile Thermotoga maritima. The structures in three different states include the apo form, the NADH bound holo form, and the ternary complex with NADH and the reaction product d-glucuronic acid, at 2.15, 1.97 and 1.85 Å resolutions, respectively. These structures reveal the step-wise route of conformational changes required in the active site to achieve the catalytically competent state, and illustrate the direct role of residues that determine the reaction mechanism. Furthermore, a structural transition of a helical region in the active site to a turn geometry resulting in the rearrangement of a unique arginine residue governs the exclusive glucopyranosiduronic acid recognition in TmAgu4B. Mutational studies show that modifications of the glycone binding site geometry lead to catalytic failure and indicate overlapping roles of specific residues in catalysis and substrate recognition. The data highlight hitherto unreported molecular features and associated active site dynamics that determine the structure-function relationships within the unique GH4 family.
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14
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Expanding the Enzyme Repertoire for Sugar Nucleotide Epimerization: The CDP-Tyvelose 2-Epimerase from Thermodesulfatator atlanticus for Glucose/Mannose Interconversion. Appl Environ Microbiol 2021; 87:AEM.02131-20. [PMID: 33277270 PMCID: PMC7851689 DOI: 10.1128/aem.02131-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Epimerization of sugar nucleotides is central to the structural diversification of monosaccharide building blocks for cellular biosynthesis. Epimerase applicability to carbohydrate synthesis can be limited, however, by the high degree of substrate specificity exhibited by most sugar nucleotide epimerases. Here, we discovered a promiscuous type of CDP-tyvelose 2-epimerase (TyvE)-like enzyme that promotes C2-epimerization in all nucleotide (CDP, UDP, GDP, ADP, TDP)-activated forms of d-glucose. This new epimerase, originating from Thermodesulfatator atlanticus, is a functional homodimer that contains one tightly bound NAD+/subunit and shows optimum activity at 70°C and pH 9.5. The enzyme exhibits a k cat with CDP-dglucose of ∼1.0 min-1 (pH 7.5, 60°C). To characterize the epimerase kinetically and probe its substrate specificity, we developed chemo-enzymatic syntheses for CDP-dmannose, CDP-6-deoxy-dglucose, CDP-3-deoxy-dglucose and CDP-6-deoxy-dxylo-hexopyranos-4-ulose. Attempts to obtain CDP-dparatose and CDP-dtyvelose were not successful. Using high-resolution carbohydrate analytics and in situ NMR to monitor the enzymatic conversions (60°C, pH 7.5), we show that the CDP-dmannose/CDP-dglucose ratio at equilibrium is 0.67 (± 0.1), determined from the kinetic Haldane relationship and directly from the reaction. We further show that deoxygenation at sugar C6 enhances the enzyme activity 5-fold compared to CDP-dglucose whereas deoxygenation at C3 renders the substrate inactive. Phylogenetic analysis places the T. atlanticus epimerase into a distinct subgroup within the sugar nucleotide epimerase family of SDR (short-chain dehydrogenases/reductases), for which the current study now provides the functional context. Collectively, our results expand an emerging toolbox of epimerase-catalyzed reactions for sugar nucleotide synthesis.IMPORTANCE Epimerases of the sugar nucleotide-modifying class of enzymes have attracted considerable interest in carbohydrate (bio)chemistry, for the mechanistic challenges and the opportunities for synthesis involved in the reactions catalyzed. Discovery of new epimerases with expanded scope of sugar nucleotide substrates used is important to promote the mechanistic inquiry and can facilitate the development of new enzyme applications. Here, a CDP-tyvelose 2-epimerase-like enzyme from Thermodesulfatator atlanticus is shown to catalyze sugar C2 epimerization in CDP-glucose and other nucleotide-activated forms of dglucose. The reactions are new to nature in the context of enzymatic sugar nucleotide modification. The current study explores the substrate scope of the discovered C2-epimerase and, based on modeling, suggests structure-function relationships that may be important for specificity and catalysis.
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15
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Barnawi H, Woodward L, Fava N, Roubakha M, Shaw SD, Kubinec C, Naismith JH, Creuzenet C. Structure-function studies of the C3/C5 epimerases and C4 reductases of the Campylobacter jejuni capsular heptose modification pathways. J Biol Chem 2021; 296:100352. [PMID: 33524389 PMCID: PMC7949155 DOI: 10.1016/j.jbc.2021.100352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/14/2023] Open
Abstract
Many bacteria produce polysaccharide-based capsules that protect them from environmental insults and play a role in virulence, host invasion, and other functions. Understanding how the polysaccharide components are synthesized could provide new means to combat bacterial infections. We have previously characterized two pairs of homologous enzymes involved in the biosynthesis of capsular sugar precursors GDP-6-deoxy-D-altro-heptose and GDP-6-OMe-L-gluco-heptose in Campylobacter jejuni. However, the substrate specificity and mechanism of action of these enzymes-C3 and/or C5 epimerases DdahB and MlghB and C4 reductases DdahC and MlghC-are unknown. Here, we demonstrate that these enzymes are highly specific for heptose substrates, using mannose substrates inefficiently with the exception of MlghB. We show that DdahB and MlghB feature a jellyroll fold typical of cupins, which possess a range of activities including epimerizations, GDP occupying a similar position as in cupins. DdahC and MlghC contain a Rossman fold, a catalytic triad, and a small C-terminal domain typical of short-chain dehydratase reductase enzymes. Integrating structural information with site-directed mutagenesis allowed us to identify features unique to each enzyme and provide mechanistic insight. In the epimerases, mutagenesis of H67, D173, N121, Y134, and Y132 suggested the presence of alternative catalytic residues. We showed that the reductases could reduce GDP-4-keto-6-deoxy-mannulose without prior epimerization although DdahC preferred the pre-epimerized substrate and identified T110 and H180 as important for substrate specificity and catalytic efficacy. This information can be exploited to identify inhibitors for therapeutic applications or to tailor these enzymes to synthesize novel sugars useful as glycobiology tools.
