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Popović I, Dončević L, Biba R, Košpić K, Barbalić M, Marinković M, Cindrić M. Advancements in Adenine Nucleotides Extraction and Quantification from a Single Drop of Human Blood. Molecules 2024; 29:5630. [PMID: 39683788 DOI: 10.3390/molecules29235630] [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: 10/31/2024] [Revised: 11/25/2024] [Accepted: 11/26/2024] [Indexed: 12/18/2024] Open
Abstract
Adenine nucleotides (ANs)-adenosine 5'-triphosphate (ATP), adenosine 5'-diphosphate (ADP), and adenosine 5'-monophosphate (AMP)-are essential for energy transfer and the supply of countless processes within cellular metabolism. Their concentrations can be expressed as adenylate energy charge (AEC), a measure of cellular metabolic energy that directly correlates with the homeostasis of the organism. AEC index has broad diagnostic potential, as reduced ATP levels are associated to various conditions, such as inflammatory diseases, metabolic disorders, and cancer. We introduce a novel methodology for rapid isolation, purification, and quantification of ANs from a single drop of capillary blood. Of all the stationary phases tested, activated carbon proved to be the most efficient for the purification of adenine nucleotides, using an automated micro-solid phase extraction (µ-SPE) platform. An optimized µ-SPE method, coupled with RP-HPLC and a run time of 30 min, provides a reliable analytical framework for adenine nucleotide analysis of diverse biological samples. AN concentrations measured in capillary blood samples were 1393.1 µM, 254.8 µM, and 76.9 µM for ATP, ADP, and AMP molecules aligning with values reported in the literature. Overall, this study presents a streamlined and precise approach for analyzing ANs from microliters of blood, offering promising applications in clinical diagnostics.
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Affiliation(s)
- Ivana Popović
- Doctoral Study of Biophysics, Faculty of Science, University of Split, 21000 Split, Croatia
- Faculty of Science, University of Split, 21000 Split, Croatia
| | - Lucija Dončević
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Renata Biba
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Karla Košpić
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Maja Barbalić
- Faculty of Science, University of Split, 21000 Split, Croatia
| | - Mija Marinković
- Faculty of Science, University of Split, 21000 Split, Croatia
| | - Mario Cindrić
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
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2
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Rodrigues TB, Cunha RL, Barci PEP, Santos-Neto ÁJ, Lanças FM. Analysis of human biological samples using porous graphitic carbon columns and liquid chromatography-mass spectrometry: a review. Anal Bioanal Chem 2024; 416:5233-5253. [PMID: 39158631 DOI: 10.1007/s00216-024-05458-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) has emerged as a powerful analytical technique for analyzing complex biological samples. Among various chromatographic stationary phases, porous graphitic carbon (PGC) columns have attracted significant attention due to their unique properties-such as the ability to separate both polar and non-polar compounds and their stability through all pH ranges and to high temperatures-besides the compatibility with LC-MS. This review discusses the applicability of PGC for SPE and separation in LC-MS-based analyses of human biological samples, highlighting the diverse applications of PGC-LC-MS in analyzing endogenous metabolites, pharmaceuticals, and biomarkers, such as glycans, proteins, oligosaccharides, sugar phosphates, and nucleotides. Additionally, the fundamental principles underlying PGC column chemistry and its advantages, challenges, and advances in method development are explored. This comprehensive review aims to provide researchers and practitioners with a valuable resource for understanding the capabilities and limitations of PGC columns in LC-MS-based analysis of human biological samples, thereby facilitating advancements in analytical methodologies and biomedical research.
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Affiliation(s)
- Taís Betoni Rodrigues
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil.
| | - Ricardo Leal Cunha
- Forensic Toxicology Laboratory, Scientific Police, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Paulo Emílio Pereira Barci
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil
| | - Álvaro José Santos-Neto
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil
| | - Fernando Mauro Lanças
- Laboratory of Chromatography (CROMA), São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, São Paulo, 13560-970, Brazil
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3
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Jo S, El-Demerdash A, Owen C, Srivastava V, Wu D, Kikuchi S, Reed J, Hodgson H, Harkess A, Shu S, Plott C, Jenkins J, Williams M, Boston LB, Lacchini E, Qu T, Goossens A, Grimwood J, Schmutz J, Leebens-Mack J, Osbourn A. Unlocking saponin biosynthesis in soapwort. Nat Chem Biol 2024:10.1038/s41589-024-01681-7. [PMID: 39043959 DOI: 10.1038/s41589-024-01681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 06/18/2024] [Indexed: 07/25/2024]
Abstract
Soapwort (Saponaria officinalis) is a flowering plant from the Caryophyllaceae family with a long history of human use as a traditional source of soap. Its detergent properties are because of the production of polar compounds (saponins), of which the oleanane-based triterpenoid saponins, saponariosides A and B, are the major components. Soapwort saponins have anticancer properties and are also of interest as endosomal escape enhancers for targeted tumor therapies. Intriguingly, these saponins share common structural features with the vaccine adjuvant QS-21 and, thus, represent a potential alternative supply of saponin adjuvant precursors. Here, we sequence the S. officinalis genome and, through genome mining and combinatorial expression, identify 14 enzymes that complete the biosynthetic pathway to saponarioside B. These enzymes include a noncanonical cytosolic GH1 (glycoside hydrolase family 1) transglycosidase required for the addition of D-quinovose. Our results open avenues for accessing and engineering natural and new-to-nature pharmaceuticals, drug delivery agents and potential immunostimulants.
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Affiliation(s)
- Seohyun Jo
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Amr El-Demerdash
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
| | - Charlotte Owen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Vikas Srivastava
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Botany, School of Life Sciences, Central University of Jammu, Jammu, India
| | - Dewei Wu
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Shingo Kikuchi
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - James Reed
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hannah Hodgson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Tongtong Qu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, USA
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK.
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4
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Rahm M, Kwast H, Wessels HJCT, Noga MJ, Lefeber DJ. Mixed-phase weak anion-exchange/reversed-phase LC-MS/MS for analysis of nucleotide sugars in human fibroblasts. Anal Bioanal Chem 2024; 416:3595-3604. [PMID: 38676823 PMCID: PMC11156716 DOI: 10.1007/s00216-024-05313-w] [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: 11/21/2023] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
Nucleotide sugars (NS) fulfil important roles in all living organisms and in humans, related defects result in severe clinical syndromes. NS can be seen as the "activated" sugars used for biosynthesis of a wide range of glycoconjugates and serve as substrates themselves for the synthesis of other nucleotide sugars. NS analysis is complicated by the presence of multiple stereoisomers without diagnostic transition ions, therefore requiring separation by liquid chromatography. In this paper, we explored weak anion-exchange/reversed-phase chromatography on a hybrid column for the separation of 17 nucleotide sugars that can occur in humans. A robust and reproducible method was established with intra- and inter-day coefficients of variation below 10% and a linear range spanning three orders of magnitude. Application to patient fibroblasts with genetic defects in mannose-1-phosphate guanylyltransferase beta, CDP-L-ribitol pyrophosphorylase A, and UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase showed abnormal levels of guanosine-5'-diphosphate-α-D-mannose (GDP-Man), cytidine-5'-diphosphate-L-ribitol (CDP-ribitol), and cytidine-5'-monophosphate-N-acetyl-β-D-neuraminic acid (CMP-Neu5Ac), respectively, in consonance with expectations based on the diagnosis. In conclusion, a novel, semi-quantitative method was established for the analysis of nucleotide sugars that can be applied to diagnose several genetic glycosylation disorders in fibroblasts and beyond.
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Affiliation(s)
- Moritz Rahm
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Hanneke Kwast
- Translational Metabolic Laboratory (TML), Department of Human Genetics, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory (TML), Department of Human Genetics, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Marek J Noga
- Laboratory of Clinical Genetics, Inborn Errors of Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Translational Metabolic Laboratory (TML), Department of Human Genetics, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525 GA, Nijmegen, The Netherlands.
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Huang J, Ma S, Zhou M, Liu Z, Liang Q. Cytochemical localization and synthesis mechanism of the glucomannan in pseudobulbs of Bletilla striata Reichb. f. HORTICULTURE RESEARCH 2024; 11:uhae092. [PMID: 38799126 PMCID: PMC11116825 DOI: 10.1093/hr/uhae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
The dried pseudobulbs of Bletilla striata, an important traditional Chinese medicine named BaiJi, have an extraordinary polysaccharide content and excellent prospects for medicinal effects. However, the distribution and molecular mechanism underlying biosynthesis are poorly understood. In this study, chemical and immunologic analyses were performed in representative tissues of B. striata, and the results showed that what are conventionally termed Bletilla striata polysaccharides (BSPs) are water-soluble polysaccharides deposited only in pseudobulbs. The structural component of BSPs is glucomannan, with a mannose:glucose mass ratio of ~3:2. BSPs are present in the parenchyma of the pseudobulbs in cells known as glucomannan idioblasts and distributed in the cytoplasm within cellular membranes, but are not contained in the vacuole. Comparative transcriptomics and bioinformatics analyses mapped the pathway from sucrose to BSP and identified BsGPI, BsmanA, and BsCSLAs as the key genes of BSP biosynthesis, suggesting that the functional differentiation of the cellulose synthase-like family A (CSLA) may be critical for the flow of glucomannan to the BSP or cell wall. Subsequently, virus-mediated gene silencing showed that silencing of two CSLAs (Bs03G11846 and Bs03G11849) led to a decrease in BSP content, and yeast two-hybrid and luciferase complementation experiments confirmed that four CSLAs (Bs03G11846, Bs03G11847, Bs03G11848, and Bs03G11849) can form homo- or heterodimers, suggesting that multiple CSLAs may form a large complex that functions in BSP synthesis. Our results provide cytological evidence of BSP and describe the isolation and characterization of candidate genes involved in BSP synthesis, laying a solid foundation for further research on its regulation mechanisms and the genetic engineering breeding of B. striata.
