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Ahn H, Lee GS. Amino Sugar-Enriched Fraction of Korean Red Ginseng Extract Induces the Priming Step of NLRP3 Inflammasome. Molecules 2024; 29:1455. [PMID: 38611734 PMCID: PMC11013037 DOI: 10.3390/molecules29071455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Intracellular protein complexes, known as inflammasomes, activate caspase-1 and induce the secretion of pro-inflammatory cytokines, namely interleukin (IL)-1β and -18. Korean Red Ginseng extract (RGE) is a known immunomodulator and a potential candidate for the regulation of inflammasomes. The saponins, such as ginsenosides, of RGE inhibit inflammasome signaling, while non-saponin substances containing amino sugars promote the priming step, up-regulating inflammasome components (pro-IL-1β, NLRP3, caspase-1, and Asc). In this study, the amino sugar-enriched fraction (ASEF), which increases only non-saponin components, including amino sugars, without changing the concentration of saponin substances, was used to investigate whether saponin or non-saponin components of RGE would have a greater impact on the priming step. When murine macrophages were treated with ASEF, the gene expression of inflammatory cytokines (IL-1α, TNFα, IL-6, and IL-10) increased. Additionally, ASEF induced the priming step but did not affect the inflammasome activation step, such as the secretion of IL-1β, cleavage of caspase-1, and formation of Asc pyroptosome. Furthermore, the upregulation of gene expression of inflammasome components by ASEF was blocked by inhibitors of Toll-like receptor 4 signaling. Maltol, the main constituent of ASEF, promoted the priming step but inhibited the activation step of the inflammasome, while arginine, sugars, arginine-fructose-glucose, and fructose-arginine, the other main constituents of ASEF, had no effect on either step. Thus, certain amino sugars in RGE, excluding maltol, are believed to be the components that induce the priming step. The priming step that prepares the NLRP3 inflammasome for activation appears to be induced by amino sugars in RGE, thereby contributing to the immune-boosting effects of RGE.
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Affiliation(s)
| | - Geun-Shik Lee
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Republic of Korea;
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2
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Wang S, Zhu XM, Hong SD, Zheng SJ, Wang YB, Huang XC, Tian YC, Li WT, Lu YZ, Wu J, Zeng RJ, Dai K, Zhang F. Unveiling the Occurrence and Non-Negligible Role of Amino Sugars in Waste Activated Sludge Fermentation by an Enriched Chitin-Degradation Consortium. Environ Sci Technol 2024; 58:1966-1975. [PMID: 38153028 DOI: 10.1021/acs.est.3c09302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Polysaccharides in extracellular polymeric substances (EPS) can form a hybrid matrix network with proteins, impeding waste-activated sludge (WAS) fermentation. Amino sugars, such as N-acetyl-d-glucosamine (GlcNAc) polymers and sialic acid, are the non-negligible components in the EPS of aerobic granules or biofilm. However, the occurrence of amino sugars in WAS and their degradation remains unclear. Thus, amino sugars (∼6.0%) in WAS were revealed, and the genera of Lactococcus and Zoogloea were identified for the first time. Chitin was used as the substrate to enrich a chitin-degrading consortium (CDC). The COD balances for methane production ranged from 83.3 and 95.1%. Chitin was gradually converted to oligosaccharides and GlcNAc after dosing with the extracellular enzyme. After doing enriched CDC in WAS, the final methane production markedly increased to 60.4 ± 0.6 mL, reflecting an increase of ∼62%. Four model substrates of amino sugars (GlcNAc and sialic acid) and polysaccharides (cellulose and dextran) could be used by CDC. Treponema (34.3%) was identified as the core bacterium via excreting chitinases (EC 3.2.1.14) and N-acetyl-glucosaminidases (EC 3.2.1.52), especially the genetic abundance of chitinases in CDC was 2.5 times higher than that of WAS. Thus, this study provides an elegant method for the utilization of amino sugar-enriched organics.
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Affiliation(s)
- Shuai Wang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiao-Mei Zhu
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Si-Di Hong
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Si-Jie Zheng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yi-Bo Wang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xing-Chen Huang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ye-Chao Tian
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wen-Tao Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yong-Ze Lu
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Jianrong Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Kun Dai
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Fang Zhang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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Li Q, Song Z, Xia S, Kuzyakov Y, Yu C, Fang Y, Chen J, Wang Y, Shi Y, Luo Y, Li Y, Chen J, Wang W, Zhang J, Fu X, Vancov T, Van Zwieten L, Liu CQ, Wang H. Microbial Necromass, Lignin, and Glycoproteins for Determining and Optimizing Blue Carbon Formation. Environ Sci Technol 2024; 58:468-479. [PMID: 38141044 DOI: 10.1021/acs.est.3c08229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Coastal wetlands contribute to the mitigation of climate change through the sequestration of "blue carbon". Microbial necromass, lignin, and glycoproteins (i.e., glomalin-related soil proteins (GRSP)), as important components of soil organic carbon (SOC), are sensitive to environmental change. However, their contributions to blue carbon formation and the underlying factors remain largely unresolved. To address this paucity of knowledge, we investigated their contributions to blue carbon formation along a salinity gradient in coastal marshes. Our results revealed decreasing contributions of microbial necromass and lignin to blue carbon as the salinity increased, while GRSP showed an opposite trend. Using random forest models, we showed that their contributions to SOC were dependent on microbial biomass and resource stoichiometry. In N-limited saline soils, contributions of microbial necromass to SOC decreased due to increased N-acquisition enzyme activity. Decreases in lignin contributions were linked to reduced mineral protection offered by short-range-ordered Fe (FeSRO). Partial least-squares path modeling (PLS-PM) further indicated that GRSP could increase microbial necromass and lignin formation by enhancing mineral protection. Our findings have implications for improving the accumulation of refractory and mineral-bound organic matter in coastal wetlands, considering the current scenario of heightened nutrient discharge and sea-level rise.