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Affiliation(s)
- Heba Barnawi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Laura Woodward
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK
| | - Natalie Fava
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Mikhail Roubakha
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Steve D Shaw
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Chelsea Kubinec
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - James H Naismith
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK; Rosalind Franklin Institute, Research Complex at Harwell, Harwell Campus, Didcot, UK; Division of Structural Biology, Oxford University, Oxford, UK.
| | - Carole Creuzenet
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
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16
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Borg AJE, Beerens K, Pfeiffer M, Desmet T, Nidetzky B. Stereo-electronic control of reaction selectivity in short-chain dehydrogenases: Decarboxylation, epimerization, and dehydration. Curr Opin Chem Biol 2020; 61:43-52. [PMID: 33166830 DOI: 10.1016/j.cbpa.2020.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/18/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022]
Abstract
Sugar nucleotide-modifying enzymes of the short-chain dehydrogenase/reductase type use transient oxidation-reduction by a tightly bound nicotinamide cofactor as a common strategy of catalysis to promote a diverse set of reactions, including decarboxylation, single- or double-site epimerization, and dehydration. Although the basic mechanistic principles have been worked out decades ago, the finely tuned control of reactivity and selectivity in several of these enzymes remains enigmatic. Recent evidence on uridine 5'-diphosphate (UDP)-glucuronic acid decarboxylases (UDP-xylose synthase, UDP-apiose/UDP-xylose synthase) and UDP-glucuronic acid-4-epimerase suggests that stereo-electronic constraints established at the enzyme's active site control the selectivity, and the timing of the catalytic reaction steps, in the conversion of the common substrate toward different products. The mechanistic idea of stereo-electronic control is extended to epimerases and dehydratases that deprotonate the Cα of the transient keto-hexose intermediate. The human guanosine 5'-diphosphate (GDP)-mannose 4,6-dehydratase was recently shown to use a minimal catalytic machinery, exactly as predicted earlier from theoretical considerations, for the β-elimination of water from the keto-hexose species.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria
| | - Koen Beerens
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria
| | - Tom Desmet
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria.
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17
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Agostino M. Comprehensive analysis of carbohydrate-protein recognition in the Protein Data Bank. Carbohydr Res 2020; 498:108180. [PMID: 33096507 DOI: 10.1016/j.carres.2020.108180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
Carbohydrate-protein interactions underpin wide-ranging aspects of biology. However, such interactions remain relatively unexplored in pharmaceutical and biotechnological applications, in part due to the challenges associated with their structural characterisation, both experimentally and computationally. Knowledge-based approaches have shown great success in the prediction of drug-protein and protein-protein interactions, although have not been comprehensively investigated for carbohydrate-protein interactions. In this work, carbohydrate-protein complexes from the Protein Data Bank were comprehensively obtained and analysed to identify patterns in how carbohydrate-protein interactions are mediated.
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Affiliation(s)
- Mark Agostino
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Bentley, Australia.
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18
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Gevaert O, Van Overtveldt S, Da Costa M, Beerens K, Desmet T. GDP-altrose as novel product of GDP-mannose 3,5-epimerase: Revisiting its reaction mechanism. Int J Biol Macromol 2020; 165:1862-1868. [PMID: 33075338 DOI: 10.1016/j.ijbiomac.2020.10.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Abstract
GDP-mannose 3,5-epimerase (GM35E) catalyzes the double epimerization of GDP-mannose to yield GDP-l-galactose. GDP-l-gulose (C5-epimer) has previously been detected as a byproduct of this reaction, indicating that C3,5-epimerization occurs through an initial epimerization at C5. Given these products, GM35E constitutes a valuable bridge between d- and l-hexoses. In order to fully exploit this potential, the enzyme might be subjected to specificity engineering for which profound mechanistic insights are beneficial. Accordingly, this study further elucidated GM35E's reaction mechanism. For the first time, the production of the C3-epimer GDP-altrose was demonstrated, resulting in an adjustment of the acknowledged reaction mechanism. As GM35E converts GDP-mannose to GDP-l-gulose, GDP-altrose and GDP-l-galactose in a 72:4:4:20 ratio, this indicates that the enzyme does not discriminate between the C3 and C5 position as initial epimerization site. This was also confirmed by a structural investigation. Based on a mutational analysis of the active site, residues S115 and R281 were attributed a stabilizing function, which is believed to support the reactivation process of the catalytic residues. This paper eventually reflected on some engineering strategies that aim to change the enzyme towards a single specificity.
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Affiliation(s)
- Ophelia Gevaert
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Matthieu Da Costa
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
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19
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Van Overtveldt S, Da Costa M, Gevaert O, Joosten HJ, Beerens K, Desmet T. Determinants of the Nucleotide Specificity in the Carbohydrate Epimerase Family 1. Biotechnol J 2020; 15:e2000132. [PMID: 32761842 DOI: 10.1002/biot.202000132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/20/2020] [Indexed: 11/09/2022]
Abstract
In recent years, carbohydrate epimerases have attracted increasing attention as promising biocatalysts for the production of specialty sugars and derivatives. The vast majority of these enzymes are active on nucleotide-activated sugars, rather than on their free counterparts. Although such epimerases are known to have a clear preference for a particular nucleotide (UDP, GDP, CDP, or ADP), very little is known about the determinants of the respective specificities. In this work, sequence motifs are identified that correlate with the different nucleotide specificities in one of the main epimerase superfamilies, carbohydrate epimerase 1 (CEP1). To confirm their relevance, GDP- and CDP-specific residues are introduced into the UDP-glucose 4-epimerase from Thermus thermophilus, resulting in a 3-fold and 13-fold reduction in KM for GDP-Glc and CDP-Glc, respectively. Moreover, several variants are severely crippled in UDP-Glc activity, which further underlines the crucial role of the identified positions. Hence, the analysis should prove to be valuable for the further exploration and application of epimerases involved in carbohydrate synthesis.