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Affiliation(s)
- Junfeng Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Shuang Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ming Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhihao Liu
- Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi City 435002, China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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6
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Liu YM, Wang S, Dickenson A, Mao J, Bai X, Liao X. An on-line SPE-LC-MS/MS method for quantification of nucleobases and nucleosides present in biological fluids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2505-2512. [PMID: 38584507 PMCID: PMC11151739 DOI: 10.1039/d4ay00100a] [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] [Indexed: 04/09/2024]
Abstract
Solid phase extraction (SPE) and liquid chromatographic (LC) separation of nucleobases and nucleosides are challenging due to the high hydrophilicity of these compounds. Herein we report a novel on-line SPE-LC-MS/MS method for their quantification after pre-column derivatization with chloroacetaldehyde (CAA). The method proposed is selective and sensitive with limits of detection at the nano-molar level. Analysis of urine and saliva samples by using this method is demonstrated. Adenine, guanine, cytosine, adenosine, guanosine, and cytidine were found in the range from 0.19 (guanosine) to 1.83 μM (cytidine) in urine and from 0.015 (guanosine) to 0.79 μM (adenine) in saliva. Interestingly, methylation of cytidine was found to be significantly different in urine from that in saliva. While 5-hydroxymethylcytidine was detected at a very low level (<0.05 μM) in saliva, it was found to be the most prominent methylated cytidine in urine at a high level of 3.33 μM. Since on-line SPE is deployed, the proposed LC-MS/MS quantitative assay is convenient to carry out and offers good assay accuracy and repeatability.
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Affiliation(s)
- Yi-Ming Liu
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Shuguan Wang
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Amani Dickenson
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Jinghe Mao
- Department of Biology, Tougaloo College, Tougaloo, MS 39174, USA
| | - Xiaolin Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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7
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Imae R, Manya H, Tsumoto H, Umezawa K, Miura Y, Endo T. Changes in the amount of nucleotide sugars in aged mouse tissues. Glycobiology 2024; 34:cwae032. [PMID: 38598324 DOI: 10.1093/glycob/cwae032] [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: 01/21/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024] Open
Abstract
Aging affects tissue glycan profiles, which may alter cellular functions and increase the risk of age-related diseases. Glycans are biosynthesized by glycosyltransferases using the corresponding nucleotide sugar, and the availability of nucleotide sugars affects glycosylation efficiency. However, the effects of aging on nucleotide sugar profiles and contents are yet to be elucidated. Therefore, this study aimed to investigate the effects of aging on nucleotide sugars using a new LC-MS/MS method. Specifically, the new method was used to determine the nucleotide sugar contents of various tissues (brain, liver, heart, skeletal muscle, kidney, lung, and colon) of male C57BL/6NCr mice (7- or 26-month-old). Characteristic age-associated nucleotide sugar changes were observed in each tissue sample. Particularly, there was a significant decrease in UDP-glucuronic acid content in the kidney of aged mice and a decrease in the contents of several nucleotide sugars, including UDP-N-acetylgalactosamine, in the brain of aged mice. Additionally, there were variations in nucleotide sugar profiles among the tissues examined regardless of the age. The kidneys had the highest concentration of UDP-glucuronic acid among the seven tissues. In contrast, the skeletal muscle had the lowest concentration of total nucleotide sugars among the tissues; however, CMP-N-acetylneuraminic acid and CDP-ribitol were relatively enriched. Conclusively, these findings may contribute to the understanding of the roles of glycans in tissue aging.
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Affiliation(s)
- Rieko Imae
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Hiroshi Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Hiroki Tsumoto
- Proteome Research, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Keitaro Umezawa
- Proteome Research, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Yuri Miura
- Proteome Research, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Tamao Endo
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
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8
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Marotta NJ, Weinert EE. Insights into the metabolism, signaling, and physiological effects of 2',3'-cyclic nucleotide monophosphates in bacteria. Crit Rev Biochem Mol Biol 2023; 58:118-131. [PMID: 38064689 PMCID: PMC10877235 DOI: 10.1080/10409238.2023.2290473] [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: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 02/03/2024]
Abstract
2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have been discovered within both prokaryotes and eukaryotes in the past decade and a half, raising questions about their conserved existence in cells. In plants and mammals, wounding has been found to cause increased levels of 2',3'-cNMPs. Roles for 2',3'-cNMPs in plant immunity suggest that their regulation may be valuable for both plant hosts and microbial pathogens. In support of this hypothesis, a plethora of microbial enzymes have been found with activities related to these molecules. Studies in bacteria suggest that 2',3'-cNMPs are also produced in response to cellular stress and modulate expression of numerous genes. 2',3'-cNMP levels affect bacterial phenotypes, including biofilm formation, motility, and growth. Within E. coli and Salmonella enterica, 2',3'-cNMPs are produced by RNA degradation by RNase I, highlighting potential roles for Type 2 RNases producing 2',3'-cNMPs in a range of organisms. Development of cellular tools to modulate 2',3'-cNMP levels in bacteria has allowed for interrogation of the effects of 2',3'-cNMP concentration on bacterial transcriptomes and physiology. Pull-downs of cellular 2',3'-cNMP binding proteins have identified the ribosome and in vitro studies demonstrated that 2',3'-cNMPs decrease translation, suggesting a direct mechanism for 2',3-cNMP-dependent control of bacterial phenotypes. Future studies dissecting the cellular roles of 2',3'-cNMPs will highlight novel signaling pathways within prokaryotes and which can potentially be engineered to control bacterial physiology.
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Affiliation(s)
- Nick J. Marotta
- Graduate Program in Molecular, Cellular, and Integrative
Biosciences, Penn State University, University Park, PA, 16803, USA
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Penn
State University, University Park, PA, 16803, USA
- Department of Chemistry, Penn State University, University
Park, PA, 16803, USA
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9
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Jia X, Zhang H, Qin H, Li K, Liu X, Wang W, Ye M, Yin H. Protein O-GlcNAcylation impairment caused by N-acetylglucosamine phosphate mutase deficiency leads to growth variations in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:613-635. [PMID: 36799458 DOI: 10.1111/tpj.16156] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/10/2023]
Abstract
As an essential enzyme in the uridine diphosphate (UDP)-GlcNAc biosynthesis pathway, the significant role of N-acetylglucosamine phosphate mutase (AGM) remains unknown in plants. In the present study, a functional plant AGM (AtAGM) was identified from Arabidopsis thaliana. AtAGM catalyzes the isomerization of GlcNAc-1-P and GlcNAc-6-P, and has broad catalytic activity on different phosphohexoses. UDP-GlcNAc contents were significantly decreased in AtAGM T-DNA insertional mutants, which caused temperature-dependent growth defects in seedlings and vigorous growth in adult plants. Further analysis revealed that protein O-GlcNAcylation but not N-glycosylation was dramatically impaired in Atagm mutants due to UDP-GlcNAc shortage. Combined with the results from O-GlcNAcylation or N-glycosylation deficient mutants, and O-GlcNAcase inhibitor all suggested that protein O-GlcNAcylation impairment mainly leads to the phenotypic variations of Atagm plants. In conclusion, based on the essential role in UDP-GlcNAc biosynthesis, AtAGM is important for plant growth mainly via protein O-GlcNAcylation-level regulation.
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Affiliation(s)
- Xiaochen Jia
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Hongyan Zhang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kuikui Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Xiaoyan Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wenxia Wang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
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10
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Reed J, Orme A, El-Demerdash A, Owen C, Martin LBB, Misra RC, Kikuchi S, Rejzek M, Martin AC, Harkess A, Leebens-Mack J, Louveau T, Stephenson MJ, Osbourn A. Elucidation of the pathway for biosynthesis of saponin adjuvants from the soapbark tree. Science 2023; 379:1252-1264. [PMID: 36952412 DOI: 10.1126/science.adf3727] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/02/2023] [Indexed: 03/25/2023]
Abstract
The Chilean soapbark tree (Quillaja saponaria) produces soap-like molecules called QS saponins that are important vaccine adjuvants. These highly valuable compounds are sourced by extraction from the bark, and their biosynthetic pathway is unknown. Here, we sequenced the Q. saponaria genome. Through genome mining and combinatorial expression in tobacco, we identified 16 pathway enzymes that together enable the production of advanced QS pathway intermediates that represent a bridgehead for adjuvant bioengineering. We further identified the enzymes needed to make QS-7, a saponin with excellent therapeutic properties and low toxicity that is present in low abundance in Q. saponaria bark extract. Our results enable the production of Q. saponaria vaccine adjuvants in tobacco and open the way for new routes to access and engineer natural and new-to-nature immunostimulants.
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Affiliation(s)
- James Reed
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anastasia Orme
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Charlotte Owen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Rajesh C Misra
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shingo Kikuchi
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Rejzek
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Thomas Louveau
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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11
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Caron P, Van Long FN, Rouleau M, Bujold E, Fortin P, Mohammadi S, Lévesque É, Breton S, Guillemette C. A liquid chromatography-mass spectrometry assay for the quantification of nucleotide sugars in human plasma and urine specimens and its clinical application. J Chromatogr A 2022; 1677:463296. [DOI: 10.1016/j.chroma.2022.463296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/16/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
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12
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Lan C, Zhao B, Yang L, Zhou Y, Guo S, Zhang X, Zhang J. Determination of UDP-Glucose and UDP-Galactose in Maize by Hydrophilic Interaction Liquid Chromatography and Tandem Mass Spectrometry. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2022; 2022:7015311. [PMID: 35800972 PMCID: PMC9256458 DOI: 10.1155/2022/7015311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/06/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Nucleotide sugars, the activated forms of monosaccharides, are important intermediates of carbohydrate metabolism in all organisms. Here, we describe a method for the detection and quantification of UDP-glucose and UDP-galactose in maize in order to compare their metabolism in both wild-type and mutated plants. Triple quadrupole operating in a multiple reaction monitoring mode was used to quantify nucleotide sugars. The limits of detection for UDP-glucose and UDP-galactose were 0.50 and 0.70 ng·mL-1, respectively. The recoveries of the method ranged from 98.3% to 103.6% with the relative standard deviations less than 6.3%. To prove the applicability of this method, we analyzed several sets of maize extracts obtained from different cultivars grown under standardized greenhouse conditions. All the results demonstrated the suitability of the developed method to quantify UDP-glucose and UDP-galactose in maize extracts.
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Affiliation(s)
- Chen Lan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lu Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yusen Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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13
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Chodasiewicz M, Kerber O, Gorka M, Moreno JC, Maruri-Lopez I, Minen RI, Sampathkumar A, Nelson ADL, Skirycz A. 2',3'-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana. PLANT PHYSIOLOGY 2022; 188:1966-1978. [PMID: 35043968 PMCID: PMC8968299 DOI: 10.1093/plphys/kiac013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
The role of the RNA degradation product 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) is poorly understood. Recent studies have identified 2',3'-cAMP in plant material and determined its role in stress signaling. The level of 2',3'-cAMP increases upon wounding, in the dark, and under heat, and 2',3'-cAMP binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insights into the function of 2',3'-cAMP, we used a multi-omics approach by combining transcriptomics, metabolomics, and proteomics to dissect the response of Arabidopsis (Arabidopsis thaliana) to 2',3'-cAMP treatment. We demonstrated that 2',3'-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide-adenosine pathway of human cells might also exist in plants. Transcriptomics analysis revealed only minor overlap between 2',3'-cAMP- and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2',3'-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses, including protein and RNA degradation products, glucosinolates, chaperones, and SG components. Finally, we demonstrated that 2',3'-cAMP treatment influences the movement of processing bodies, confirming the role of 2',3'-cAMP in the formation and motility of membraneless organelles.