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Affiliation(s)
- Qiang Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300192, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Zhaoliang Song
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300192, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Shaopan Xia
- Institute of Resource, Ecosystem and Environment of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen 37077, Germany
- Institute of Environmental Sciences, Kazan Federal University, Kazan 420049, Russia
- Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Changxun Yu
- Department of Biology and Environmental Science, Linnaeus University, Kalmar 39231, Sweden
| | - Yunying Fang
- Australian Rivers Institute, School of Environment and Science, Griffith University, Nathan 4111, Australia
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
- Department of Agroecology, Aarhus University, Tjele 8830, Denmark
| | - Yidong Wang
- Tianjin Key Laboratory of Water Resources and Environment, & School of Geographic and Environmental Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Yu Shi
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yu Luo
- Institute of Soil & Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yongchun Li
- School of Environmental and Resource Sciences, Zhejiang A&F University, Zhejiang, Hangzhou 311300, China
| | - Junhui Chen
- School of Environmental and Resource Sciences, Zhejiang A&F University, Zhejiang, Hangzhou 311300, China
| | - Wei Wang
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Jianchao Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300192, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Xiaoli Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300192, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Tony Vancov
- NSW Department of Planning, Industry & Environment, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Lukas Van Zwieten
- Wollongbar Primary Industries Institute, NSW Department of Primary Industries, Wollongbar, NSW 2477, Australia
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300192, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Hailong Wang
- Institute of Soil & Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
- School of Environmental and Chemical Engineering, Foshan University, Foshan, Guangdong 528000, China
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Oliva RL, Vogt C, Bublitz TA, Camenzind T, Dyckmans J, Joergensen RG. Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances. ISME Commun 2024; 4:ycae038. [PMID: 38616925 PMCID: PMC11014887 DOI: 10.1093/ismeco/ycae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Extracellular polymeric substances (EPS) are produced by microorganisms and interact to form a complex matrix called biofilm. In soils, EPS are important contributors to the microbial necromass and, thus, to soil organic carbon (SOC). Amino sugars (AS) are used as indicators for microbial necromass in soil, although the origin of galactosamine and mannosamine is largely unknown. However, indications exist that they are part of EPS. In this study, two bacteria and two fungi were grown in starch medium either with or without a quartz matrix to induce EPS production. Each culture was separated in two fractions: one that directly underwent AS extraction (containing AS from both biomass and EPS), and another that first had EPS extracted, followed then by AS determination (exclusively containing AS from EPS). We did not observe a general effect of the quartz matrix neither of microbial type on AS production. The quantified amounts of galactosamine and mannosamine in the EPS fraction represented on average 100% of the total amounts of these two AS quantified in cell cultures, revealing they are integral parts of the biofilm. In contrast, muramic acid and glucosamine were also quantified in the EPS, but with much lower contribution rates to total AS production, of 18% and 33%, respectively, indicating they are not necessarily part of EPS. Our results allow a meaningful ecological interpretation of mannosamine and galactosamine data in the future as indicators of microbial EPS, and also attract interest of future studies to investigate the role of EPS to SOC and its dynamics.
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Affiliation(s)
- Rebeca Leme Oliva
- Soil Biology and Plant Nutrition, University of Kassel, 37213 Witzenhausen, Germany
| | - Carla Vogt
- Soil Biology and Plant Nutrition, University of Kassel, 37213 Witzenhausen, Germany
| | - Tábata Aline Bublitz
- Soil Biology and Plant Nutrition, University of Kassel, 37213 Witzenhausen, Germany
| | - Tessa Camenzind
- Institute of Biology, Department of Plant Ecology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Jens Dyckmans
- Centre for Stable Isotope Research Analysis, University of Göttingen, 37077 Göttingen, Germany
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Jing YL, Li XH, Zhang Y, Zhang XY, Liu M, Feng QH. [Effects of thinning on accumulation of soil microbial residue carbon of Picea asperata plantations in sub-alpine region of western Sichuan, China]. Ying Yong Sheng Tai Xue Bao 2024; 35:169-176. [PMID: 38511453 DOI: 10.13287/j.1001-9332.202401.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Microbial residues are an important component of soil organic carbon (SOC). It is unclear how long-term thinning affects the accumulation characteristics of microbial residue carbon (C). We analyzed the differences in soil physicochemical properties, microbial communities, extracellular enzyme activities, and microbial residue C in topsoil (0-10 cm) and subsoil (20-30 cm) in Picea asperata plantation of non-thinned (control, 4950 trees·hm-2) and thinned for 14 years (1160 trees·hm-2) stands, aiming to reveal the regulatory mechanism of thinning on microbial residue C accumulation. The results showed that thinning significantly increased SOC content, total nitrogen content, available phosphorus content, the proportion of particulate organic C, soil water content, C-cycle hydrolase, and acid phosphatase activities, but significantly reduced the proportion of mineral-associated organic C. Thinning significantly affected the content of fungal and microbial residue C, and the contribution of microbial residue C to SOC, and these effects were independent of soil layer. The content of fungal and microbial residue C was 25.0% and 24.5% higher under thinning treatments. However, thinning significantly decreased the contribution of microbial residue C to SOC by 12.3%, indicating an increase in the proportion of plant-derived C in SOC. Stepwise regression analysis showed that total nitrogen and soil water content were key factors influencing fungal and micro-bial residue C accumulation. In summary, thinning promoted microbial residue C sequestration by altering soil pro-perties and changed the composition of SOC sources.
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Affiliation(s)
- Yan-Li Jing
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, Sichuan, China
| | - Xu-Hua Li
- Ecological Restoration and Conservation for Forest and Wetland Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu 610081, China
| | - Yuan Zhang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, Sichuan, China
| | - Xin-Yue Zhang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, Sichuan, China
| | - Mei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, Sichuan, China
| | - Qiu-Hong Feng
- Ecological Restoration and Conservation for Forest and Wetland Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu 610081, China
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Ohnuma T, Tsujii J, Kataoka C, Yoshimoto T, Takeshita D, Lampela O, Juffer AH, Suginta W, Fukamizo T. Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation. Sci Rep 2023; 13:20558. [PMID: 37996461 PMCID: PMC10667598 DOI: 10.1038/s41598-023-47253-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc)n (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients and the negative control of chitin signal transduction in Vibrios. Most translocation processes by SBPs across the inner membrane have been explained thus far by two-domain open/closed mechanism. Here we propose three-domain mechanism of the (GlcNAc)n translocation based on experiments using a recombinant VcCBP, SBP specific for (GlcNAc)n from Vibrio cholerae. X-ray crystal structures of unliganded or (GlcNAc)3-liganded VcCBP solved at 1.2-1.6 Å revealed three distinct domains, the Upper1, Upper2 and Lower domains for this protein. Molecular dynamics simulation indicated that the motions of the three domains are independent and that in the (GlcNAc)3-liganded state the Upper2/Lower interface fluctuated more intensively, compared to the Upper1/Lower interface. The Upper1/Lower interface bound two GlcNAc residues tightly, while the Upper2/Lower interface appeared to loosen and release the bound sugar molecule. The three-domain mechanism proposed here was fully supported by binding data obtained by thermal unfolding experiments and ITC, and may be applicable to other translocation systems involving SBPs belonging to the same cluster.
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Affiliation(s)
- Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan.
| | - Jun Tsujii
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Chikara Kataoka
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Teruki Yoshimoto
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Daijiro Takeshita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-Shi, Ibaraki, 305-8566, Japan
| | - Outi Lampela
- Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
| | - André H Juffer
- Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O.Box 5000, FI-90014, Oulu, Finland
| | - Wipa Suginta
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand.