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Affiliation(s)
- Stevie Van Overtveldt
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Matthieu Da Costa
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, Nijmegen, 6511 AA, The Netherlands
| | - Koen Beerens
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Gent, 9000, Belgium
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Borg AJE, Dennig A, Weber H, Nidetzky B. Mechanistic characterization of UDP-glucuronic acid 4-epimerase. FEBS J 2020; 288:1163-1178. [PMID: 32645249 PMCID: PMC7984243 DOI: 10.1111/febs.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/22/2020] [Accepted: 07/06/2020] [Indexed: 12/27/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) is a central precursor in sugar nucleotide biosynthesis and common substrate for C4-epimerases and decarboxylases releasing UDP-galacturonic acid (UDP-GalA) and UDP-pentose products, respectively. Despite the different reactions catalyzed, the enzymes are believed to share mechanistic analogy rooted in their joint membership to the short-chain dehydrogenase/reductase (SDR) protein superfamily: Oxidation at the substrate C4 by enzyme-bound NAD+ initiates the catalytic pathway. Here, we present mechanistic characterization of the C4-epimerization of UDP-GlcA, which in comparison with the corresponding decarboxylation has been largely unexplored. The UDP-GlcA 4-epimerase from Bacillus cereus functions as a homodimer and contains one NAD+ /subunit (kcat = 0.25 ± 0.01 s-1 ). The epimerization of UDP-GlcA proceeds via hydride transfer from and to the substrate's C4 while retaining the enzyme-bound cofactor in its oxidized form (≥ 97%) at steady state and without trace of decarboxylation. The kcat for UDP-GlcA conversion shows a kinetic isotope effect of 2.0 (±0.1) derived from substrate deuteration at C4. The proposed enzymatic mechanism involves a transient UDP-4-keto-hexose-uronic acid intermediate whose formation is rate-limiting overall, and is governed by a conformational step before hydride abstraction from UDP-GlcA. Precise positioning of the substrate in a kinetically slow binding step may be important for the epimerase to establish stereo-electronic constraints in which decarboxylation of the labile β-keto acid species is prevented effectively. Mutagenesis and pH studies implicate the conserved Tyr149 as the catalytic base for substrate oxidation and show its involvement in the substrate positioning step. Collectively, this study suggests that based on overall mechanistic analogy, stereo-electronic control may be a distinguishing feature of catalysis by SDR-type epimerases and decarboxylases active on UDP-GlcA.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Austria
| | - Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
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Bearne SL. Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases. Chemistry 2020; 26:10367-10390. [DOI: 10.1002/chem.201905826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/09/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry & Molecular BiologyDepartment of ChemistryDalhousie University Halifax, Nova Scotia B3H 4R2 Canada
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Bell A, Severi E, Lee M, Monaco S, Latousakis D, Angulo J, Thomas GH, Naismith JH, Juge N. Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. J Biol Chem 2020; 295:13724-13736. [PMID: 32669363 PMCID: PMC7535918 DOI: 10.1074/jbc.ra120.014454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut symbiont Ruminococcus gnavus scavenges host-derived N-acetylneuraminic acid (Neu5Ac) from mucins by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into R. gnavus ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D NMR, we elucidated the multistep enzymatic mechanism of the oxidoreductase (RgNanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-2-deoxy-2,3-dehydro-N-acetylneuraminic acid intermediate and NAD+ regeneration. The crystal structure of RgNanOx in complex with the NAD+ cofactor showed a protein dimer with a Rossman fold. Guided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of RgNanOx homologues across Gram-negative and Gram-positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionization spray MS that the Escherichia coli homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that E. coli could catabolize 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using E. coli mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in E. coli depended on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in E. coli.
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Affiliation(s)
- Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Micah Lee
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Dimitrios Latousakis
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-US), Sevilla, Spain
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.
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Novel Insights into the Existence of the Putative UDP-Glucuronate 5-Epimerase Specificity. Catalysts 2020. [DOI: 10.3390/catal10020222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
C5-epimerases are promising tools for the production of rare l-hexoses from their more common d-counterparts. On that account, UDP-glucuronate 5-epimerase (UGA5E) attracts attention as this enzyme could prove to be useful for the synthesis of UDP-l-iduronate. Interestingly, l-iduronate is known as a precursor for the production of heparin, an effective anticoagulant. To date, the UGA5E specificity has only been detected in rabbit skin extract, and the respective enzyme has not been characterized in detail or even identified at the molecular level. Accordingly, the current work aimed to shed more light on the properties of UGA5E. Therefore, the pool of putative UGA5Es present in the UniProt database was scrutinized and their sequences were clustered in a phylogenetic tree. However, the examination of two of these enzymes revealed that they actually epimerize UDP-glucuronate at the 4- rather than 5-position. Furthermore, in silico analysis indicated that this should be the case for all sequences that are currently annotated as UGA5E and, hence, that such activity has not yet been discovered in nature. The detected l-iduronate synthesis in rabbit skin extract can probably be assigned to the enzyme chondroitin-glucuronate C5-epimerase, which catalyzes the conversion of d-glucuronate to l-iduronate on a polysaccharide level.
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Ciancia M, Matulewicz MC, Tuvikene R. Structural Diversity in Galactans From Red Seaweeds and Its Influence on Rheological Properties. FRONTIERS IN PLANT SCIENCE 2020; 11:559986. [PMID: 33013979 PMCID: PMC7511586 DOI: 10.3389/fpls.2020.559986] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/21/2020] [Indexed: 05/08/2023]
Abstract
Galactans are important components of many plant cell walls. Besides, they are the major polysaccharides in extracellular matrixes from different seaweeds, and other marine organisms, which have an acidic character due to the presence of sulfate groups in their structures. In particular, most of the red seaweeds biosynthesize sulfated galactans with very special linear backbones, constituted by alternating (1→3)-β-d-galactopyranose units (A-unit) and (1→4)-α-galactopyranose residues (B-unit). In the industrially significant seaweeds as source of hydrocolloids, B-units belong either to the d-series and they produce carrageenans (as in the order Gigartinales), or to the l-series, and they are sources of agarose and/or structurally related polymers (i.e., Gelidiales, Gracilariales). In both cases, the latter units appear as cyclized 3,6-anhydro-α-galactose in certain amounts, which can be increased by alkaline cyclization of α-galactose 6-sulfate units. Besides, it has been clearly shown that some red algae produce different amounts of both galactan structures, known as d/l-hybrids. It is not yet clear if they comprise both diasteromeric types of units in the same molecule, or if they are mixtures of carrageenans and agarans that are very difficult to separate. It has been reported that the biosynthesis of these galactans, showing that the nucleotide transport for d-galactopyranose units is UDP-d-Gal, while for l-galactose, it is GDP-l-Gal, so, there is a different pathway in the biosynthesis of agarans. However, at least in those seaweeds that produce carrageenans as major galactans, but also agarans, both synthetic pathways should coexist. Another interesting characteristic of these galactans is the important variation in the sulfation patterns, which modulate their physical behavior in aqueous solutions. Although the most common carrageenans are of the κ/ι- and λ-types (with A-units sulfated at the 4- and 2-positions, respectively) and usually in agarans, when sulfated, is at the 6-position, many other sulfate arrangements have been reported, greatly influencing the functional properties of the corresponding galactans. Other substituents can modify their structures, as methyl ethers, pyruvic acid ketals, acetates, and single stubs of xylose or other monosaccharides. It has been shown that structural heterogeneity at some extent is essential for the proper functional performance of red algal galactans.