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Affiliation(s)
| | - Olga Kerber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michal Gorka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Romina I Minen
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
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14
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Mahour R, Lee JW, Grimpe P, Boecker S, Grote V, Klamt S, Seidel‐Morgenstern A, Rexer TFT, Reichl U. Cell-Free Multi-Enzyme Synthesis and Purification of Uridine Diphosphate Galactose. Chembiochem 2022; 23:e202100361. [PMID: 34637168 PMCID: PMC9299652 DOI: 10.1002/cbic.202100361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/10/2021] [Indexed: 11/26/2022]
Abstract
High costs and low availability of UDP-galactose hampers the enzymatic synthesis of valuable oligosaccharides such as human milk oligosaccharides. Here, we report the development of a platform for the scalable, biocatalytic synthesis and purification of UDP-galactose. UDP-galactose was produced with a titer of 48 mM (27.2 g/L) in a small-scale batch process (200 μL) within 24 h using 0.02 genzyme /gproduct . Through in-situ ATP regeneration, the amount of ATP (0.6 mM) supplemented was around 240-fold lower than the stoichiometric equivalent required to achieve the final product yield. Chromatographic purification using porous graphic carbon adsorbent yielded UDP-galactose with a purity of 92 %. The synthesis was transferred to 1 L preparative scale production in a stirred tank bioreactor. To further reduce the synthesis costs here, the supernatant of cell lysates was used bypassing expensive purification of enzymes. Here, 23.4 g/L UDP-galactose were produced within 23 h with a synthesis yield of 71 % and a biocatalyst load of 0.05 gtotal_protein /gproduct . The costs for substrates per gram of UDP-galactose synthesized were around 0.26 €/g.
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Affiliation(s)
- Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Bioprocess EngineeringSandtorstrasse 139106MagdeburgGermany
- Present Address: c-LEcta GmbHLeipzigGermany
| | - Ju Weon Lee
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Physical and Chemical Foundations of Process EngineeringSandtorstrasse 139106MagdeburgGermany
| | - Pia Grimpe
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Bioprocess EngineeringSandtorstrasse 139106MagdeburgGermany
| | - Simon Boecker
- Max Planck Institute for Dynamics of Complex Technical SystemsResearch group Analysis and Redesign of Biological NetworksSandtorstrasse 139106MagdeburgGermany
| | - Valerian Grote
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Bioprocess EngineeringSandtorstrasse 139106MagdeburgGermany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical SystemsResearch group Analysis and Redesign of Biological NetworksSandtorstrasse 139106MagdeburgGermany
| | - Andreas Seidel‐Morgenstern
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Physical and Chemical Foundations of Process EngineeringSandtorstrasse 139106MagdeburgGermany
- Otto-von-Guericke University MagdeburgChair of Chemical Process EngineeringUniversitätsplatz 239106MagdeburgGermany
| | - Thomas F. T. Rexer
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Bioprocess EngineeringSandtorstrasse 139106MagdeburgGermany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical SystemsDepartment of Bioprocess EngineeringSandtorstrasse 139106MagdeburgGermany
- Otto-von-Guericke University MagdeburgChair of Bioprocess EngineeringUniversitätsplatz 239106MagdeburgGermany
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15
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Approaching Sites of Action of Temozolomide for Pharmacological and Clinical Studies in Glioblastoma. Biomedicines 2021; 10:biomedicines10010001. [PMID: 35052681 PMCID: PMC8772814 DOI: 10.3390/biomedicines10010001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
Temozolomide (TMZ), together with bulk resection and focal radiotherapy, is currently a standard of care for glioblastoma. Absorption, distribution, metabolism, and excretion (ADME) parameters, together with the mode of action of TMZ, make its biochemical and biological action difficult to understand. Accurate understanding of the mode of action of TMZ and the monitoring of TMZ at its anatomical, cellular, and molecular sites of action (SOAs) would greatly benefit precision medicine and the development of novel therapeutic approaches in combination with TMZ. In the present perspective article, we summarize the known ADME parameters and modes of action of TMZ, and we review the possible methodological options to monitor TMZ at its SOAs. We focus our descriptions of methodologies on mass spectrometry-based approaches, and all related considerations are taken into account regarding the avoidance of artifacts in mass spectrometric analysis during sampling, sample preparation, and the evaluation of results. Finally, we provide an overview of potential applications for precision medicine and drug development.
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16
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Braun F, Recalde A, Bähre H, Seifert R, Albers SV. Putative Nucleotide-Based Second Messengers in the Archaeal Model Organisms Haloferax volcanii and Sulfolobus acidocaldarius. Front Microbiol 2021; 12:779012. [PMID: 34880846 PMCID: PMC8646023 DOI: 10.3389/fmicb.2021.779012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
Research on nucleotide-based second messengers began in 1956 with the discovery of cyclic adenosine monophosphate (3',5'-cAMP) by Earl Wilbur Sutherland and his co-workers. Since then, a broad variety of different signaling molecules composed of nucleotides has been discovered. These molecules fulfill crucial tasks in the context of intracellular signal transduction. The vast majority of the currently available knowledge about nucleotide-based second messengers originates from model organisms belonging either to the domain of eukaryotes or to the domain of bacteria, while the archaeal domain is significantly underrepresented in the field of nucleotide-based second messenger research. For several well-stablished eukaryotic and/or bacterial nucleotide-based second messengers, it is currently not clear whether these signaling molecules are present in archaea. In order to shed some light on this issue, this study analyzed cell extracts of two major archaeal model organisms, the euryarchaeon Haloferax volcanii and the crenarchaeon Sulfolobus acidocaldarius, using a modern mass spectrometry method to detect a broad variety of currently known nucleotide-based second messengers. The nucleotides 3',5'-cAMP, cyclic guanosine monophosphate (3',5'-cGMP), 5'-phosphoadenylyl-3',5'-adenosine (5'-pApA), diadenosine tetraphosphate (Ap4A) as well as the 2',3'-cyclic isomers of all four RNA building blocks (2',3'-cNMPs) were present in both species. In addition, H. volcanii cell extracts also contain cyclic cytosine monophosphate (3',5'-cCMP), cyclic uridine monophosphate (3',5'-cUMP) and cyclic diadenosine monophosphate (3',5'-c-di-AMP). The widely distributed bacterial second messengers cyclic diguanosine monophosphate (3',5'-c-di-GMP) and guanosine (penta-)/tetraphosphate [(p)ppGpp] could not be detected. In summary, this study gives a comprehensive overview on the presence of a large set of currently established or putative nucleotide-based second messengers in an eury- and a crenarchaeal model organism.
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Affiliation(s)
- Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Alejandra Recalde
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Roland Seifert
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
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17
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Silva JVV, Ganesan S, Wickramasinghe HKJP, Stepanchenko N, Kaya CA, Beitz DC, Appuhamy JADRN. Effects of branched-chain amino acids on glucose uptake and lactose synthesis rates in bovine mammary epithelial cells and lactating mammary tissue slices. J Dairy Sci 2021; 105:1717-1730. [PMID: 34802743 DOI: 10.3168/jds.2021-20950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022]
Abstract
Even though supplementations of essential AA (EAA) are often related to increased lactose yields in dairy cows, underlying mechanisms connecting EAA availability to the mammary glands and lactose synthesis are poorly understood. The objective of this study was to examine the effects of branched-chain AA (BCAA) including Leu, Ile, and Val on (1) glucose transporter (GLUT1) abundance and glucose uptake, (2) the abundance of proteins regulating lactose synthesis pathway, and (3) fractional synthesis rates of lactose (FSR) using bovine mammary epithelial cells (BMEC) and mammary tissues slices (MTS). The BMEC (n = 4) were allocated randomly to regular Dulbecco's Modified Eagle Medium with Ham's F12 (DMEM/F12) media (+EAA) or +EAA deficient (by 90%) in all EAA (-EAA), all BCAA (-BCAA), only Leu (-Leu), only Ile (-Ile) or only Val (-Val). Western immunoblotting analyses, depletion of glucose in media, and a proteomic analysis were performed to determine the abundance of GLUT1 in the cell membrane, net glucose uptake, and the abundance of enzymes involved in lactose synthesis pathway in BMEC, respectively. The MTS (n = 6) were allocated randomly to DMEM/F12 media having all EAA and 13C-glucose at concentrations similar to plasma concentrations of cows (+EAAp), and +EAAp deprived of all BCAA (-BCAAp) or only Leu (-Leup) for 3 h. The 13C enrichments of free glucose pool in MTS (EGlu-free) and the enrichments of glucose incorporated into lactose in MTS and media [ELactose-bound (T&M)] were determined and used in calculating FSR. In BMEC, -BCAA increased the fraction of total GLUT1 translocated to the cell membrane and the fraction that was potentially glycosylated compared with +EAA. Among individual BCAA, only -Leu was associated with a 63% increase in GLUT1 translocated to the cell membrane and a 40% increase in glucose uptake of BMEC. The -BCAA tended to be related to a 75% increase in the abundance of hexokinase in BMEC. Deprivation of Leu tended to increase glucose uptake of MTS but did not affect EGlu-free, ELactose-bound (T&M), or FSR relative to +EAAp. On the other hand, -BCAAp did not affect glucose uptake of MTS but was related to lower ELactose-bound (T&M), or FSR relative to +EAAp. Considering together, decreasing Leu supply to mammary tissues enhances GLUT1 and thus glucose uptake, which, however, does not affect lactose synthesis rates. Moreover, the deficiency of other BCAA, Ile, and Val alone or together with the deficiency of Leu seemed to decrease lactose synthesis rates without affecting glucose uptake. The data also emphasize the importance of addressing the effect of the supply of other nutrients to the mammary glands than the precursor supply in describing the synthesis of a milk component.