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Li SJ, Sheng MJ, Li G, Wang R, Li J, Zhang GL, Xiu WM. [Impacts of Land Use Intensification Level on Fluvo-aquic Cropland Soil Microbial Community Abundance and Necromass Accumulation in North China]. Huan Jing Ke Xue 2023; 44:4611-4622. [PMID: 37694654 DOI: 10.13227/j.hjkx.202209304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Despite the essential role of soil microorganisms in nutrient turnover in soil ecological systems and the recognized paramount significance of microbial necromass to soil organic carbon accumulation, how microbial community abundance and necromass respond to land use intensification level regulation remains poorly understood. To address this knowledge gap, based on the land use intensification level, three treatments were set up[annual wheat-maize rotation (CC), alternating temporary grassland with wheat planting (TG), and perennial grassland (PG)], and a long-term fixed filed experiment was established to investigate the influences of the regulation of land use intensification level on bacterial and fungal community abundances; the accumulation of bacterial, fungal, and total microbial necromass; and their contributions to SOC sequestration using droplet digital PCR and amino sugar detection technologies. We further sought to determine the key factors driving the bacterial, fungal, and total microbial necromass C accumulation. Our results demonstrated that fungal community abundance was strongly affected by land use intensification level regulation compared to that of the bacterial community, which increased with decreasing land use intensification level. The total microbial necromass C predominated the SOC accumulation across all three land use intensification levels, which contributed 52.78%, 58.36%, and 68.87% to SOC, respectively, exhibiting an increasing trend with the decline in land use intensification level. Fungal necromass C accounted for more than 80% of the total microbial necromass C, indicating its predominance in the accumulation of the total microbial necromass C and active variation via the reduction in land use intensification level. There was no significant difference in bacterial necromass C (MurA) content, with the trend of CC
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Affiliation(s)
- Sheng-Jun Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Mei-Jun Sheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Gang Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Rui Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Jie Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Gui-Long Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Wei-Ming Xiu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
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8
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Abstract
Microbe-mediated carbon transformation plays an important role in soil carbon sequestration, which is considered to be one of the key strategies to achieve carbon neutrality in the long term. Assessing the efficiency of microbial necromass accumulation relative to plant carbon input or microbial respiration will help to identify ways to promote soil carbon sequestration from an ecosystem perspective.
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Affiliation(s)
- Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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9
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Yang J, Xie D, Ma X. Recent Advances in Chemical Synthesis of Amino Sugars. Molecules 2023; 28:4724. [PMID: 37375279 DOI: 10.3390/molecules28124724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Amino sugars are a kind of carbohydrates with one or more hydroxyl groups replaced by an amino group. They play crucial roles in a broad range of biological activities. Over the past few decades, there have been continuing efforts on the stereoselective glycosylation of amino sugars. However, the introduction of glycoside bearing basic nitrogen is challenging using conventional Lewis acid-promoted pathways owing to competitive coordination of the amine to the Lewis acid promoter. Additionally, diastereomeric mixtures of O-glycoside are often produced if aminoglycoside lack a C2 substituent. This review focuses on the updated overview of the way to stereoselective synthesis of 1,2-cis-aminoglycoside. The scope, mechanism, and the applications in the synthesis of complex glycoconjugates for the representative methodologies were also included.
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Affiliation(s)
- Jian Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Demeng Xie
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiaofeng Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Zhou W, Ma T, Yin X, Wu X, Li Q, Rupakheti D, Xiong X, Zhang Q, Mu C, de Foy B, Rupakheti M, Kang S, Qin D. Dramatic Carbon Loss in a Permafrost Thaw Slump in the Tibetan Plateau is Dominated by the Loss of Microbial Necromass Carbon. Environ Sci Technol 2023; 57:6910-6921. [PMID: 37074051 DOI: 10.1021/acs.est.2c07274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Thaw slumps can lead to considerable carbon loss in permafrost regions, while the loss of components from two major origins, i.e., microbial and plant-derived carbon, during this process remains poorly understood. Here, we provide direct evidence that microbial necromass carbon is a major component of lost carbon in a retrogressive permafrost thaw slump by analyzing soil organic carbon (SOC), biomarkers (amino sugars and lignin phenols), and soil environmental variables in a typical permafrost thaw slump in the Tibetan Plateau. The retrogressive thaw slump led to a ∼61% decrease in SOC and a ∼25% SOC stock loss. As evident in the levels of amino sugars (average of 55.92 ± 18.79 mg g-1 of organic carbon, OC) and lignin phenols (average of 15.00 ± 8.05 mg g-1 OC), microbial-derived carbon (microbial necromass carbon) was the major component of the SOC loss, accounting for ∼54% of the SOC loss in the permafrost thaw slump. The variation of amino sugars was mainly related to the changes in soil moisture, pH, and plant input, while changes in lignin phenols were mainly related to the changes in soil moisture and soil bulk density.
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Affiliation(s)
- Wenting Zhou
- Cryosphere Research Station on the Qinghai-Tibet Plateau, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Ma
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xiufeng Yin
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiaodong Wu
- Cryosphere Research Station on the Qinghai-Tibet Plateau, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin 150025, China
| | - Quanlian Li
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Dipesh Rupakheti
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xin Xiong
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Qianggong Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuicui Mu
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Observation and Research Station on Eco-Environment of Frozen Ground in the Qilian Mountains, Lanzhou University, Lanzhou 730000, China
| | - Benjamin de Foy
- Department of Earth and Atmospheric Sciences, Saint Louis University, St. Louis, Missouri 63108, United States
| | - Maheswar Rupakheti
- Research Institute for Sustainability-Helmholtz Centre Potsdam, Potsdam 14467, Germany
| | - Shichang Kang
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Dahe Qin
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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11
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Zhou R, Liu Y, Dungait JAJ, Kumar A, Wang J, Tiemann LK, Zhang F, Kuzyakov Y, Tian J. Microbial necromass in cropland soils: A global meta-analysis of management effects. Glob Chang Biol 2023; 29:1998-2014. [PMID: 36751727 DOI: 10.1111/gcb.16613] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 05/28/2023]
Abstract
Microbial necromass is a large and persistent component of soil organic carbon (SOC), especially under croplands. The effects of cropland management on microbial necromass accumulation and its contribution to SOC have been measured in individual studies but have not yet been summarized on the global scale. We conducted a meta-analysis of 481-paired measurements from cropland soils to examine the management effects on microbial necromass and identify the optimal conditions for its accumulation. Nitrogen fertilization increased total microbial necromass C by 12%, cover crops by 14%, no or reduced tillage (NT/RT) by 20%, manure by 21%, and straw amendment by 21%. Microbial necromass accumulation was independent of biochar addition. NT/RT and straw amendment increased fungal necromass and its contribution to SOC more than bacterial necromass. Manure increased bacterial necromass higher than fungal, leading to decreased ratio of fungal-to-bacterial necromass. Greater microbial necromass increases after straw amendments were common under semi-arid and in cool climates in soils with pH <8, and were proportional to the amount of straw input. In contrast, NT/RT increased microbial necromass mainly under warm and humid climates. Manure application increased microbial necromass irrespective of soil properties and climate. Management effects were especially strong when applied during medium (3-10 years) to long (10+ years) periods to soils with larger initial SOC contents, but were absent in sandy soils. Close positive links between microbial biomass, necromass and SOC indicate the important role of stabilized microbial products for C accrual. Microbial necromass contribution to SOC increment (accumulation efficiency) under NT/RT, cover crops, manure and straw amendment ranged from 45% to 52%, which was 9%-16% larger than under N fertilization. In summary, long-term cropland management increases SOC by enhancing microbial necromass accumulation, and optimizing microbial necromass accumulation and its contribution to SOC sequestration requires site-specific management.