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Affiliation(s)
- Marina Ciancia
- Universidad de Buenos Aires, Facultad de Agronomía, Departamento de Biología Aplicada y Alimentos, Cátedra de Química de Biomoléculas (CIHIDECAR,CONICET-UBA), Buenos Aires, Argentina
| | - María Cristina Matulewicz
- Universidad de Buenos Aires – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigación de Hidratos de Carbono (CIHIDECAR), Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Buenos Aires, Argentina
- *Correspondence: María Cristina Matulewicz,
| | - Rando Tuvikene
- Tallinn University, School of Natural Sciences and Health, Tallinn, Estonia
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25
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Multi-enzyme systems and recombinant cells for synthesis of valuable saccharides: Advances and perspectives. Biotechnol Adv 2019; 37:107406. [DOI: 10.1016/j.biotechadv.2019.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/30/2019] [Accepted: 06/08/2019] [Indexed: 02/07/2023]
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Characterization of the First Bacterial and Thermostable GDP-Mannose 3,5-Epimerase. Int J Mol Sci 2019; 20:ijms20143530. [PMID: 31330931 PMCID: PMC6678494 DOI: 10.3390/ijms20143530] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/25/2023] Open
Abstract
GDP-mannose 3,5-epimerase (GM35E) catalyzes the conversion of GDP-mannose towards GDP-l-galactose and GDP-l-gulose. Although this reaction represents one of the few enzymatic routes towards the production of l-sugars and derivatives, it has not yet been exploited for that purpose. One of the reasons is that so far only GM35Es from plants have been characterized, yielding biocatalysts that are relatively unstable and difficult to express heterologously. Through the mining of sequence databases, we succeeded in identifying a promising bacterial homologue. The gene from the thermophilic organism Methylacidiphilum fumariolicum was codon optimized for expression in Escherichia coli, resulting in the production of 40 mg/L of recombinant protein. The enzyme was found to act as a self-sufficient GM35E, performing three chemical reactions in the same active site. Furthermore, the biocatalyst was highly stable at temperatures up to 55 °C, making it well suited for the synthesis of new carbohydrate products with application in the pharma industry.
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Fenech M, Amaya I, Valpuesta V, Botella MA. Vitamin C Content in Fruits: Biosynthesis and Regulation. FRONTIERS IN PLANT SCIENCE 2019; 9:2006. [PMID: 30733729 PMCID: PMC6353827 DOI: 10.3389/fpls.2018.02006] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/31/2018] [Indexed: 05/19/2023]
Abstract
Throughout evolution, a number of animals including humans have lost the ability to synthesize ascorbic acid (ascorbate, vitamin C), an essential molecule in the physiology of animals and plants. In addition to its main role as an antioxidant and cofactor in redox reactions, recent reports have shown an important role of ascorbate in the activation of epigenetic mechanisms controlling cell differentiation, dysregulation of which can lead to the development of certain types of cancer. Although fruits and vegetables constitute the main source of ascorbate in the human diet, rising its content has not been a major breeding goal, despite the large inter- and intraspecific variation in ascorbate content in fruit crops. Nowadays, there is an increasing interest to boost ascorbate content, not only to improve fruit quality but also to generate crops with elevated stress tolerance. Several attempts to increase ascorbate in fruits have achieved fairly good results but, in some cases, detrimental effects in fruit development also occur, likely due to the interaction between the biosynthesis of ascorbate and components of the cell wall. Plants synthesize ascorbate de novo mainly through the Smirnoff-Wheeler pathway, the dominant pathway in photosynthetic tissues. Two intermediates of the Smirnoff-Wheeler pathway, GDP-D-mannose and GDP-L-galactose, are also precursors of the non-cellulosic components of the plant cell wall. Therefore, a better understanding of ascorbate biosynthesis and regulation is essential for generation of improved fruits without developmental side effects. This is likely to involve a yet unknown tight regulation enabling plant growth and development, without impairing the cell redox state modulated by ascorbate pool. In certain fruits and developmental conditions, an alternative pathway from D-galacturonate might be also relevant. We here review the regulation of ascorbate synthesis, its close connection with the cell wall, as well as different strategies to increase its content in plants, with a special focus on fruits.
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Affiliation(s)
- Mario Fenech
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Consejo Superior de Investigaciones Científicas, Universidad de Málaga, Málaga, Spain
| | - Iraida Amaya
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Area de Genómica y Biotecnología, Centro de Málaga, Spain
| | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Consejo Superior de Investigaciones Científicas, Universidad de Málaga, Málaga, Spain
| | - Miguel A. Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Consejo Superior de Investigaciones Científicas, Universidad de Málaga, Málaga, Spain
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28
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Yu S, Shen H, Cheng Y, Zhu Y, Li X, Mu W. Structural and Functional Basis of Difructose Anhydride III Hydrolase, Which Sequentially Converts Inulin Using the Same Catalytic Residue. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuhuai Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Hui Shen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuanyuan Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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Narnoliya LK, Sangwan RS, Singh SP. Transcriptome mining and in silico structural and functional analysis of ascorbic acid and tartaric acid biosynthesis pathway enzymes in rose-scanted geranium. Mol Biol Rep 2018; 45:315-326. [DOI: 10.1007/s11033-018-4164-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/11/2018] [Indexed: 11/30/2022]
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Deciphering the sugar biosynthetic pathway and tailoring steps of nucleoside antibiotic A201A unveils a GDP-l-galactose mutase. Proc Natl Acad Sci U S A 2017; 114:4948-4953. [PMID: 28438999 DOI: 10.1073/pnas.1620191114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Galactose, a monosaccharide capable of assuming two possible configurational isomers (d-/l-), can exist as a six-membered ring, galactopyranose (Galp), or as a five-membered ring, galactofuranose (Galf). UDP-galactopyranose mutase (UGM) mediates the conversion of pyranose to furanose thereby providing a precursor for d-Galf Moreover, UGM is critical to the virulence of numerous eukaryotic and prokaryotic human pathogens and thus represents an excellent antimicrobial drug target. However, the biosynthetic mechanism and relevant enzymes that drive l-Galf production have not yet been characterized. Herein we report that efforts to decipher the sugar biosynthetic pathway and tailoring steps en route to nucleoside antibiotic A201A led to the discovery of a GDP-l-galactose mutase, MtdL. Systematic inactivation of 18 of the 33 biosynthetic genes in the A201A cluster and elucidation of 10 congeners, coupled with feeding and in vitro biochemical experiments, enabled us to: (i) decipher the unique enzyme, GDP-l-galactose mutase associated with production of two unique d-mannose-derived sugars, and (ii) assign two glycosyltransferases, four methyltransferases, and one desaturase that regiospecifically tailor the A201A scaffold and display relaxed substrate specificities. Taken together, these data provide important insight into the origin of l-Galf-containing natural product biosynthetic pathways with likely ramifications in other organisms and possible antimicrobial drug targeting strategies.