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Affiliation(s)
- J V V Silva
- Department of Animal Science, Iowa State University, Ames 50011
| | - S Ganesan
- Department of Animal Science, Iowa State University, Ames 50011
| | | | - N Stepanchenko
- Department of Animal Science, Iowa State University, Ames 50011
| | - C A Kaya
- Department of Livestock and Crop Production, Dicle University, Diyarbakir, 21280, Turkey
| | - D C Beitz
- Department of Animal Science, Iowa State University, Ames 50011
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18
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Chiu KY, Wang Q, Gunawardena HP, Held M, Faik A, Chen H. Desalting Paper Spay Mass Spectrometry (DPS-MS) for Rapid Detection of Glycans and Glycoconjugates. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116688. [PMID: 35386843 PMCID: PMC8981528 DOI: 10.1016/j.ijms.2021.116688] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The detection of glycans and glycoconjugates has gained increasing attention in biological fields. Traditional mass spectrometry (MS)-based methods for glycoconjugate analysis are challenged with poor intensity when dealing with complex biological samples. We developed a desalting paper spray mass spectrometry (DPS-MS) strategy to overcome the issue of signal suppression of carbohydrates in salted buffer. Glycans and glycoconjugates (i.e., glycopeptides, nucleotide sugars, etc.) in non-volatile buffer (e.g., Tris buffer) can be loaded on the paper substrate from which buffers can be removed by washing with ACN/H2O (90/10 v/v) solution. Glycans or glycoconjugates can then be eluted and spray ionized by adding ACN/H2O/formic acid (FA) (10/90/1 v/v/v) solvent and applying a high voltage (HV) to the paper substrate. This work also showed that DPS-MS is applicable for direct detection of intact glycopeptides and nucleotide sugars as well as determination of glycosylation profiling of antibody, such as NIST monoclonal antibody IgG (NISTmAb). NISTmAb was deglycosylated with PNGase F to release N-linked oligosaccharides. Twenty-six N-linked oligosaccharides were detected by DPS-MS within a 5-minute timeframe without the need for further enrichment or derivatization. This work demonstrates that DPS-MS allows fast and sensitive detection of glycans/oligosaccharides and glycosylated species in complex matrices and has great potential in bioanalysis.
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Affiliation(s)
- Kai-Yuan Chiu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
| | - Qi Wang
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
| | - Harsha P Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania, USA, 19477
| | - Michael Held
- Deparment of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio USA, 45701
| | - Ahmed Faik
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, Ohio USA, 45701
- Department of Environmental and Plant Biology, Ohio University, Athens Ohio, USA, 45701
| | - Hao Chen
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA, 07102
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19
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Scherpenzeel M, Conte F, Büll C, Ashikov A, Hermans E, Willems A, Tol W, Kragt E, Noga M, Moret EE, Heise T, Langereis JD, Rossing E, Zimmermann M, Rubio-Gozalbo ME, de Jonge MI, Adema GJ, Zamboni N, Boltje T, Lefeber DJ. Dynamic tracing of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs. Glycobiology 2021; 32:239-250. [PMID: 34939087 PMCID: PMC8966471 DOI: 10.1093/glycob/cwab106] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 11/14/2022] Open
Abstract
Synthetic sugar analogs are widely applied in metabolic oligosaccharide engineering (MOE) and as novel drugs to interfere with glycoconjugate biosynthesis. However, mechanistic insights on their exact cellular metabolism over time are mostly lacking. We combined ion-pair ultrahigh performance liquid chromatography–triple quadrupole mass spectrometry mass spectrometry using tributyl- and triethylamine buffers for sensitive analysis of sugar metabolites in cells and organisms and identified low abundant nucleotide sugars, such as UDP-arabinose in human cell lines and CMP-sialic acid (CMP-NeuNAc) in Drosophila. Furthermore, MOE revealed that propargyloxycarbonyl (Poc)-labeled ManNPoc was metabolized to both CMP-NeuNPoc and UDP-GlcNPoc. Finally, time-course analysis of the effect of antitumor compound 3Fax-NeuNAc by incubation of B16-F10 melanoma cells with N-acetyl-D-[UL-13C6]glucosamine revealed full depletion of endogenous ManNAc 6-phosphate and CMP-NeuNAc within 24 h. Thus, dynamic tracing of sugar metabolic pathways provides a general approach to reveal time-dependent insights into the metabolism of synthetic sugars, which is important for the rational design of analogs with optimized effects.
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Affiliation(s)
- Monique Scherpenzeel
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,GlycoMScan B.V., Kloosterstraat 9, RE0329, 5349 AB Oss, The Netherlands
| | - Federica Conte
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Christian Büll
- Department of Radiation Oncology, Radiotherapy & OncoImmunology Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, Nijmegen, The Netherlands
| | - Angel Ashikov
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Esther Hermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Anke Willems
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Walinka Tol
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Else Kragt
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Marek Noga
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Ed E Moret
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Torben Heise
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Jeroen D Langereis
- Radboud Center for Infectious Diseases, Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Emiel Rossing
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands
| | | | - M Estela Rubio-Gozalbo
- Department of Clinical Genetics, department of Pediatrics, Maastricht University Medical Centre, Universiteitssingel 50, P.O. Box 616, box 16, 6200 MD, Maastricht, The Netherlands
| | - Marien I de Jonge
- Radboud Center for Infectious Diseases, Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Gosse J Adema
- Department of Radiation Oncology, Radiotherapy & OncoImmunology Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 32, Nijmegen, The Netherlands
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Thomas Boltje
- Cluster for Molecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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20
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Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
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Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
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Wei-Qi K, Yuan Z, Yu Z, Xue-Song F. An Overview of Pretreatment and Analysis of Nucleotides in Different Samples (Update since 2010). Crit Rev Anal Chem 2021; 52:1624-1643. [PMID: 33840326 DOI: 10.1080/10408347.2021.1907173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nucleotides, which are important low-molecular-weight compounds present in organisms, are precursors of nucleic acids and participate in various regulatory and metabolic functions. Sensitive and valid methods for monitoring and determining nucleotides and nucleosides in different samples are urgently required. Due to the presence of numerous endogenous interferences in complex matrices and the high polarity of the molecules of the phosphate moiety, the determination of nucleotide content is challenging. This review summarizes the pretreatment and analysis methods of nucleotides in different samples. Advanced pretreatment methods, including different microextraction methods, solid-phase extraction based on novel materials, QuEChERS, are clearly displayed, and continuous progress which has been made in LC, LC-MS/MS and capillary electrophoresis methods are discussed. Moreover, the strengths and weaknesses of different methods are discussed and compared. Highlight:Advanced pretreatment and detection methods of nucleotides were critically reviewed.Microextraction technology was one of the trends of nucleotides pretreatment in the future.Applications of novel materials and supercritical fluid were highlighted.The evolution and advance of HRMS analyzers were in detailed.
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Affiliation(s)
- Kang Wei-Qi
- School of Pharmacy, China Medical University, Shenyang, China
| | - Zhang Yuan
- School of Pharmacy, China Medical University, Shenyang, China
| | - Zhou Yu
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Feng Xue-Song
- School of Pharmacy, China Medical University, Shenyang, China
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22
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Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
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Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
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23
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Ma J, Wu C, Hart GW. Analytical and Biochemical Perspectives of Protein O-GlcNAcylation. Chem Rev 2021; 121:1513-1581. [DOI: 10.1021/acs.chemrev.0c00884] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Gerald W. Hart
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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24
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Xu Z, He WQ, Liu CS, Kong JQ. Enzymatic synthesis of myricetin 3-O-galactoside through a whole-cell biocatalyst. CHINESE HERBAL MEDICINES 2020; 12:384-389. [PMID: 36120167 PMCID: PMC9476700 DOI: 10.1016/j.chmed.2020.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/12/2020] [Accepted: 03/27/2020] [Indexed: 11/17/2022] Open
Abstract
Objective Myricetin 3-O-galactoside is an active compound with pharmaceutical potential. The insufficient supply of this compound becomes a bottleneck in the druggability study of myricetin 3-O-galactoside. Thus, it is necessary to develop a biosynthetic process for myricetin 3-O-galactoside through metabolic engineering. Methods Two genes OcSUS1 and OcUGE1 encoding sucrose synthase and UDP-glucose 4-epimerase were introduced into BL21(DE3) to reconstruct a UDP-D-galactose (UDP-Gal) biosynthetic pathway in Escherichia coli. The resultant chassis strain was able to produce UDP-Gal. Subsequently, a flavonol 3-O-galactosyltransferase DkFGT gene was transformed into the chassis strain producing UDP-Gal. An artificial pathway for myricetin 3-O-galactoside biosynthesis was thus constructed in E. coli. Results The obtained engineered strain was demonstrated to be capable of producing myricetin 3-O-galactoside, reaching 29.7 mg/L. Conclusion Biosynthesis of myricetin 3-O-galactoside through engineered E. coli could be achieved. This result lays the foundation for the large-scale preparation of myricetin 3-O-galactoside.
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25
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Liu Y, Kong Z, Liu J, Zhang P, Wang Q, Huan X, Li L, Qin P. Non-targeted metabolomics of quinoa seed filling period based on liquid chromatography-mass spectrometry. Food Res Int 2020; 137:109743. [PMID: 33233308 DOI: 10.1016/j.foodres.2020.109743] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/02/2020] [Accepted: 09/18/2020] [Indexed: 01/07/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.), an herb belonging to the amaranth family, is rich in minerals, amino acids, vitamins, proteins, and flavonoids. Its grain, compared with other major grains, has unique nutritional value with tremendous applications. This study used four independently bred high-generation lines (seed colors) of quinoa as materials to further understand the metabolic differences in the filling periods of quinoa varieties. Additionally, the non-targeted metabolome of quinoa seeds 35 and 42 days after flowering, respectively, were studied via liquid chromatography-mass spectrometry. The two filling periods of yellow, white, black, and red quinoa grains resulted in significant differences in the metabolites, particularly in L-methionine, S-adenosyl-L-homocysteine, S-adenosyl-L-methionine, pyruvate, fumarate, and oxaloacetate. Soluble sugar, amino acid, and fatty acid contents in quinoa increased after 42 days of flowering. There were metabolic differences between the sugar phosphates (L-fucose, D-mannose-6-phosphate, xylulose-5-phosphate, sedoheptulose-7-phosphate), amino acid (alanine), and organic compounds (kynurenate, tryptamine, serotonin, bilirubin) among the four quinoa varieties. The relative difference in the metabolites was largest when the yellow quinoa grain was compared with the other quinoa varieties and smallest when the red and black varieties were compare. The results of this study provide a basis for the reproduction and identification of new quinoa varieties, as well as for screening potential quality control target genes by combining genomics and transcriptomics.
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Affiliation(s)
- Yongjiang Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Zhiyou Kong
- College of Natural Resources and Environment, Baoshan University, Baoshan 678000, PR China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Xiuju Huan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, PR China.