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Affiliation(s)
- Ranran Zhou
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, P.R. China
| | - Yuan Liu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jennifer A J Dungait
- Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, UK
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Amit Kumar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, UAE
| | - Jinsong Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Lisa K Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Fusuo Zhang
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, P.R. China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
| | - Jing Tian
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, P.R. China
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12
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Li T, Yuan Y, Mou Z, Li Y, Kuang L, Zhang J, Wu W, Wang F, Wang J, Lambers H, Sardans J, Peñuelas J, Ren H, Liu Z. Faster accumulation and greater contribution of glomalin to the soil organic carbon pool than amino sugars do under tropical coastal forest restoration. Glob Chang Biol 2023; 29:533-546. [PMID: 36251710 DOI: 10.1111/gcb.16467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Microbial metabolic products play a vital role in maintaining ecosystem multifunctionality, such as soil physical structure and soil organic carbon (SOC) preservation. Afforestation is an effective strategy to restore degraded land. Glomalin-related soil proteins (GRSP) and amino sugars are regarded as stable microbial-derived C, and their distribution within soil aggregates affects soil structure stability and SOC sequestration. However, the information about how afforestation affects the microbial contribution to SOC pools within aggregates is poorly understood. We assessed the accumulation and contribution of GRSP and amino sugars within soil aggregates along a restoration chronosequence (Bare land, Eucalyptus exserta plantation, native species mixed forest, and native forest) in tropical coastal terraces. Amino sugars and GRSP concentrations increased, whereas their contributions to the SOC pool decreased along the restoration chronosequence. Although microaggregates harbored greater microbial abundances, amino sugars and GRSP concentrations were not significantly affected by aggregate sizes. Interestingly, the contributions of amino sugars and GRSP to SOC pools decreased with decreasing aggregate size which might be associated with increased accumulation of plant-derived C. However, the relative change rate of GRSP was consistently greater in all restoration chronosequences than that of amino sugars. The accumulation of GRSP and amino sugars in SOC pools was closely associated with the dynamics of soil fertility and the microbial community. Our findings suggest that GRSP accumulates faster and contributes more to SOC pools during restoration than amino sugars did which was greatly affected by aggregate sizes. Afforestation substantially enhanced soil quality with native forest comprising species sequestering more SOC than the monoculture plantation did. Such information is invaluable for improving our mechanistic understanding of microbial control over SOC preservation during degraded ecosystem restoration. Our findings also show that plantations using arbuscular mycorrhizal plants can be an effective practice to sequester more soil carbon during restoration.
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Affiliation(s)
- Tengteng Li
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Ye Yuan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhijian Mou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yue Li
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Luhui Kuang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Jing Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Wenjia Wu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Faming Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Jun Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Catalonia, Spain
- CREAF, Catalonia, Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Catalonia, Spain
- CREAF, Catalonia, Spain
| | - Hai Ren
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, China
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13
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Whalen ED, Grandy AS, Sokol NW, Keiluweit M, Ernakovich J, Smith RG, Frey SD. Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding. Glob Chang Biol 2022; 28:7167-7185. [PMID: 36043234 DOI: 10.1111/gcb.16413] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Predicting and mitigating changes in soil carbon (C) stocks under global change requires a coherent understanding of the factors regulating soil organic matter (SOM) formation and persistence, including knowledge of the direct sources of SOM (plants vs. microbes). In recent years, conceptual models of SOM formation have emphasized the primacy of microbial-derived organic matter inputs, proposing that microbial physiological traits (e.g., growth efficiency) are dominant controls on SOM quantity. However, recent quantitative studies have challenged this view, suggesting that plants make larger direct contributions to SOM than is currently recognized by this paradigm. In this review, we attempt to reconcile these perspectives by highlighting that variation across estimates of plant- versus microbial-derived SOM may arise in part from methodological limitations. We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings, highlighting the uncertainty in our current quantitative estimates. We demonstrate that there is significant overlap in the chemical signatures of compounds produced by microbes, plant roots, and through the extracellular decomposition of plant litter, which introduces uncertainty into the use of common biomarkers for parsing plant- and microbial-derived SOM, especially in the mineral-associated organic matter (MAOM) fraction. Although the studies that we review have contributed to a deeper understanding of microbial contributions to SOM, limitations with current methods constrain quantitative estimates. In light of recent advances, we suggest that now is a critical time to re-evaluate long-standing methods, clearly define their limitations, and develop a strategic plan for improving the quantification of plant- and microbial-derived SOM. From our synthesis, we outline key questions and challenges for future research on the mechanisms of SOM formation and stabilization from plant and microbial pathways.
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Affiliation(s)
- Emily D Whalen
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - A Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Noah W Sokol
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Marco Keiluweit
- School of Earth & Sustainability and Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jessica Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Richard G Smith
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Serita D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
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14
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Merx J, Hintzen JCJ, Proietti G, Elferink H, Wang Y, Porzberg MRB, Sondag D, Bilgin N, Park J, Mecinović J, Boltje TJ. Investigation of in vitro histone H3 glycosylation using H3 tail peptides. Sci Rep 2022; 12:19251. [PMID: 36357422 DOI: 10.1038/s41598-022-21883-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/05/2022] [Indexed: 11/12/2022] Open
Abstract
Posttranslational modifications (PTMs) on histone tails regulate eukaryotic gene expression by impacting the chromatin structure and by modulating interactions with other cellular proteins. One such PTM has been identified as serine and threonine glycosylation, the introduction of the ß-N-acetylglucosamine (GlcNAc) moiety on histone H3 tail at position Ser10 and Thr32. The addition of the ß-O-GlcNAc moiety on serine or threonine residues is facilitated by the O-GlcNAc transferase (OGT), and can be removed by the action of O-GlcNAcase (OGA). Conflicting reports on histone tail GlcNAc modification in vivo prompted us to investigate whether synthetic histone H3 tail peptides in conjunction with other PTMs are substrates for OGT and OGA in vitro. Our enzymatic assays with recombinantly expressed human OGT revealed that the unmodified and PTM-modified histone H3 tails are not substrates for OGT at both sites, Ser10 and Thr32. In addition, full length histone H3 was not a substrate for OGT. Conversely, our work demonstrates that synthetic peptides containing the GlcNAc functionality at Ser10 are substrates for recombinantly expressed human OGA, yielding deglycosylated histone H3 peptides. We also show that the catalytic domains of human histone lysine methyltransferases G9a, GLP and SETD7 and histone lysine acetyltransferases PCAF and GCN5 do somewhat tolerate glycosylated H3Ser10 close to lysine residues that undergo methylation and acetylation reactions, respectively. Overall, this work indicates that GlcNAcylation of histone H3 tail peptide in the presence of OGT does not occur in vitro.