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Beerens K, Van Overtveldt S, Desmet T. The “epimerring” highlights the potential of carbohydrate epimerases for rare sugar production. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1306738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Koen Beerens
- Unit for Biocatalysis and Enzyme Engineering, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Stevie Van Overtveldt
- Unit for Biocatalysis and Enzyme Engineering, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Unit for Biocatalysis and Enzyme Engineering, Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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32
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The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development. Nat Commun 2016; 7:12119. [PMID: 27381418 PMCID: PMC4935801 DOI: 10.1038/ncomms12119] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/01/2016] [Indexed: 02/06/2023] Open
Abstract
Nucleotide sugar transport across Golgi membranes is essential for the luminal biosynthesis of glycan structures. Here we identify GDP-fucose transporter 1 (GFT1), an Arabidopsis nucleotide sugar transporter that translocates GDP-L-fucose into the Golgi lumen. Using proteo-liposome-based transport assays, we show that GFT preferentially transports GDP-L-fucose over other nucleotide sugars in vitro, while GFT1-silenced plants are almost devoid of L-fucose in cell wall-derived xyloglucan and rhamnogalacturonan II. Furthermore, these lines display reduced L-fucose content in N-glycan structures accompanied by severe developmental growth defects. We conclude that GFT1 is the major nucleotide sugar transporter for import of GDP-L-fucose into the Golgi and is required for proper plant growth and development. Nucleotide sugars are transported from the cytoplasm to the Golgi lumen where they are incorporated into cell wall polysaccharides and used for glycosylation of proteins and lipids. Here the authors identify GFT1, an Arabidopsis Golgi-localized GDP-fucose transporter that is required for plant growth and development
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Van Overtveldt S, Verhaeghe T, Joosten HJ, van den Bergh T, Beerens K, Desmet T. A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications. Biotechnol Adv 2015; 33:1814-28. [DOI: 10.1016/j.biotechadv.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/15/2015] [Accepted: 10/22/2015] [Indexed: 12/26/2022]
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Höller S, Ueda Y, Wu L, Wang Y, Hajirezaei MR, Ghaffari MR, von Wirén N, Frei M. Ascorbate biosynthesis and its involvement in stress tolerance and plant development in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2015; 88:545-60. [PMID: 26129988 DOI: 10.1007/s11103-015-0341-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/23/2015] [Indexed: 05/26/2023]
Abstract
Ascorbic acid (AsA) biosynthesis and its implications for stress tolerance and plant development were investigated in a set of rice knock-out (KO) mutants for AsA biosynthetic genes and their wild-types. KO of two isoforms of GDP-D-mannose epimerase (OsGME) reduced the foliar AsA level by 20-30%, and KO of GDP-L-galactose phosphorylase (OsGGP) by 80%, while KO of myo-inositol oxygenase (OsMIOX) did not affect foliar AsA levels. AsA concentration was negatively correlated with lipid peroxidation in foliar tissue under ozone stress and zinc deficiency, but did not affect the sensitivity to iron toxicity. Lack of AsA reduced the photosynthetic efficiency as represented by the maximum carboxylation rate of Rubisco (Vmax), the maximum electron transport rate (Jmax) and the chlorophyll fluorescence parameter ΦPSII. Mutants showed lower biomass production than their wild-types, especially when OsGGP was lacking (around 80% reductions). All plants except for KO mutants of OsGGP showed distinct peaks in foliar AsA concentrations during the growth, which were consistent with up-regulation of OsGGP, suggesting that OsGGP plays a pivotal role in regulating foliar AsA levels during different growth stages. In conclusion, our data demonstrate multiple roles of AsA in stress tolerance and development of rice.
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Affiliation(s)
- Stefanie Höller
- Institute of Crop Science and Resource Conservation (INRES), Abiotic Stress Tolerance in Crops, University of Bonn, Karlrobert-Kreiten Strasse 13, 53115, Bonn, Germany
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Mizrachi E, Maloney VJ, Silberbauer J, Hefer CA, Berger DK, Mansfield SD, Myburg AA. Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus. THE NEW PHYTOLOGIST 2015; 206:1351-63. [PMID: 25388807 DOI: 10.1111/nph.13152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/25/2014] [Indexed: 05/13/2023]
Abstract
Tension wood has distinct physical and chemical properties, including altered fibre properties, cell wall composition and ultrastructure. It serves as a good system for investigating the genetic regulation of secondary cell wall biosynthesis and wood formation. The reference genome sequence for Eucalyptus grandis allows investigation of the global transcriptional reprogramming that accompanies tension wood formation in this global wood fibre crop. We report the first comprehensive analysis of physicochemical wood property changes in tension wood of Eucalyptus measured in a hybrid (E. grandis × Eucalyptus urophylla) clone, as well as genome-wide gene expression changes in xylem tissues 3 wk post-induction using RNA sequencing. We found that Eucalyptus tension wood in field-grown trees is characterized by an increase in cellulose, a reduction in lignin, xylose and mannose, and a marked increase in galactose. Gene expression profiling in tension wood-forming tissue showed corresponding down-regulation of monolignol biosynthetic genes, and differential expression of several carbohydrate active enzymes. We conclude that alterations of cell wall traits induced by tension wood formation in Eucalyptus are a consequence of a combination of down-regulation of lignin biosynthesis and hemicellulose remodelling, rather than the often proposed up-regulation of the cellulose biosynthetic pathway.
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Affiliation(s)
- Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Victoria J Maloney
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Janine Silberbauer
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Charles A Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Dave K Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJG, Adams PD, Petzold CJ, Pauly M, Willats WGT, Heazlewood JL, Scheller HV. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. THE PLANT CELL 2015; 27:1218-27. [PMID: 25804536 PMCID: PMC4558686 DOI: 10.1105/tpc.114.133827] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/05/2015] [Indexed: 05/02/2023]
Abstract
Most glycosylation reactions require activated glycosyl donors in the form of nucleotide sugars to drive processes such as posttranslational modifications and polysaccharide biosynthesis. Most plant cell wall polysaccharides are biosynthesized in the Golgi apparatus from cytosolic-derived nucleotide sugars, which are actively transferred into the Golgi lumen by nucleotide sugar transporters (NSTs). An exception is UDP-xylose, which is biosynthesized in both the cytosol and the Golgi lumen by a family of UDP-xylose synthases. The NST-based transport of UDP-xylose into the Golgi lumen would appear to be redundant. However, employing a recently developed approach, we identified three UDP-xylose transporters in the Arabidopsis thaliana NST family and designated them UDP-XYLOSE TRANSPORTER1 (UXT1) to UXT3. All three transporters localize to the Golgi apparatus, and UXT1 also localizes to the endoplasmic reticulum. Mutants in UXT1 exhibit ∼30% reduction in xylose in stem cell walls. These findings support the importance of the cytosolic UDP-xylose pool and UDP-xylose transporters in cell wall biosynthesis.