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26
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Pecher D, Zelinkova Z, Lucenicova J, Peppelenbosch M, Dokupilova S, Mikusova V, Mikus P. Porous graphitic carbon based chromatography hyphenated with mass spectrometry: A new strategy for profiling thiopurine nucleotides in patients with inflammatory bowel diseases. Anal Chim Acta 2020; 1137:64-73. [PMID: 33153610 DOI: 10.1016/j.aca.2020.08.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/19/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Thiopurine (TP) treatment is discontinued in up to 30% of patients suffering from inflammatory bowel diseases (IBD) due to various adverse effects. Therapeutic drug monitoring of biologically active TP metabolites, i.e. thiopurine nucleotides (TPN), can help to optimize the efficacy and safety of the TP treatment. In our work, a novel strategy for TPN profiling, based on a porous graphitic carbon (PGC) chromatography, was developed. The validated PGC-MS method was compared with ion-exchange LC-MS, a currently leading analytical approach established for the determination of TPN. The innovative approach enabled an enhancement of several key performance parameters demanded in a clinical routine use, namely (i) selectivity (time- and mass-recognition of all 12 TPN in one run), (ii) sensitivity (2-5-fold increase in intensities of the analytical signals), (iii) sample throughput (25% shorter analysis time). Application of the novel TPN profiling strategy to a pilot clinical study (12 patients) revealed significantly higher levels of 6-methylthioguanine 5'-diphosphate (MeTGDP) in non-responsive IDB patients treated with azathioprine. Some other TPN are very close to the critical level (p = 0.05) and they will need larger groups of IBD patients to confirm definitively their relevance. In conclusion, the developed PGC-MS method represents a significant improvement to currently available methods for detailed profiling of TPN and its use in bigger clinical studies should lead to a better understanding of the relationship between TPN profiles and therapeutic outcome.
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Affiliation(s)
- Daniel Pecher
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic.
| | - Zuzana Zelinkova
- Department of Gastroenterology, St Michael's Hospital, Satinskeho 1, SK-811 08, Bratislava, Slovak Republic.
| | - Jana Lucenicova
- Department of Biochemistry & Hematology, St Michael's Hospital, Satinskeho 1, SK-811 08, Bratislava, Slovak Republic.
| | - Maikel Peppelenbosch
- Gastrolab, Erasmus Medical Center, Wytemaweg 80, 3015, CN Rotterdam, the Netherlands.
| | - Svetlana Dokupilova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic.
| | - Veronika Mikusova
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic.
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32, Bratislava, Slovak Republic.
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27
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Jia X, Zeng H, Bose SK, Wang W, Yin H. Chitosan oligosaccharide induces resistance to Pst DC3000 in Arabidopsis via a non-canonical N-glycosylation regulation pattern. Carbohydr Polym 2020; 250:116939. [PMID: 33049851 DOI: 10.1016/j.carbpol.2020.116939] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022]
Abstract
Roles of protein N-glycosylation in chitosan oligosaccharide (COS) induced resistance were investigated in the present study. Results demonstrated that N-glycosylation deficient Arabidopsis mutants (stt3a and ManI) were more susceptible against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) than wild type (WT) plants. Surprisingly, in stt3a and ManI, COS-induced resistance to Pst DC3000 was mostly intact, and the up-regulation effect on SA- and JA-mediated signalling pathways also similar like WT. Nucleotide sugars accumulation and N-glycosylation related genes expression were differently regulated after COS treatment. Global glycomics analysis quantified 157 N-glycan isomers, and 56.7, 50.3 and 47.1 % of them were significantly changed in COS, mock + Pst, and COS + Pst treated plants, respectively. Moreover, COS pretreatment could reverse the effect of Pst DC3000 on many N-glycans, suggesting that COS regulates protein N-glycosylation via a non-canonical pattern compared with plant defense, which may contribute to its obvious disease control effect when N-glycosylation impairment occurs.
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Affiliation(s)
- Xiaochen Jia
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haihong Zeng
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Santosh Kumar Bose
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Wenxia Wang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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28
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Majewska NI, Tejada ML, Betenbaugh MJ, Agarwal N. N-Glycosylation of IgG and IgG-Like Recombinant Therapeutic Proteins: Why Is It Important and How Can We Control It? Annu Rev Chem Biomol Eng 2020; 11:311-338. [DOI: 10.1146/annurev-chembioeng-102419-010001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Regulatory bodies worldwide consider N-glycosylation to be a critical quality attribute for immunoglobulin G (IgG) and IgG-like therapeutics. This consideration is due to the importance of posttranslational modifications in determining the efficacy, safety, and pharmacokinetic properties of biologics. Given its critical role in protein therapeutic production, we review N-glycosylation beginning with an overview of the myriad interactions of N-glycans with other biological factors. We examine the mechanism and drivers for N-glycosylation during biotherapeutic production and the several competing factors that impact glycan formation, including the abundance of precursor nucleotide sugars, transporters, glycosidases, glycosyltransferases, and process conditions. We explore the role of these factors with a focus on the analytical approaches used to characterize glycosylation and associated processes, followed by the current state of advanced glycosylation modeling techniques. This combination of disciplines allows for a deeper understanding of N-glycosylation and will lead to more rational glycan control.
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Affiliation(s)
- Natalia I. Majewska
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;,
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland 20878, USA
| | - Max L. Tejada
- Bioassay, Impurities and Quality, AstraZeneca, Gaithersburg, Maryland 20878, USA
| | - Michael J. Betenbaugh
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;,
| | - Nitin Agarwal
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland 20878, USA
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29
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Rautengarten C, Quarrell OW, Stals K, Caswell RC, De Franco E, Baple E, Burgess N, Jokhi R, Heazlewood JL, Offiah AC, Ebert B, Ellard S. A hypomorphic allele of SLC35D1 results in Schneckenbecken-like dysplasia. Hum Mol Genet 2020; 28:3543-3551. [PMID: 31423530 PMCID: PMC6927460 DOI: 10.1093/hmg/ddz200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
We report the case of a consanguineous couple who lost four pregnancies associated with skeletal dysplasia. Radiological examination of one fetus was inconclusive. Parental exome sequencing showed that both parents were heterozygous for a novel missense variant, p.(Pro133Leu), in the SLC35D1 gene encoding a nucleotide sugar transporter. The affected fetus was homozygous for the variant. The radiological features were reviewed, and being similar, but atypical, the phenotype was classified as a ‘Schneckenbecken-like dysplasia.’ The effect of the missense change was assessed using protein modelling techniques and indicated alterations in the mouth of the solute channel. A detailed biochemical investigation of SLC35D1 transport function and that of the missense variant p.(Pro133Leu) revealed that SLC35D1 acts as a general UDP-sugar transporter and that the p.(Pro133Leu) mutation resulted in a significant decrease in transport activity. The reduced transport activity observed for p.(Pro133Leu) was contrasted with in vitro activity for SLC35D1 p.(Thr65Pro), the loss-of-function mutation was associated with Schneckenbecken dysplasia. The functional classification of SLC35D1 as a general nucleotide sugar transporter of the endoplasmic reticulum suggests an expanded role for this transporter beyond chondroitin sulfate biosynthesis to a variety of important glycosylation reactions occurring in the endoplasmic reticulum.
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Affiliation(s)
| | - Oliver W Quarrell
- Department of Clinical Genetics, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Karen Stals
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Richard C Caswell
- University of Exeter School of Medicine, Barrack Road, Exeter EX2 5DW, UK
| | - Elisa De Franco
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Emma Baple
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,University of Exeter School of Medicine, Barrack Road, Exeter EX2 5DW, UK
| | - Nadia Burgess
- Department of Histology, Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield UK. S10 2TH, UK
| | - Roobin Jokhi
- Department of Obstetrics and Gynaecology, Sheffield Teaching Hospitals, Jessop Wing Tree Root Walk, Sheffield S10 2SF, UK
| | - Joshua L Heazlewood
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Amaka C Offiah
- University of Sheffield, Academic Unit of Child Health, Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield S10 2TH, UK
| | - Berit Ebert
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,University of Exeter School of Medicine, Barrack Road, Exeter EX2 5DW, UK
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30
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Feliu C, Peyret H, Vautier D, Djerada Z. Simultaneous quantification of 8 nucleotides and adenosine in cells and their medium using UHPLC-HRMS. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1148:122156. [PMID: 32446186 DOI: 10.1016/j.jchromb.2020.122156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Purinergic signalling is involved in physiological processes, particularly during ischemia-reperfusion injuries for which it has a protective effect. The purpose of this work was to develop a method for simultaneous quantification of eight nucleotides and adenosine in biological matrices by liquid chromatography coupled with high-resolution mass spectrometry. A method was developed that was sufficiently robust to quantify the targeted analytes in 20 min with good sensitivity. Analysis of extracellular media from cultured endothelial cells detected the release of nucleotides and adenosine during 2 h of hypoxia. The quantification of cylic adenosine monophosphate (cAMP) allowed to establish a dose-response curve after receptor stimulation. Therefore, our method allows us to study the involvement of nucleotides in various processes in both the intracellular and extracellular compartment.
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Affiliation(s)
- Catherine Feliu
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Hélène Peyret
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Damien Vautier
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Zoubir Djerada
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France.
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31
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Del Solar V, Gupta R, Zhou Y, Pawlowski G, Matta KL, Neelamegham S. Robustness in glycosylation systems: effect of modified monosaccharides, acceptor decoys and azido sugars on cellular nucleotide-sugar levels and pattern of N-linked glycosylation. Mol Omics 2020; 16:377-386. [PMID: 32352119 DOI: 10.1039/d0mo00023j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Small molecule monosaccharide analogs (e.g. 4F-GlcNAc, 4F-GalNAc) and acceptor decoys (e.g. ONAP, SNAP) are commonly used as metabolic glycoengineering tools to perturb molecular and cellular recognition processes. Azido-derivatized sugars (e.g. ManNAz, GlcNAz, GalNAz) are also used as bioorthogonal probes to assay the glycosylation status of cells and tissue. With the goal of obtaining a systems-level understanding of how these compounds work, we cultured cells with these molecules and systematically evaluated their impact on: (i) cellular nucleotide-sugar levels, and (ii) N-linked glycosylation. To this end, we developed a streamlined, simple workflow to quantify nucleotide-sugar levels using amide-based hydrophilic interaction liquid chromatography (HILIC) separation followed by negative-mode electrospray ionization mass spectrometry (ESI-MS/MS) using an Orbitrap detector. N-Glycans released from cells were also procainamide functionalized and quantified using positive-mode ESI-MS/MS. Results show that all tested compounds changed the baseline nucleotide-sugar levels, with the effect being most pronounced for the fluoro-HexNAc compounds. These molecules depressed UDP-HexNAc levels in cells by up to 80%, while concomitantly elevating UDP-4F-GalNAc and UDP-4F-GlcNAc. While the measured changes in nucleotide-sugar concentration were substantial in many cases, their impact on N-linked glycosylation was relatively small. This may be due to the high nucleotide-sugar concentrations in the Golgi, which far exceed the KM values of the glycosylating enzymes. Thus, the glycosylation system output exhibits 'robustness' even in the face of significant changes in cellular nucleotide-sugar concentrations.