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15
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Zeng L, Walker AR, Calderon PDS, Xia X, Ren F, Esquivel-Upshaw JF. The Effect of Amino Sugars on the Composition and Metabolism of a Microcosm Biofilm and the Cariogenic Potential against Teeth and Dental Materials. J Funct Biomater 2022; 13. [PMID: 36412864 DOI: 10.3390/jfb13040223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Amino sugars N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) are abundant sources of carbon and nitrogen in the oral cavity. The aim of this study was to investigate the effects of GlcNAc metabolism on the genomics and biochemistry of a saliva-derived microbial community, and on the surface integrity of human teeth and restorative surfaces. Pooled cell-containing saliva (CCS) was used to establish a microcosm biofilm in vitro in a biofilm medium (BM) containing 5 different carbohydrates. The microbial composition of each biofilm was analyzed by 16S rRNA amplicon sequencing, and the concentrations of eight organic acids were determined for selected sugars by targeted metabolomics. Meanwhile, extracted human teeth and polished titanium and ceramic disks were submerged in BM supplemented with 1% of glucose or GlcNAc, inoculated with CCS and Streptococcus mutans UA159, and incubated for 30 days. To mimic the effects of other microbial byproducts, the specimens were immersed in 10 mM hydrogen peroxide and 10 mM ammonium hydroxide for 30 days. The surface of each specimen was evaluated by profilometry for roughness (Ra) and imaged by scanning electron microscopy. The pH of the biofilm supernatant was significantly higher for the medium containing GlcNAc (p < 0.0001), and was higher in samples containing teeth than the two restorative disks for media containing the same sugar. For both teeth and titanium specimens, the samples treated with glucose-biofilm presented higher roughness values (Ra) than those with GlcNAc-biofilm and every other group. SEM images of the teeth and titanium disks largely supported the profilometry results, with glucose-biofilm samples demonstrating the largest deviation from the reference. For ceramic disks, slightly higher Ra values were obtained for the ammonia group. These findings provide the first direct evidence to support the ability of amino sugars to significantly reduce the cariogenic potential of oral biofilms by altering their biochemistry and bacterial composition. Additionally, amino sugar metabolism appears to be less detrimental to teeth and restorative surfaces than glucose metabolism.
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16
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Luo R, Kuzyakov Y, Zhu B, Qiang W, Zhang Y, Pang X. Phosphorus addition decreases plant lignin but increases microbial necromass contribution to soil organic carbon in a subalpine forest. Glob Chang Biol 2022; 28:4194-4210. [PMID: 35445477 DOI: 10.1111/gcb.16205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Increasing phosphorus (P) inputs induced by anthropogenic activities have increased P availability in soils considerably, with dramatic effects on carbon (C) cycling and storage. However, the underlying mechanisms via which P drives plant and microbial regulation of soil organic C (SOC) formation and stabilization remain unclear, hampering the accurate projection of soil C sequestration under future global change scenarios. Taking the advantage of an 8-year field experiment with increasing P addition levels in a subalpine forest on the eastern Tibetan Plateau, we explored plant C inputs, soil microbial communities, plant and microbial biomarkers, as well as SOC physical and chemical fractions. We found that continuous P addition reduced fine root biomass, but did not affect total SOC content. P addition decreased plant lignin contribution to SOC, primarily from declined vanillyl-type phenols, which was coincided with a reduction in methoxyl/N-alkyl C by 2.1%-5.5%. Despite a decline in lignin decomposition due to suppressed oxidase activity by P addition, the content of lignin-derived compounds decreased because of low C input from fine roots. In contrast, P addition increased microbial (mainly fungal) necromass and its contribution to SOC due to the slower necromass decomposition under reduced N-acquisition enzyme activity. The larger microbial necromass contribution to SOC corresponded with a 9.1%-12.4% increase in carbonyl C abundance. Moreover, P addition had no influence on the slow-cycing mineral-associated organic C pool, and SOC chemical stability indicated by aliphaticity and recalcitrance indices. Overall, P addition in the subalpine forest over 8 years influenced SOC composition through divergent alterations of plant- and microbial-derived C contributions, but did not shape SOC physical and chemical stability. Such findings may aid in accurately forecasting SOC dynamics and their potential feedbacks to climate change with future scenarios of increasing soil P availability in Earth system models.
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Affiliation(s)
- Ruyi Luo
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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17
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Vogel U, Beerens K, Desmet T. Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential. J Biol Chem 2022; 298:101809. [PMID: 35271853 PMCID: PMC8987622 DOI: 10.1016/j.jbc.2022.101809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
Nucleotide sugar (NS) dehydratases play a central role in the biosynthesis of deoxy and amino sugars, which are involved in a variety of biological functions in all domains of life. Bacteria are true masters of deoxy sugar biosynthesis as they can produce a wide range of highly specialized monosaccharides. Indeed, deoxy and amino sugars play important roles in the virulence of gram-positive and gram-negative pathogenic species and are additionally involved in the biosynthesis of diverse macrolide antibiotics. The biosynthesis of deoxy sugars relies on the activity of NS dehydratases, which can be subdivided into three groups based on their structure and reaction mechanism. The best-characterized NS dehydratases are the 4,6-dehydratases that, together with the 5,6-dehydratases, belong to the NS-short-chain dehydrogenase/reductase superfamily. The other two groups are the less abundant 2,3-dehydratases that belong to the Nudix hydrolase superfamily and 3-dehydratases, which are related to aspartame aminotransferases. 4,6-Dehydratases catalyze the first step in all deoxy sugar biosynthesis pathways, converting nucleoside diphosphate hexoses to nucleoside diphosphate-4-keto-6-deoxy hexoses, which in turn are further deoxygenated by the 2,3- and 3-dehydratases to form dideoxy and trideoxy sugars. In this review, we give an overview of the NS dehydratases focusing on the comparison of their structure and reaction mechanisms, thereby highlighting common features, and investigating differences between closely related members of the same superfamilies.