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Affiliation(s)
- Berit Ebert
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Carsten Rautengarten
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Xiaoyuan Guo
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark
| | - Guangyan Xiong
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Solomon Stonebloom
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Andreia M Smith-Moritz
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Thomas Herter
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Leanne Jade G Chan
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D Adams
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Bioengineering, University of California, Berkeley, California 94720
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - William G T Willats
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Henrik Vibe Scheller
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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Tiwari P, Singh N, Dixit A, Choudhury D. Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily. Proteins 2014; 82:2842-56. [DOI: 10.1002/prot.24647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 06/19/2014] [Accepted: 07/15/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Pratibha Tiwari
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
| | - Noopur Singh
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
| | - Aparna Dixit
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
| | - Devapriya Choudhury
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
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The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis. Proc Natl Acad Sci U S A 2014; 111:11563-8. [PMID: 25053812 DOI: 10.1073/pnas.1406073111] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Plant cells are surrounded by a cell wall that plays a key role in plant growth, structural integrity, and defense. The cell wall is a complex and diverse structure that is mainly composed of polysaccharides. The majority of noncellulosic cell wall polysaccharides are produced in the Golgi apparatus from nucleotide sugars that are predominantly synthesized in the cytosol. The transport of these nucleotide sugars from the cytosol into the Golgi lumen is a critical process for cell wall biosynthesis and is mediated by a family of nucleotide sugar transporters (NSTs). Numerous studies have sought to characterize substrate-specific transport by NSTs; however, the availability of certain substrates and a lack of robust methods have proven problematic. Consequently, we have developed a novel approach that combines reconstitution of NSTs into liposomes and the subsequent assessment of nucleotide sugar uptake by mass spectrometry. To address the limitation of substrate availability, we also developed a two-step reaction for the enzymatic synthesis of UDP-l-rhamnose (Rha) by expressing the two active domains of the Arabidopsis UDP-l-Rha synthase. The liposome approach and the newly synthesized substrates were used to analyze a clade of Arabidopsis NSTs, resulting in the identification and characterization of six bifunctional UDP-l-Rha/UDP-d-galactose (Gal) transporters (URGTs). Further analysis of loss-of-function and overexpression plants for two of these URGTs supported their roles in the transport of UDP-l-Rha and UDP-d-Gal for matrix polysaccharide biosynthesis.
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Biosynthetic Mechanism forL-Gulose in Main Polar Lipids ofThermoplasma acidophilumand Possible Resemblance to Plant Ascorbic Acid Biosynthesis. Biosci Biotechnol Biochem 2014; 77:2087-93. [DOI: 10.1271/bbb.130442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rosa JCC, Colombo LT, Alvim MCT, Avonce N, Van Dijck P, Passos FML. Metabolic engineering of Kluyveromyces lactis for L-ascorbic acid (vitamin C) biosynthesis. Microb Cell Fact 2013; 12:59. [PMID: 23799937 PMCID: PMC3699391 DOI: 10.1186/1475-2859-12-59] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND L-ascorbic acid (L-AA) is naturally synthesized in plants from D-glucose by 10 steps pathway. The pathway branch to synthesize L-galactose, the key intermediate for L-ascorbic acid biosynthesis, has been recently elucidated. Budding yeast produces an 5-carbon ascorbic acid analogue Dehydro-D-arabinono 1,4-lactone (D-DAL), which is synthesized from D-arabinose. Yeast is able to synthesize L-ascorbic acid only if it is cultivated in the presence of one of its precursors: L-galactose, L-galactono 1,4-lactone, or L-gulono 1,4-lactone extracted from plants or animals. To avoid feeding the yeast culture with this "L" enantiomer, we engineered Kluyveromyces lactis with L-galactose biosynthesis pathway genes: GDP-mannose 3,5-epimerase (GME), GDP-L-galactose phosphorylase (VTC2) and L-galactose-1-phosphate phosphatase (VTC4) isolated from Arabidopsis thaliana. RESULTS Plasmids were constructed and modified such that the cloned plant genes were targeted to the K. lactis LAC4 Locus by homologous recombination and that the expression was associated to the growth on D-galactose or lactose. Upon K. lactis transformation, GME was under the control of the native LAC4 promoter whereas VTC2 and VTC4 were expressed from the S. cerevisiae promoters GPD1 and ADH1 respectively. The expression in K. lactis, of the L-galactose biosynthesis genes was determined by Reverse Transcriptase-PCR and western blotting. The recombinant yeasts were capable to produce about 30 mg.L(-1) of L-ascorbic acid in 48 hours of cultivation when cultured on rich medium with 2% (w/v) D-galactose. We also evaluated the L-AA production culturing recombinant recombinant strains in cheese whey, a waste product during cheese production, as an alternative source of lactose. CONCLUSIONS This work is the first attempt to engineer K. lactis cells for L-ascorbic acid biosynthesis by a fermentation process without any trace of "L" isomers precursors in the culture medium. We have engineered K. lactis strains capable of converting lactose and D-galactose into L-galactose, by the integration of the genes from the A. thaliana L-galactose pathway. L-galactose is a rare sugar, which is one of the main precursors for L-AA production.
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Affiliation(s)
- Júlio César Câmara Rosa
- Laboratório de Fisiologia de Microrganismos, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Brazil
- Departamento de Microbiologia, Universidade Federal de Viçosa, campus Viçosa, Minas Gerais, Brasil
| | - Lívia Tavares Colombo
- Laboratório de Fisiologia de Microrganismos, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Brazil
- Departamento de Microbiologia, Universidade Federal de Viçosa, campus Viçosa, Minas Gerais, Brasil
| | - Mariana Caroline Tocantins Alvim
- Laboratório de Fisiologia de Microrganismos, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Brazil
- Departamento de Microbiologia, Universidade Federal de Viçosa, campus Viçosa, Minas Gerais, Brasil
| | - Nelson Avonce
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU, Leuven
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU, Leuven
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Flávia Maria Lopes Passos
- Laboratório de Fisiologia de Microrganismos, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Brazil
- Departamento de Microbiologia, Universidade Federal de Viçosa, campus Viçosa, Minas Gerais, Brasil
- Av. P. H. Rolfs s/nº, 36571-000, Laboratório de Fisiologia de Microrganismos, BIOAGRO, Universidade Federal de Viçosa, Viçosa–MG, Brazil
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Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus. Biosci Rep 2013; 33:BSR20130017. [PMID: 23611437 PMCID: PMC3699295 DOI: 10.1042/bsr20130017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Enzymes synthesizing the bacterial CP (capsular polysaccharide) are attractive antimicrobial targets. However, we lack critical information about the structure and mechanism of many of them. In an effort to reduce that gap, we have determined three different crystal structures of the enzyme CapE of the human pathogen Staphylococcus aureus. The structure reveals that CapE is a member of the SDR (short-chain dehydrogenase/reductase) super-family of proteins. CapE assembles in a hexameric complex stabilized by three major contact surfaces between protein subunits. Turnover of substrate and/or coenzyme induces major conformational changes at the contact interface between protein subunits, and a displacement of the substrate-binding domain with respect to the Rossmann domain. A novel dynamic element that we called the latch is essential for remodelling of the protein–protein interface. Structural and primary sequence alignment identifies a group of SDR proteins involved in polysaccharide synthesis that share the two salient features of CapE: the mobile loop (latch) and a distinctive catalytic site (MxxxK). The relevance of these structural elements was evaluated by site-directed mutagenesis.