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Affiliation(s)
- Virginia Del Solar
- Department of Chemical & Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA.
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32
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Sha S, Handelman G, Agarabi C, Yoon S. A high-resolution measurement of nucleotide sugars by using ion-pair reverse chromatography and tandem columns. Anal Bioanal Chem 2020; 412:3683-3693. [PMID: 32300845 DOI: 10.1007/s00216-020-02608-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/08/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
N-Linked glycosylation is a cellular process transferring sugars from glycosyl donors to proteins or lipids. Biopharmaceutical products widely produced by culturing mammalian cells such as Chinese hamster ovary (CHO) cells are typically glycosylated during biosynthesis. For some biologics, the N-linked glycan is a critical quality attribute of the drugs. Nucleotide sugars are the glycan donors and impact the intracellular glycosylation process. In current analytical methods, robust separation of nucleotide sugar isomers such as UDP glucose and UDP galactose remains a challenge because of their structural similarity. In this study, we developed a strategy to resolve the separation of major nucleotide sugars including challenging isomers based on the use of ion-pair reverse phase (IP-RP) chromatography. The strategy applies core-shell columns and connects multiple columns in tandem to increase separation power and ultimately enables high-resolution detection of nucleotide sugars from cell extracts. The key parameters in the IP-RP method, including temperature, mobile phase, and flow rates, have been systematically evaluated in this work and the theoretical mechanisms of the chromatographic behavior were proposed. Graphical abstract.
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Affiliation(s)
- Sha Sha
- Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Garry Handelman
- Biomedical & Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Cyrus Agarabi
- U.S. FDA, CDER/OBP/Division of Biotechnology Review and Research II, Silver Spring, MD, 20993, USA
| | - Seongkyu Yoon
- Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA, 01854, USA. .,Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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33
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Rautengarten C, Heazlewood JL, Ebert B. Profiling Cell Wall Monosaccharides and Nucleotide-Sugars from Plants. ACTA ACUST UNITED AC 2019; 4:e20092. [PMID: 31187943 DOI: 10.1002/cppb.20092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cell wall is an intricate mesh largely composed of polysaccharides that vary in structure and abundance. Apart from cellulose biosynthesis, the assembly of matrix polysaccharides such as pectin and hemicellulose occur in the Golgi apparatus before being transported via vesicles to the cell wall. Matrix polysaccharides are biosynthesized from activated precursors or nucleotide sugars. The composition and assembly of the cell wall is an important aspect in plant development and plant biomass utilization. The application of anion-exchange chromatography to determine the monosaccharide composition of the insoluble matrix polysaccharides enables a complete profile of all major sugars in the cell wall from a single run. While porous carbon graphite chromatography and tandem mass spectrometry delivers a sensitive and robust nucleotide sugar profile from plant extracts. Here we describe detailed methodology to quantify nucleotide sugars within the cell and profile the non-cellulosic monosaccharide composition of the cell wall. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Carsten Rautengarten
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua L Heazlewood
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Berit Ebert
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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Wagstaff BA, Rejzek M, Kuhaudomlarp S, Hill L, Mascia I, Nepogodiev SA, Dorfmueller HC, Field RA. Discovery of an RmlC/D fusion protein in the microalga Prymnesium parvum and its implications for NDP-β-l-rhamnose biosynthesis in microalgae. J Biol Chem 2019; 294:9172-9185. [PMID: 31010825 PMCID: PMC6556577 DOI: 10.1074/jbc.ra118.006440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/19/2019] [Indexed: 11/06/2022] Open
Abstract
The 6-deoxy sugar l-rhamnose (l-Rha) is found widely in plant and microbial polysaccharides and natural products. The importance of this and related compounds in host-pathogen interactions often means that l-Rha plays an essential role in many organisms. l-Rha is most commonly biosynthesized as the activated sugar nucleotide uridine 5'-diphospho-β-l-rhamnose (UDP-β-l-Rha) or thymidine 5'-diphospho-β-l-rhamnose (TDP-β-l-Rha). Enzymes involved in the biosynthesis of these sugar nucleotides have been studied in some detail in bacteria and plants, but the activated form of l-Rha and the corresponding biosynthetic enzymes have yet to be explored in algae. Here, using sugar-nucleotide profiling in two representative algae, Euglena gracilis and the toxin-producing microalga Prymnesium parvum, we show that levels of UDP- and TDP-activated l-Rha differ significantly between these two algal species. Using bioinformatics and biochemical methods, we identified and characterized a fusion of the RmlC and RmlD proteins, two bacteria-like enzymes involved in TDP-β-l-Rha biosynthesis, from P. parvum Using this new sequence and also others, we explored l-Rha biosynthesis among algae, finding that although most algae contain sequences orthologous to plant-like l-Rha biosynthesis machineries, instances of the RmlC-RmlD fusion protein identified here exist across the Haptophyta and Gymnodiniaceae families of microalgae. On the basis of these findings, we propose potential routes for the evolution of nucleoside diphosphate β-l-Rha (NDP-β-l-Rha) pathways among algae.
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Affiliation(s)
- Ben A Wagstaff
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sakonwan Kuhaudomlarp
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Lionel Hill
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ilaria Mascia
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sergey A Nepogodiev
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom,
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35
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Gika H, Virgiliou C, Theodoridis G, Plumb RS, Wilson ID. Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1117:136-147. [PMID: 31009899 DOI: 10.1016/j.jchromb.2019.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/25/2022]
Abstract
Liquid chromatography (LC) hyphenated to mass spectrometry is currently the most widely used means of determining metabolic phenotypes via both untargeted and targeted analysis. At present a range of analytical separations, including reversed-phase, hydrophilic interaction and ion-pair LC are employed to maximise metabolome coverage with ultra (high) performance liquid chromatography (UHPLC) increasingly displacing conventional high performance liquid chromatography because of the need for short analysis times and high peak capacity in such applications. However, it is widely recognized that these methodologies do not entirely solve the problems facing researchers trying to perform comprehensive metabolic phenotyping and in addition to these "routine" approaches there are continuing investigations of alternative separation methods including 2-dimensional/multi column approaches. These involve either new stationary phases or multidimensional combinations of the more conventional materials currently used, as well as application of miniaturization or "new" approaches such as supercritical HP and UHP- chromatographic separations. There is also a considerable amount of interest in the combination of chromatographic and ion mobility separations, with the latter providing both an increase in resolution and the potential to provide additional structural information via the determination of molecular collision cross section data. However, key problems remain to be solved including ensuring quality, comparability across different laboratories and the ever present difficulty of identifying unknowns.
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Affiliation(s)
- Helen Gika
- Department of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece
| | - Christina Virgiliou
- Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Georgios Theodoridis
- Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | | | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College, Exhibition Road, South Kensington, London SW7 2AZ, UK.
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Abstract
UDP-sugars are important substrates for the synthesis of various cellular glycans and glycoconjugates, many of which play essential roles in the pathobiology of diseases associated with deranged glucose metabolism, such as cancer and type 2 diabetes. Hence, their analysis from cultured cells and especially from tissue samples can give valuable information. This chapter describes a method for UDP-sugar isolation from various sources utilizing ion-pair solid-phase extraction with graphitized carbon cartridges, and their analysis using anion-exchange high-performance liquid chromatography.
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Affiliation(s)
- Sanna Oikari
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
- Institute of Dentistry, University of Eastern Finland, Kuopio, Finland.
| | - Markku I Tammi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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37
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Latousakis D, Nepravishta R, Rejzek M, Wegmann U, Le Gall G, Kavanaugh D, Colquhoun IJ, Frese S, MacKenzie DA, Walter J, Angulo J, Field RA, Juge N. Serine-rich repeat protein adhesins from Lactobacillus reuteri display strain specific glycosylation profiles. Glycobiology 2019; 29:45-58. [PMID: 30371779 PMCID: PMC6291802 DOI: 10.1093/glycob/cwy100] [Citation(s) in RCA: 12] [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: 07/27/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023] Open
Abstract
Lactobacillus reuteri is a gut symbiont inhabiting the gastrointestinal tract of numerous vertebrates. The surface-exposed serine-rich repeat protein (SRRP) is a major adhesin in Gram-positive bacteria. Using lectin and sugar nucleotide profiling of wild-type or L. reuteri isogenic mutants, MALDI-ToF-MS, LC-MS and GC-MS analyses of SRRPs, we showed that L. reuteri strains 100-23C (from rodent) and ATCC 53608 (from pig) can perform protein O-glycosylation and modify SRRP100-23 and SRRP53608 with Hex-Glc-GlcNAc and di-GlcNAc moieties, respectively. Furthermore, in vivo glycoengineering in E. coli led to glycosylation of SRRP53608 variants with α-GlcNAc and GlcNAcβ(1→6)GlcNAcα moieties. The glycosyltransferases involved in the modification of these adhesins were identified within the SecA2/Y2 accessory secretion system and their sugar nucleotide preference determined by saturation transfer difference NMR spectroscopy and differential scanning fluorimetry. Together, these findings provide novel insights into the cellular O-protein glycosylation pathways of gut commensal bacteria and potential routes for glycoengineering applications.