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Affiliation(s)
- Ulrike Vogel
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
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Ramadhan MR, Schlecht E, Dickhoefer U, Mahgoub O, Joergensen RG. Feed digestibility, digesta passage and faecal microbial biomass in desert-adapted goats exposed to mild water restriction. J Anim Physiol Anim Nutr (Berl) 2021; 106:721-732. [PMID: 34278606 DOI: 10.1111/jpn.13597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/23/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
In arid and semi-arid environments, extensively managed ruminants regularly experience drinking water shortage, especially in the dry season. The present study therefore investigated the effects of mild drinking water restriction on feed intake, feed digestibility, solid digesta passage and composition of faeces including faecal microbial biomass. A feeding trial was conducted in Oman, during the dry summer months. Nine adult male Batinah goats were subjected to three watering regimes in a 3 × 3 Latin Square design. Treatments were (1) water offered ad libitum (100%, W100); (2) water restricted to 85% ad libitum consumption (W85); and (3) water restricted to 70% ad libitum consumption (W70). Animals were offered Rhodes grass hay and whole barley grains (1:1 ratio) at 1.3 times maintenance energy requirements. Each of the three experimental periods comprised 16 days of adaptation and 8 days of measurements. During the latter, feed offered and refused as well as faeces were sampled and quantified. Gastrointestinal digesta passage was determined using ytterbium-labelled Rhodes grass hay. Ergosterol and amino sugars were used as markers for faecal microbial biomass, that is the sum of fungi and bacteria. Water restriction had no effect on feed intake and digesta passage. However, feed dry matter, organic matter and fibre digestibility increased (p < 0.05) in W70 compared with W85, and the excreted amount of faecal dry matter, organic matter, nitrogen and neutral detergent fibre decreased (p < 0.05) in W70 compared with W85. Even though water restriction did not affect total faecal microbial biomass carbon (C) concentration, that of fungal biomass C increased (p < 0.05) in W70 compared with W85. Therefore, mild water restriction seems unproblematic from a physiological and nutrient utilization perspective as it increases feed digestibility without compromising feed intake.
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Affiliation(s)
- M R Ramadhan
- Animal Husbandry in the Tropics and Subtropics, University of Kassel and Georg-August-Universität Göttingen, Witzenhausen, Germany
| | - E Schlecht
- Animal Husbandry in the Tropics and Subtropics, University of Kassel and Georg-August-Universität Göttingen, Witzenhausen, Germany
| | - U Dickhoefer
- Nutrition and Rangeland Management in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg Institute), University of Hohenheim, Stuttgart, Germany
| | - O Mahgoub
- College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - R G Joergensen
- Soil Biology and Plant Nutrition, University of Kassel, Witzenhausen, Germany
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19
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Hamala V, Červenková Šťastná L, Kurfiřt M, Cuřínová P, Dračínský M, Karban J. Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides. Beilstein J Org Chem 2021; 17:1086-1095. [PMID: 34093878 PMCID: PMC8144920 DOI: 10.3762/bjoc.17.85] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
Multiple fluorination of glycostructures has emerged as an attractive way of modulating their protein affinity, metabolic stability, and lipophilicity. Here we described the synthesis of a series of mono-, di- and trifluorinated N-acetyl-ᴅ-glucosamine and ᴅ-galactosamine analogs. The key intermediates are the corresponding multiply fluorinated glucosazide and galactosazide thioglycosides prepared from deoxyfluorinated 1,6-anhydro-2-azido-β-ᴅ-hexopyranose precursors by ring-opening reaction with phenyl trimethylsilyl sulfide. Nucleophilic deoxyfluorination at C4 and C6 by reaction with DAST, thioglycoside hydrolysis and azide/acetamide transformation completed the synthesis.
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Affiliation(s)
- Vojtěch Hamala
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
- University of Chemistry and Technology Prague, Technická 5, 16628 Praha 6, Czech Republic
| | - Lucie Červenková Šťastná
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
| | - Martin Kurfiřt
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
- University of Chemistry and Technology Prague, Technická 5, 16628 Praha 6, Czech Republic
| | - Petra Cuřínová
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
| | - Martin Dračínský
- NMR Spectroscopy group, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 542/2, 16000 Praha, Czech Republic
| | - Jindřich Karban
- Department of Bioorganic Compounds and Nanocomposites, Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic
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20
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Zhang Q, Cao HY, Wei L, Lu D, Du M, Yuan M, Shi D, Chen X, Wang P, Chen XL, Chi L, Zhang YZ, Li F. Discovery of exolytic heparinases and their catalytic mechanism and potential application. Nat Commun 2021; 12:1263. [PMID: 33627653 PMCID: PMC7904915 DOI: 10.1038/s41467-021-21441-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.
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Affiliation(s)
- Qingdong Zhang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Hai-Yan Cao
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China ,grid.4422.00000 0001 2152 3263College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lin Wei
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Danrong Lu
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Min Du
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Min Yuan
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Deling Shi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | | | - Peng Wang
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xiu-Lan Chen
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lianli Chi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China ,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Fuchuan Li
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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21
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Zhu X, Jackson RD, DeLucia EH, Tiedje JM, Liang C. The soil microbial carbon pump: From conceptual insights to empirical assessments. Glob Chang Biol 2020; 26:6032-6039. [PMID: 32844509 DOI: 10.1111/gcb.15319] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
The global soil carbon (C) pool is massive, so relatively small changes in soil organic carbon (SOC) stocks can significantly alter atmospheric C and global climate. The recently proposed concept of the soil microbial carbon pump (MCP) emphasizes the active role of soil microbes in SOC storage by integrating the continual microbial transformation of organic C from labile to persistent anabolic forms. However, the concept has not been evaluated with data. Here, we combine datasets, including microbial necromass biomarker amino sugars and SOC, from two long-term agricultural field studies conducted by large United States bioenergy research programs. We interrogate the soil MCP concept by investigating the asynchronous responses of microbial necromass and SOC to land-use change. Microbial necromass appeared to preferentially accumulate in soil and be the dominant contributor to SOC accrual in diversified perennial bioenergy crops. Specifically, ~92% of the additional SOC enhanced by plant diversity was estimated to be microbial necromass C, and >76% of the additional SOC enhanced by land-use transition from annual to perennial crops was estimated to be microbial necromass. This suggests that the soil MCP was stimulated in diversified perennial agroecosystems. We further delineate and suggest two parameters-soil MCP capacity and efficacy-reflecting the conversion of plant C into microbial necromass and the contribution of microbial necromass to SOC, respectively, that should serve as valuable metrics for future studies evaluating SOC storage under alternative management in changing climates.