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42
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McCallum M, Shaw GS, Creuzenet C. Comparison of predicted epimerases and reductases of the Campylobacter jejuni D-altro- and L-gluco-heptose synthesis pathways. J Biol Chem 2013; 288:19569-80. [PMID: 23689373 DOI: 10.1074/jbc.m113.468066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uniquely modified heptoses found in surface carbohydrates of bacterial pathogens are potential therapeutic targets against such pathogens. Our recent biochemical characterization of the GDP-6-deoxy-D-manno- and GDP-6-deoxy-D-altro-heptose biosynthesis pathways has provided the foundation for elucidation of the more complex L-gluco-heptose synthesis pathway of Campylobacter jejuni strain NCTC 11168. In this work we use GDP-4-keto,6-deoxy-D-lyxo-heptose as a surrogate substrate to characterize three enzymes predicted to be involved in this pathway: WcaGNCTC (also known as Cj1427), MlghB (Cj1430), and MlghC (Cj1428). We compare them with homologues involved in d-altro-heptose production: WcaG81176 (formerly WcaG), DdahB (Cjj1430), and DdahC (Cjj1427). We show that despite high levels of similarity, the enzymes have pathway-specific catalytic activities and substrate specificities. MlghB forms three products via C3 and C5 epimerization activities, whereas its DdahB homologue only had C3 epimerase activity along its cognate pathway. MlghC is specific for the double C3/C5 epimer generated by MlghB and produces L-gluco-heptose via stereospecific C4 reductase activity. In contrast, its homologue DdahC only uses the C3 epimer to yield d-altro-heptose via C4 reduction. Finally, we show that WcaGNCTC is not necessary for L-gluco-heptose synthesis and does not affect its production by MlghB and MlghC, in contrast to its homologue WcaG81176, that has regulatory activity on d-altro-heptose synthesis. These studies expand our fundamental understanding of heptose modification, provide new glycobiology tools to synthesize novel heptose derivatives with biomedical applications, and provide a foundation for the structure function analysis of these enzymes.
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Affiliation(s)
- Matthew McCallum
- Department of Microbiology and Immunology, Infectious Diseases Research Group, University of Western Ontario, London, Ontario N6A 5C1, Canada
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43
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Mortimer JC, Yu X, Albrecht S, Sicilia F, Huichalaf M, Ampuero D, Michaelson LV, Murphy AM, Matsunaga T, Kurz S, Stephens E, Baldwin TC, Ishii T, Napier JA, Weber AP, Handford MG, Dupree P. Abnormal glycosphingolipid mannosylation triggers salicylic acid-mediated responses in Arabidopsis. THE PLANT CELL 2013; 25:1881-94. [PMID: 23695979 PMCID: PMC3694712 DOI: 10.1105/tpc.113.111500] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The Arabidopsis thaliana protein GOLGI-LOCALIZED NUCLEOTIDE SUGAR TRANSPORTER (GONST1) has been previously identified as a GDP-d-mannose transporter. It has been hypothesized that GONST1 provides precursors for the synthesis of cell wall polysaccharides, such as glucomannan. Here, we show that in vitro GONST1 can transport all four plant GDP-sugars. However, gonst1 mutants have no reduction in glucomannan quantity and show no detectable alterations in other cell wall polysaccharides. By contrast, we show that a class of glycosylated sphingolipids (glycosylinositol phosphoceramides [GIPCs]) contains Man and that this mannosylation is affected in gonst1. GONST1 therefore is a Golgi GDP-sugar transporter that specifically supplies GDP-Man to the Golgi lumen for GIPC synthesis. gonst1 plants have a dwarfed phenotype and a constitutive hypersensitive response with elevated salicylic acid levels. This suggests an unexpected role for GIPC sugar decorations in sphingolipid function and plant defense signaling. Additionally, we discuss these data in the context of substrate channeling within the Golgi.
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Affiliation(s)
- Jenny C. Mortimer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Sandra Albrecht
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Francesca Sicilia
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Mariela Huichalaf
- Department of Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Diego Ampuero
- Department of Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Louise V. Michaelson
- Biological Chemistry Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Alex M. Murphy
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Toshiro Matsunaga
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
- National Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8666, Japan
| | - Samantha Kurz
- Institute of Plant Biochemistry, Heinrich-Heine-Universität, 40225 Duesseldorf, Germany
| | - Elaine Stephens
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Timothy C. Baldwin
- School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1SB, United Kingdom
| | - Tadashi Ishii
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Johnathan A. Napier
- Biological Chemistry Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Andreas P.M. Weber
- Institute of Plant Biochemistry, Heinrich-Heine-Universität, 40225 Duesseldorf, Germany
| | - Michael G. Handford
- Department of Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Address correspondence to
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Kim MS, Lim A, Yang SW, Park J, Lee D, Shin DH. Structure andin silicosubstrate-binding mode of ADP-L-glycero-D-manno-heptose 6-epimerase fromBurkholderia thailandensis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:658-68. [DOI: 10.1107/s0907444913001030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/11/2013] [Indexed: 11/11/2022]
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Handford M, Rodríguez-Furlán C, Marchant L, Segura M, Gómez D, Alvarez-Buylla E, Xiong GY, Pauly M, Orellana A. Arabidopsis thaliana AtUTr7 encodes a golgi-localized UDP-glucose/UDP-galactose transporter that affects lateral root emergence. MOLECULAR PLANT 2012; 5:1263-80. [PMID: 22933714 DOI: 10.1093/mp/sss074] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nucleotide sugar transporters (NSTs) are antiporters comprising a gene family that plays a fundamental role in the biosynthesis of complex cell wall polysaccharides and glycoproteins in plants. However, due to the limited number of related mutants that have observable phenotypes, the biological function(s) of most NSTs in cell wall biosynthesis and assembly have remained elusive. Here, we report the characterization of AtUTr7 from Arabidopsis (Arabidopsis thaliana (L.) Heynh.), which is homologous to multi-specific UDP-sugar transporters from Drosophila melanogaster, humans, and Caenorhabditis elegans. We show that AtUTr7 possesses the common structural characteristics conserved among NSTs. Using a green fluorescent protein (GFP) tagged version, we demonstrate that AtUTr7 is localized in the Golgi apparatus. We also show that AtUTr7 is widely expressed, especially in the roots and in specific floral organs. Additionally, the results of an in vitro nucleotide sugar transport assay carried out with a tobacco and a yeast expression system suggest that AtUTr7 is capable of transferring UDP-Gal and UDP-Glc, but not a range of other UDP- and GDP-sugars, into the Golgi lumen. Mutants lacking expression of AtUTr7 exhibited an early proliferation of lateral roots as well as distorted root hairs when cultivated at high sucrose concentrations. Furthermore, the distribution of homogalacturonan with a low degree of methyl esterification differed in lateral root tips of the mutant compared to wild-type plants, although additional analytical procedures revealed no further differences in the composition of the root cell walls. This evidence suggests that the transport of UDP-Gal and UDP-Glc into the Golgi under conditions of high root biomass production plays a role in lateral root and root hair development.