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Affiliation(s)
- Dimitrios Latousakis
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Udo Wegmann
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Gwenaelle Le Gall
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Devon Kavanaugh
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ian J Colquhoun
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Donald A MacKenzie
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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Li Z, Zhang HX, Li Y, Lam CWK, Wang CY, Zhang WJ, Wong VKW, Pang SS, Yao MC, Zhang W. Method for Quantification of Ribonucleotides and Deoxyribonucleotides in Human Cells Using (Trimethylsilyl)diazomethane Derivatization Followed by Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2018; 91:1019-1026. [PMID: 30525455 DOI: 10.1021/acs.analchem.8b04281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Investigation into intracellular ribonucleotides (RNs) and deoxyribonucleotides (dRNs) is important for studies of the mechanism of many biological processes, such as RNA and DNA synthesis and DNA repair, as well as metabolic and therapeutic efficacy of nucleoside analogues. However, current methods are still unsatisfactory for determination of nucleotides in complex matrixes. Here we describe a novel method for the determination of RN and dRN pools in cells based on fast derivatization with (trimethylsilyl)diazomethane (TMSD) followed by quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Derivatization was accomplished in 3 min, and each derivatized nucleotide not only had a sufficient retention on reversed-phase column by introduction of methyl groups but also exhibited a unique ion transition which consequently eliminated mutual interference in LC-MS/MS. Chromatographic separation was performed on a C18 column with a simple acetonitrile-water gradient elution system, which avoided contamination and ion suppression caused by ion-pairing reagents. The developed method was fully validated and applied to the analysis of RNs and dRNs in cell samples. Moreover, results demonstrated that the applicability of this method could be extended to nucleoside analogues and their metabolites and could facilitate many applications in future studies.
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Affiliation(s)
- Zheng Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Hui-Xia Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Yan Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Christopher Wai Kei Lam
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Cai-Yun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Wei-Jia Zhang
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guang Zhou 510275 , China
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Su-Seng Pang
- Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Mei-Cun Yao
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guang Zhou 510275 , China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
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39
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Naik HM, Majewska NI, Betenbaugh MJ. Impact of nucleotide sugar metabolism on protein N-glycosylation in Chinese Hamster Ovary (CHO) cell culture. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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40
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Wagstaff BA, Rejzek M, Field RA. Identification of a Kdn biosynthesis pathway in the haptophyte Prymnesium parvum suggests widespread sialic acid biosynthesis among microalgae. J Biol Chem 2018; 293:16277-16290. [PMID: 30171074 PMCID: PMC6200933 DOI: 10.1074/jbc.ra118.004921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/31/2018] [Indexed: 01/08/2023] Open
Abstract
Sialic acids are a family of more than 50 structurally distinct acidic sugars on the surface of all vertebrate cells where they terminate glycan chains and are exposed to many interactions with the surrounding environment. In particular, sialic acids play important roles in cell-cell and host-pathogen interactions. The sialic acids or related nonulosonic acids have been observed in Deuterostome lineages, Eubacteria, and Archaea but are notably absent from plants. However, the structurally related C8 acidic sugar 3-deoxy-d-manno-2-octulosonic acid (Kdo) is present in Gram-negative bacteria and plants as a component of bacterial lipopolysaccharide and pectic rhamnogalacturonan II in the plant cell wall. Until recently, sialic acids were not thought to occur in algae, but as in plants, Kdo has been observed in algae. Here, we report the de novo biosynthesis of the deaminated sialic acid, 3-deoxy-d-glycero-d-galacto-2-nonulosonic acid (Kdn), in the toxin-producing microalga Prymnesium parvum Using biochemical methods, we show that this alga contains CMP-Kdn and identified and recombinantly expressed the P. parvum genes encoding Kdn-9-P synthetase and CMP-Kdn synthetase enzymes that convert mannose-6-P to CMP-Kdn. Bioinformatics analysis revealed sequences related to those of the two P. parvum enzymes, suggesting that sialic acid biosynthesis is likely more widespread among microalgae than previously thought and that this acidic sugar may play a role in host-pathogen interactions involving microalgae. Our findings provide evidence that P. parvum has the biosynthetic machinery for de novo production of the deaminated sialic acid Kdn and that sialic acid biosynthesis may be common among microalgae.
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Affiliation(s)
- Ben A Wagstaff
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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41
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Sarin LP, Kienast SD, Leufken J, Ross RL, Dziergowska A, Debiec K, Sochacka E, Limbach PA, Fufezan C, Drexler HCA, Leidel SA. Nano LC-MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels. RNA (NEW YORK, N.Y.) 2018; 24:1403-1417. [PMID: 30012570 PMCID: PMC6140458 DOI: 10.1261/rna.065482.117] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/11/2018] [Indexed: 05/14/2023]
Abstract
Post-transcriptional chemical modifications of (t)RNA molecules are crucial in fundamental biological processes, such as translation. Despite their biological importance and accumulating evidence linking them to various human diseases, technical challenges have limited their detection and accurate quantification. Here, we present a sensitive capillary nanoflow liquid chromatography mass spectrometry (nLC-MS) pipeline for quantitative high-resolution analysis of ribonucleoside modifications from complex biological samples. We evaluated two porous graphitic carbon (PGC) materials and one end-capped C18 reference material as stationary phases for reversed-phase separation. We found that these matrices have complementing retention and separation characteristics, including the capability to separate structural isomers. PGC and C18 matrices yielded excellent signal-to-noise ratios in nLC-MS while differing in the separation capability and sensitivity for various nucleosides. This emphasizes the need for tailored LC-MS setups for optimally detecting as many nucleoside modifications as possible. Detection ranges spanning up to six orders of magnitude enable the analysis of individual ribonucleosides down to femtomol concentrations. Furthermore, normalizing the obtained signal intensities to a stable isotope labeled spike-in enabled direct comparison of ribonucleoside levels between different samples. In conclusion, capillary columns coupled to nLC-MS constitute a powerful and sensitive tool for quantitative analysis of modified ribonucleosides in complex biological samples. This setup will be invaluable for further unraveling the intriguing and multifaceted biological roles of RNA modifications.
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Affiliation(s)
- L Peter Sarin
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Sandra D Kienast
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Johannes Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Agnieszka Dziergowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Katarzyna Debiec
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, 48143, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
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42
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Abstract
Disturbances in cardiac metabolism underlie most cardiovascular diseases. Metabolomics, one of the newer omics technologies, has emerged as a powerful tool for defining changes in both global and cardiac-specific metabolism that occur across a spectrum of cardiovascular disease states. Findings from metabolomics studies have contributed to better understanding of the metabolic changes that occur in heart failure and ischemic heart disease and have identified new cardiovascular disease biomarkers. As technologies advance, the metabolomics field continues to evolve rapidly. In this review, we will discuss the current state of metabolomics technologies, including consideration of various metabolomics platforms and elements of study design; the emerging utility of stable isotopes for metabolic flux studies; and the use of metabolomics to better understand specific cardiovascular diseases, with an emphasis on recent advances in the field.
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Affiliation(s)
- Robert W McGarrah
- From the Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute (R.W.M., S.B.C., G.F.Z., S.H.S., C.B.N.)
- Division of Cardiology (R.W.M., S.H.S.)
- Department of Medicine (R.W.M., G.F.Z., S.H.S., C.B.N.)
| | - Scott B Crown
- From the Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute (R.W.M., S.B.C., G.F.Z., S.H.S., C.B.N.)
| | - Guo-Fang Zhang
- From the Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute (R.W.M., S.B.C., G.F.Z., S.H.S., C.B.N.)
- Division of Endocrinology (G.F.Z., C.B.N.)
- Department of Medicine (R.W.M., G.F.Z., S.H.S., C.B.N.)
| | - Svati H Shah
- From the Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute (R.W.M., S.B.C., G.F.Z., S.H.S., C.B.N.)
- Division of Cardiology (R.W.M., S.H.S.)
- Department of Medicine (R.W.M., G.F.Z., S.H.S., C.B.N.)
| | - Christopher B Newgard
- From the Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute (R.W.M., S.B.C., G.F.Z., S.H.S., C.B.N.)
- Division of Endocrinology (G.F.Z., C.B.N.)
- Department of Medicine (R.W.M., G.F.Z., S.H.S., C.B.N.)
- Departments of Pharmacology and Cancer Biology (C.B.N.), Duke University Medical Center, Durham, NC
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Schatschneider S, Abdelrazig S, Safo L, Henstra AM, Millat T, Kim DH, Winzer K, Minton NP, Barrett DA. Quantitative Isotope-Dilution High-Resolution-Mass-Spectrometry Analysis of Multiple Intracellular Metabolites in Clostridium autoethanogenum with Uniformly 13C-Labeled Standards Derived from Spirulina. Anal Chem 2018. [PMID: 29533656 DOI: 10.1021/acs.analchem.7b04758] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have investigated the applicability of commercially available lyophilized spirulina ( Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze-thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves ( R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood-Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation.
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Affiliation(s)
- Sarah Schatschneider
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Laudina Safo
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Anne M Henstra
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Thomas Millat
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Klaus Winzer
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Nigel P Minton
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
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44
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Bustamante S, Jayasena T, Richani D, Gilchrist RB, Wu LE, Sinclair DA, Sachdev PS, Braidy N. Quantifying the cellular NAD+ metabolome using a tandem liquid chromatography mass spectrometry approach. Metabolomics 2017; 14:15. [PMID: 30830318 PMCID: PMC6519110 DOI: 10.1007/s11306-017-1310-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Nicotinamide adenine dinucleotide (NAD+) is an essential pyridine nucleotide that serves as a key hydride transfer coenzyme for several oxidoreductases. It is also the substrate for intracellular secondary messenger signalling by CD38 glycohydrolases, DNA repair by poly(adenosine diphosphate ribose) polymerase, and epigenetic regulation of gene expression by a class of histone deacetylase enzymes known as sirtuins. The measurement of NAD+ and its related metabolites (hereafter, the NAD+ metabolome) represents an important indicator of cellular function. OBJECTIVES A study was performed to develop a sensitive, selective, robust, reproducible, and rapid method for the concurrent quantitative determination of intracellular levels of the NAD+ metabolome in glial and oocyte cell extracts using liquid chromatography coupled to mass spectrometry (LC/MS/MS). METHODS The metabolites were separated on a versatile amino column using a dual HILIC-RP gradient with heated electrospray (HESI) tandem mass spectrometry detection in mixed polarity multiple reaction monitoring mode. RESULTS Quantification of 17 metabolites in the NAD+ metabolome in U251 human astroglioma cells could be achieved. Changes in NAD+ metabolism in U251 cell line, and murine oocytes under different culture conditions were also investigated. CONCLUSION This method can be used as a sensitive profiling tool, tailoring chromatography for metabolites that express significant pathophysiological changes in several disease conditions and is indispensable for targeted analysis.