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Affiliation(s)
- Xuefeng Zhu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Randall D Jackson
- Department of Agronomy & DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Evan H DeLucia
- Department of Plant Biology, University of Illinois, Urbana, IL, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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22
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Chen L, Chakraborty B, Zou J, Burne RA, Zeng L. Amino Sugars Modify Antagonistic Interactions between Commensal Oral Streptococci and Streptococcus mutans. Appl Environ Microbiol 2019; 85:e00370-19. [PMID: 30877119 DOI: 10.1128/AEM.00370-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/12/2019] [Indexed: 02/05/2023] Open
Abstract
N-Acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 of Streptococcus gordonii against the caries pathogen Streptococcus mutans Here, we examine how amino sugars affect the interaction of five low-passage-number clinical isolates of abundant commensal streptococci with S. mutans by utilizing a dual-species biofilm model. Compared to that for glucose, growth on GlcN or GlcNAc significantly reduced the viability of S. mutans in cocultures with most commensals, shifting the proportions of species. Consistent with these results, production of H2O2 was increased in most commensals when growing on amino sugars, and inhibition of S. mutans by Streptococcus cristatus, Streptococcus oralis, or S. gordonii was enhanced by amino sugars on agar plates. All commensals except S. oralis had higher arginine deiminase activities when grown on GlcN and, in some cases, GlcNAc. In ex vivo biofilms formed using pooled cell-containing saliva (CCS), the proportions of S. mutans were drastically diminished when GlcNAc was the primary carbohydrate. Increased production of H2O2 could account in large part for the inhibitory effects of CCS biofilms. Surprisingly, amino sugars appeared to improve mutacin production by S. mutans on agar plates, suggesting that the commensals have mechanisms to actively subvert antagonism by S. mutans in cocultures. Collectively, these findings demonstrate that amino sugars can enhance the beneficial properties of low-passage-number commensal oral streptococci and highlight their potential for moderating the cariogenicity of oral biofilms.IMPORTANCE Dental caries is driven by dysbiosis of oral biofilms in which dominance by acid-producing and acid-tolerant bacteria results in loss of tooth mineral. Our previous work demonstrated the beneficial effects of amino sugars GlcNAc and GlcN in promoting the antagonistic properties of a health-associated oral bacterium, Streptococcus gordonii, in competition with the major caries pathogen Streptococcus mutans Here, we investigated 5 low-passage-number clinical isolates of the most common streptococcal species to establish how amino sugars may influence the ecology and virulence of oral biofilms. Using multiple in vitro models, including a human saliva-derived microcosm biofilm, experiments showed significant enhancement by at least one amino sugar in the ability of most of these bacteria to suppress the caries pathogen. Therefore, our findings demonstrated the mechanism of action by which amino sugars may affect human oral biofilms to promote health.
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23
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Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ. Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus. FEBS Lett 2018; 593:52-66. [PMID: 30411345 DOI: 10.1002/1873-3468.13289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/13/2022]
Abstract
N-Acetylglucosamine-6-phosphate deacetylase (NagA) and glucosamine-6-phosphate deaminase (NagB) are branch point enzymes that direct amino sugars into different pathways. For Staphylococcus aureus NagA, analytical ultracentrifugation and small-angle X-ray scattering data demonstrate that it is an asymmetric dimer in solution. Initial rate experiments show hysteresis, which may be related to pathway regulation, and kinetic parameters similar to other bacterial isozymes. The enzyme binds two Zn2+ ions and is not substrate inhibited, unlike the Escherichia coli isozyme. S. aureus NagB adopts a novel dimeric structure in solution and shows kinetic parameters comparable to other Gram-positive isozymes. In summary, these functional data and solution structures are of use for understanding amino sugar metabolism in S. aureus, and will inform the design of inhibitory molecules.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
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24
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Craig ME, Turner BL, Liang C, Clay K, Johnson DJ, Phillips RP. Tree mycorrhizal type predicts within-site variability in the storage and distribution of soil organic matter. Glob Chang Biol 2018; 24:3317-3330. [PMID: 29573504 DOI: 10.1111/gcb.14132] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/08/2018] [Indexed: 05/14/2023]
Abstract
Forest soils store large amounts of carbon (C) and nitrogen (N), yet how predicted shifts in forest composition will impact long-term C and N persistence remains poorly understood. A recent hypothesis predicts that soils under trees associated with arbuscular mycorrhizas (AM) store less C than soils dominated by trees associated with ectomycorrhizas (ECM), due to slower decomposition in ECM-dominated forests. However, an incipient hypothesis predicts that systems with rapid decomposition-e.g. most AM-dominated forests-enhance soil organic matter (SOM) stabilization by accelerating the production of microbial residues. To address these contrasting predictions, we quantified soil C and N to 1 m depth across gradients of ECM-dominance in three temperate forests. By focusing on sites where AM- and ECM-plants co-occur, our analysis controls for climatic factors that covary with mycorrhizal dominance across broad scales. We found that while ECM stands contain more SOM in topsoil, AM stands contain more SOM when subsoil to 1 m depth is included. Biomarkers and soil fractionations reveal that these patterns are driven by an accumulation of microbial residues in AM-dominated soils. Collectively, our results support emerging theory on SOM formation, demonstrate the importance of subsurface soils in mediating plant effects on soil C and N, and indicate that shifts in the mycorrhizal composition of temperate forests may alter the stabilization of SOM.
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Affiliation(s)
- Matthew E Craig
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Chao Liang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, IN, USA
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25
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Jing YL, Liu SR, Yin Y, Yao RS, Zhang SQ, Mao RX. [Effects of N-fixing tree species (Alnus sibirica)on amino sugars in soil aggregates of Larix kaempferi plantation in eastern Liaoning Province, China.]. Ying Yong Sheng Tai Xue Bao 2018; 29:1753-1758. [PMID: 29974682 DOI: 10.13287/j.1001-9332.201806.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Soil microbial residues are important components of soil stable carbon (C) pools. How N-fixing tree species influence microbial residues in soil aggregates in larch plantations is still unclear. To determine the effects of N-fixing tree species on the distribution of microbial residues in different aggregates, we compared the distribution of amino sugars, biomarker of microbial residues, among aggregates in a pure larch (Larix kaempferi) plantation and a mixed plantation of larch (Larix kaempferi) and alder (Alnus sibirica) in eastern Liaoning Province. The results showed that alder did not affect the distribution of amino sugars, but significantly increased amino sugars content in soil aggregates. The total amino sugars in different soil aggregates were enriched by 130%-170% in the mixed larch plantation compared with those in pure larch plantation. The contributions of glucosamine, galactosamine and muramic acid to the increases of total amino sugars caused by alder introduction were 66.5%-66.9%, 30.0%-30.6% and 2.5%-3.2%, respectively. Alder introduction significantly accelerated the glucosamine/muramic acid ratios in >2000 μm and <250 μm aggregates, but not in 250-2000 μm aggregates. Moreover, alder introduction increased the microbial contribution to soil organic C in all aggregates, but did not influence this contribution among aggregates, indicating that the effects of alder introduction on microbial contribution to aggregates were homogeneous.