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Russo L, Zanini S, Giannoni P, Landi E, Villa A, Sandri M, Riccardi C, Quarto R, Doglia SM, Nicotra F, Cipolla L. The influence of plasma technology coupled to chemical grafting on the cell growth compliance of 3D hydroxyapatite scaffolds. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2012; 23:2727-2738. [PMID: 22875605 DOI: 10.1007/s10856-012-4727-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 07/23/2012] [Indexed: 06/01/2023]
Abstract
The development of advanced materials with biomimetic features in order to elicit desired biological responses and to guarantee tissue biocompatibility is recently gaining attention for tissue engineering applications. Bioceramics, such as hydroxyapatite-based biomaterials are now used in a number of different applications throughout the body, covering all areas of the skeleton, due to their biological and chemical similarity to the inorganic phases of bones. When bioactive sintered hydroxyapatite (HA) is desired, biomolecular modification of these materials is needed. In the present work, we investigated the influence of plasma surface modification coupled to chemical grafting on the cell growth compliance of HA 3D scaffolds.
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Affiliation(s)
- Laura Russo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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47
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McCallum M, Shaw SD, Shaw GS, Creuzenet C. Complete 6-deoxy-D-altro-heptose biosynthesis pathway from Campylobacter jejuni: more complex than anticipated. J Biol Chem 2012; 287:29776-88. [PMID: 22787156 DOI: 10.1074/jbc.m112.390492] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Campylobacter jejuni capsule is important for colonization and virulence in various infection models. In most strains, the capsule includes a modified heptose whose biological role and biosynthetic pathway are unknown. To decipher the biosynthesis pathway for the 6-deoxy-D-altro-heptose of strain 81-176, we previously showed that the 4,6-dehydratase WcbK and the reductase WcaG generated GDP-6-deoxy-D-manno-heptose, but the C3 epimerase necessary to form GDP-6-deoxy-D-altro-heptose was not identified. Herein, we characterized the putative C3/C5 epimerase Cjj1430 and C3/C5 epimerase/C4 reductase Cjj1427 from the capsular cluster. We demonstrate that GDP-6-deoxy-D-altro-heptose biosynthesis is more complex than anticipated and requires the sequential action of WcbK, Cjj1430, and Cjj1427. We show that Cjj1430 serves as C3 epimerase devoid of C5 epimerization activity and that Cjj1427 has no epimerization activity and only serves as a reductase to produce GDP-6-deoxy-D-altro-heptose. Cjj1430 and Cjj1427 are the only members of the C3/C5 epimerases and C3/C5 epimerase/C4 reductase families shown to have activity on a heptose substrate and to exhibit only one of their two to three potential activities, respectively. Furthermore, we show that although the reductase WcaG is not part of the main pathway, its presence and its product affect the outcome of the pathway in a complex regulatory loop involving Cjj1427. This work provides the grounds for the elucidation of similar pathways found in other C. jejuni strains and other pathogens. It provides new molecular tools for the synthesis of carbohydrate antigens useful for vaccination and for the screening of enzymatic inhibitors that may have antibacterial effects.
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Affiliation(s)
- Matthew McCallum
- Department of Microbiology and Immunology, Infectious Diseases Research Group, University of Western Ontario, London, Ontario N6A 5C1, Canada
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48
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Highly selective l-threonine 3-dehydrogenase from Cupriavidus necator and its use in determination of l-threonine. Anal Biochem 2011; 410:44-56. [DOI: 10.1016/j.ab.2010.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/29/2010] [Accepted: 11/03/2010] [Indexed: 12/12/2022]
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49
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Negri AS, Robotti E, Prinsi B, Espen L, Marengo E. Proteins involved in biotic and abiotic stress responses as the most significant biomarkers in the ripening of Pinot Noir skins. Funct Integr Genomics 2011; 11:341-55. [PMID: 21234783 DOI: 10.1007/s10142-010-0205-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 11/14/2010] [Accepted: 12/18/2010] [Indexed: 12/30/2022]
Abstract
We propose an integrated approach, obtained by the combination of multivariate statistics and proteomics, useful to isolate candidate biomarkers for the evaluation of grape ripening. We carried out a comparative 2-DE analysis of grape skins collected in three moments of ripening and analyzed the spot volume dataset through the application of principal component analysis followed by forward stepwise-linear discriminant analysis. This technique allowed to discriminate véraison, quite mature and mature samples, and to sort the matched spots according to their significance. We identified 36 spots showing high discriminating coefficients through liquid chromatography - electrospray ionization - tandem mass spectrometry (LC-ESI-MS/MS). Most of them were involved in biotic and abiotic stress responses indicating these enzymes as good candidate markers of berry ripening. These evidences hint at a likely developmental role of these proteins, in addition to their reported activity in stress events. Restricting the same statistical analysis to the samples belonging to the two last stages, it was indicated that this approach can clearly distinguish these close and similar phases of berry development. Taken all together, these results bear out that the employment of the combination of 2-DE and multivariate statistics is a reliable tool in the identification of new protein markers for describing the ripening phases and to assess the overall quality of the fruit.
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Affiliation(s)
- Alfredo Simone Negri
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, via Celoria 2, Facoltà di Agraria, Milan, Italy
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50
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Harris LG, Schofield WCE, Doores KJ, Davis BG, Badyal JPS. Rewritable glycochips. J Am Chem Soc 2009; 131:7755-61. [PMID: 19438244 DOI: 10.1021/ja901294r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe microarraying of carbohydrates for protein screening using either disulfide bridge or Schiff base imine immobilization chemistries on plasmachemical deposited functional nanolayers. The commonly observed issue of nonspecific background binding of proteins is overcome by spotting carbohydrates through a protein-resistant overlayer yielding spatially localized interaction with a reactive functional underlayer.
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Affiliation(s)
- L G Harris
- Department of Chemistry, Science Laboratories, Durham University, Durham DH1 3LE, UK
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