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Affiliation(s)
- Sonia Bustamante
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Tharusha Jayasena
- Faculty of Medicine, School of Psychiatry, Centre for Healthy Brain Ageing, University of New South Wales Sydney, Sydney, Australia
| | - Dulama Richani
- Faculty of Medicine, School of Women's and Children's Health, University of New South Wales Sydney, Sydney, Australia
| | - Robert Bruce Gilchrist
- Faculty of Medicine, School of Women's and Children's Health, University of New South Wales Sydney, Sydney, Australia
| | - Lindsay E Wu
- Department of Pharmacology, School of Medical Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - David A Sinclair
- Department of Pharmacology, School of Medical Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
- Department of Genetics, Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA, 02115, USA
| | - Perminder Singh Sachdev
- Faculty of Medicine, School of Psychiatry, Centre for Healthy Brain Ageing, University of New South Wales Sydney, Sydney, Australia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, Australia
| | - Nady Braidy
- Faculty of Medicine, School of Psychiatry, Centre for Healthy Brain Ageing, University of New South Wales Sydney, Sydney, Australia.
- UNSW School of Psychiatry, NPI, Euroa Centre, Prince of Wales Hospital, Barker Street, Randwick, Sydney, NSW, 2031, Australia.
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45
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Exploring the Glycans of Euglena gracilis. BIOLOGY 2017; 6:biology6040045. [PMID: 29244725 PMCID: PMC5745450 DOI: 10.3390/biology6040045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/05/2017] [Accepted: 12/08/2017] [Indexed: 12/13/2022]
Abstract
Euglena gracilis is an alga of great biotechnological interest and extensive metabolic capacity, able to make high levels of bioactive compounds, such as polyunsaturated fatty acids, vitamins and β-glucan. Previous work has shown that Euglena expresses a wide range of carbohydrate-active enzymes, suggesting an unexpectedly high capacity for the synthesis of complex carbohydrates for a single-celled organism. Here, we present an analysis of some of the carbohydrates synthesised by Euglena gracilis. Analysis of the sugar nucleotide pool showed that there are the substrates necessary for synthesis of complex polysaccharides, including the unusual sugar galactofuranose. Lectin- and antibody-based profiling of whole cells and extracted carbohydrates revealed a complex galactan, xylan and aminosugar based surface. Protein N-glycan profiling, however, indicated that just simple high mannose-type glycans are present and that they are partially modified with putative aminoethylphosphonate moieties. Together, these data indicate that Euglena possesses a complex glycan surface, unrelated to plant cell walls, while its protein glycosylation is simple. Taken together, these findings suggest that Euglena gracilis may lend itself to the production of pharmaceutical glycoproteins.
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46
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Abstract
Contemporary investigations regarding the (patho)physiological roles of the non-canonical cyclic nucleoside monophosphates (cNMP) cytidine 3',5'-cyclic monophosphate (cCMP) and uridine 3',5'-cyclic monophosphate (cUMP) have been hampered by the lack of highly specific and sensitive analytic methods for these analytes. In addition, the existence of 2',3'-cNMP besides 3',5'-cNMP has been described recently. HPLC coupled with tandem mass spectrometry (HPLC-MS/MS) is the method of choice for identification and quantification of low-molecular weight endogenous metabolites. In this chapter, recommendations for an HPLC-MS/MS method for 3',5'- and 2',3'-cNMP are summarized.
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47
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Jackson EK. Discovery and Roles of 2',3'-cAMP in Biological Systems. Handb Exp Pharmacol 2017; 238:229-252. [PMID: 26721674 DOI: 10.1007/164_2015_40] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In 2009, investigators using ultra-performance liquid chromatography-tandem mass spectrometry to measure, by selected reaction monitoring, 3',5'-cAMP in the renal venous perfusate from isolated, perfused kidneys detected a large signal at the same m/z transition (330 → 136) as 3',5'-cAMP but at a different retention time. Follow-up experiments demonstrated that this signal was due to a positional isomer of 3',5'-cAMP, namely, 2',3'-cAMP. Soon thereafter, investigative teams reported the detection of 2',3'-cAMP and other 2',3'-cNMPs (2',3'-cGMP, 2',3'-cCMP, and 2',3'-cUMP) in biological systems ranging from bacteria to plants to animals to humans. Injury appears to be the major stimulus for the release of these unique noncanonical cNMPs, which likely are formed by the breakdown of RNA. In mammalian cells in culture, in intact rat and mouse kidneys, and in mouse brains in vivo, 2',3'-cAMP is metabolized to 2'-AMP and 3'-AMP; and these AMPs are subsequently converted to adenosine. In rat and mouse kidneys and mouse brains, injury releases 2',3'-cAMP, 2'-AMP, and 3'-AMP into the extracellular compartment; and in humans, traumatic brain injury is associated with large increases in 2',3'-cAMP, 2'-AMP, 3'-AMP, and adenosine in the cerebrospinal fluid. These findings motivate the extracellular 2',3'-cAMP-adenosine pathway hypothesis: intracellular production of 2',3'-cAMP → export of 2',3'-cAMP → extracellular metabolism of 2',3'-cAMP to 2'-AMP and 3'-AMP → extracellular metabolism of 2'-AMP and 3'-AMP to adenosine. Since 2',3'-cAMP has been shown to activate mitochondrial permeability transition pores (mPTPs) leading to apoptosis and necrosis and since adenosine is generally tissue protective, the extracellular 2',3'-cAMP-adenosine pathway may be a protective mechanism [i.e., removes 2',3'-cAMP (an intracellular toxin) and forms adenosine (a tissue protectant)]. This appears to be the case in the brain where deficiency in CNPase (the enzyme that metabolizes 2',3'-cAMP to 2-AMP) leads to increased susceptibility to brain injury and neurological diseases. Surprisingly, CNPase deficiency in the kidney actually protects against acute kidney injury, perhaps by preventing the formation of 2'-AMP (which turns out to be a renal vasoconstrictor) and by augmenting the mitophagy of damaged mitochondria. With regard to 2',3'-cNMPs and their downstream metabolites, there is no doubt much more to be discovered.
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Affiliation(s)
- Edwin K Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA, 15219, USA.
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48
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Gehring C, Turek IS. Cyclic Nucleotide Monophosphates and Their Cyclases in Plant Signaling. FRONTIERS IN PLANT SCIENCE 2017; 8:1704. [PMID: 29046682 PMCID: PMC5632652 DOI: 10.3389/fpls.2017.01704] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/19/2017] [Indexed: 05/19/2023]
Abstract
The cyclic nucleotide monophosphates (cNMPs), and notably 3',5'-cyclic guanosine monophosphate (cGMP) and 3',5'-cyclic adenosine monophosphate (cAMP) are now accepted as key signaling molecules in many processes in plants including growth and differentiation, photosynthesis, and biotic and abiotic defense. At the single molecule level, we are now beginning to understand how cNMPs modify specific target molecules such as cyclic nucleotide-gated channels, while at the systems level, a recent study of the Arabidopsis cNMP interactome has identified novel target molecules with specific cNMP-binding domains. A major advance came with the discovery and characterization of a steadily increasing number of guanylate cyclases (GCs) and adenylate cyclases (ACs). Several of the GCs are receptor kinases and include the brassinosteroid receptor, the phytosulfokine receptor, the Pep receptor, the plant natriuretic peptide receptor as well as a nitric oxide sensor. We foresee that in the near future many more molecular mechanisms and biological roles of GCs and ACs and their catalytic products will be discovered and further establish cNMPs as a key component of plant responses to the environment.
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Affiliation(s)
- Chris Gehring
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ilona S. Turek
- Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Leibniz Institute of Plant Biochemistry, Halle, Germany
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49
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Zhang ZW, Luo S, Zhang GC, Feng LY, Zheng C, Zhou YH, Du JB, Yuan M, Chen YE, Wang CQ, Liu WJ, Xu XC, Hu Y, Bai SL, Kong DD, Yuan S, He YK. Nitric oxide induces monosaccharide accumulation through enzyme S-nitrosylation. PLANT, CELL & ENVIRONMENT 2017; 40:1834-1848. [PMID: 28556250 DOI: 10.1111/pce.12989] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 05/05/2023]
Abstract
Nitric oxide (NO) is extensively involved in various growth processes and stress responses in plants; however, the regulatory mechanism of NO-modulated cellular sugar metabolism is still largely unknown. Here, we report that NO significantly inhibited monosaccharide catabolism by modulating sugar metabolic enzymes through S-nitrosylation (mainly by oxidizing dihydrolipoamide, a cofactor of pyruvate dehydrogenase). These S-nitrosylation modifications led to a decrease in cellular glycolysis enzymes and ATP synthase activities as well as declines in the content of acetyl coenzyme A, ATP, ADP-glucose and UDP-glucose, which eventually caused polysaccharide-biosynthesis inhibition and monosaccharide accumulation. Plant developmental defects that were caused by high levels of NO included delayed flowering time, retarded root growth and reduced starch granule formation. These phenotypic defects could be mediated by sucrose supplementation, suggesting an essential role of NO-sugar cross-talks in plant growth and development. Our findings suggest that molecular manipulations could be used to improve fruit and vegetable sweetness.
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Affiliation(s)
- Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Sha Luo
- The High School Attached to Tsinghua University, Beijing, 100084, China
| | - Gong-Chang Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling-Yang Feng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chong Zheng
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yang-Hong Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun-Bo Du
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming Yuan
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yang-Er Chen
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Chang-Quan Wang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wen-Juan Liu
- Center of Analysis and Testing, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Xiao-Chao Xu
- College of Bioindustry, Chengdu University, Chengdu, 610106, China
| | - Yong Hu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Su-Lan Bai
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Dong-Dong Kong
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yi-Kun He
- College of Life Science, Capital Normal University, Beijing, 100048, China
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50
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Analysis of mononucleotides by tandem mass spectrometry: investigation of fragmentation pathways for phosphate- and ribose-modified nucleotide analogues. Sci Rep 2017; 7:8931. [PMID: 28827558 PMCID: PMC5567097 DOI: 10.1038/s41598-017-09416-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/24/2017] [Indexed: 12/23/2022] Open
Abstract
Synthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5′-mono-, 5′-di-, and 5′-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination. While positive-ion mode yielded fragments derived mainly from nucleobases, negative-ion mode provided insight into the structures of phosphoryl and phosphoribosyl moieties, enabling the determination of structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. Based on these data, we proposed fragmentation pathways that were confirmed by experiments with [18O]-isotopologues. We demonstrated the utility of ESI(−)/MS/MS in the analysis of structurally related compounds by analysing isomeric and isobaric nucleotides and applying ESI(−)/MS/MS to rapid identification of nucleotide synthesis products. We formulated general rules regarding nucleotide structure–fragmentation pattern relationships and indicating characteristic fragmentation ions for the interpretation of ESI(−)/MS/MS spectra of nucleotides and their analogues. The ESI(−)/MS/MS spectra of all nucleotides are available in an on-line database, msTide, at www.msTide-db.com.
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