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Affiliation(s)
- Yan Li Jing
- Shenyang Agricultural University, Shenyang 110866, China
| | - Shi Rong Liu
- State Forestry Administration Key Laboratory of Forest Ecology and Environment, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - You Yin
- Shenyang Agricultural University, Shenyang 110866, China
| | - Rong Sheng Yao
- Liaoning Provincial Institute of Forest Management, Dandong 118002, Liaoning, China
| | - Shao Qiang Zhang
- Forestry Beureau of Benxi Manchu Autonomous County, Benxi 117100, Liaoning, China
| | - Ri Xin Mao
- Forestry Beureau of Benxi Manchu Autonomous County, Benxi 117100, Liaoning, China
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26
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Malyarenko TV, Ivanchina NV, Malyarenko OS, Kalinovsky AI, Dmitrenok PS, Evtushenko EV, Minh CV, Kicha AA. Two New Steroidal Monoglycosides, Anthenosides A₁ and A₂, and Revision of the Structure of Known Anthenoside A with Unusual Monosaccharide Residue from the Starfish Anthenea aspera. Molecules 2018; 23:E1077. [PMID: 29751557 DOI: 10.3390/molecules23051077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/28/2018] [Accepted: 05/01/2018] [Indexed: 11/16/2022] Open
Abstract
Two new polyhydroxysteroidal glycosides, anthenosides A₁ (1) and A₂ (2), and one previously known steroidal glycoside anthenoside A (3) were isolated from extract of the tropical starfish Anthenea aspera. Structures of 1⁻3 were determined by analysis of the spectroscopic data as well as chemical transformations. As a result, the structure of anthenoside A has been revised and the structures of 1 and 2 were established. Glycosides 1⁻3 contain a 2-acetamido-2-deoxy-4-O-methyl-β-d-glucopyranosyl residue, found in the starfish steroidal glycosides for the first time. All the isolated compounds slightly inhibited cell viability of human cancer T-47D cells and did not show cytotoxic effects against RPMI-7951 cells. Glycoside 1 slightly inhibited colony formation of human cancer RPMI-7951 cells by 16% while compound 2 decreased the number of colonies of T-47D cells by 40%.
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Fullam E, Prokes I, Fütterer K, Besra GS. Structural and functional analysis of the solute-binding protein UspC from Mycobacterium tuberculosis that is specific for amino sugars. Open Biol 2017; 6:rsob.160105. [PMID: 27335320 PMCID: PMC4929945 DOI: 10.1098/rsob.160105] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/26/2016] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the aetiological agent of tuberculosis, has evolved to scavenge nutrients from the confined environment of host macrophages with mycobacterial ATP-binding cassette (ABC) transporters playing a key role in nutrient acquisition. Mtb-UspC (Rv2318) is the solute-binding protein of the essential transporter UspABC, one of four Mtb ABC transporters implicated by homology in sugar acquisition. Herein, we report the structural and functional characterization of Mtb-UspC. The 1.5 Å resolution structure of UspC reveals a two subdomain architecture that forms a highly acidic carbohydrate-substrate binding cleft. This has allowed a distinct preference of Mtb-UspC for amino sugars as determined by thermal shift analysis and solution saturation transfer difference-NMR. Taken together our data support the functional assignment of UspABC as an amino-sugar transporter. Given the limited availability of carbohydrates within the phagosomal environmental niche during Mtb intracellular infection, our studies suggest that UspABC enables Mtb to optimize the use of scarce nutrients during intracellular infection, linking essentiality of this protein to a potential role in recycling components of cell-wall peptidoglycan.
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Affiliation(s)
- Elizabeth Fullam
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ivan Prokes
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Klaus Fütterer
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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28
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Horník Š, Červenková Šťastná L, Cuřínová P, Sýkora J, Káňová K, Hrstka R, Císařová I, Dračínský M, Karban J. Synthesis and in vitro cytotoxicity of acetylated 3-fluoro, 4-fluoro and 3,4-difluoro analogs of D-glucosamine and D-galactosamine. Beilstein J Org Chem 2016; 12:750-9. [PMID: 27340467 PMCID: PMC4901990 DOI: 10.3762/bjoc.12.75] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/30/2016] [Indexed: 11/23/2022] Open
Abstract
Background: Derivatives of D-glucosamine and D-galactosamine represent an important family of the cell surface glycan components and their fluorinated analogs found use as metabolic inhibitors of complex glycan biosynthesis, or as probes for the study of protein–carbohydrate interactions. This work is focused on the synthesis of acetylated 3-deoxy-3-fluoro, 4-deoxy-4-fluoro and 3,4-dideoxy-3,4-difluoro analogs of D-glucosamine and D-galactosamine via 1,6-anhydrohexopyranose chemistry. Moreover, the cytotoxicity of the target compounds towards selected cancer cells is determined. Results: Introduction of fluorine at C-3 was achieved by the reaction of 1,6-anhydro-2-azido-2-deoxy-4-O-benzyl-β-D-glucopyranose or its 4-fluoro analog with DAST. The retention of configuration in this reaction is discussed. Fluorine at C-4 was installed by the reaction of 1,6:2,3-dianhydro-β-D-talopyranose with DAST, or by fluoridolysis of 1,6:3,4-dianhydro-2-azido-β-D-galactopyranose with KHF2. The amino group was introduced and masked as an azide in the synthesis. The 1-O-deacetylated 3-fluoro and 4-fluoro analogs of acetylated D-galactosamine inhibited proliferation of the human prostate cancer cell line PC-3 more than cisplatin and 5-fluorouracil (IC50 28 ± 3 μM and 54 ± 5 μM, respectively). Conclusion: A complete series of acetylated 3-fluoro, 4-fluoro and 3,4-difluoro analogs of D-glucosamine and D-galactosamine is now accessible by 1,6-anhydrohexopyranose chemistry. Intermediate fluorinated 1,6-anhydro-2-azido-hexopyranoses have potential as synthons in oligosaccharide assembly.
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Affiliation(s)
- Štěpán Horník
- Institute of Chemical Process Fundamentals of the CAS, Rozvojová 135, 165 02 Praha, Czech Republic
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the CAS, Rozvojová 135, 165 02 Praha, Czech Republic
| | - Petra Cuřínová
- Institute of Chemical Process Fundamentals of the CAS, Rozvojová 135, 165 02 Praha, Czech Republic
| | - Jan Sýkora
- Institute of Chemical Process Fundamentals of the CAS, Rozvojová 135, 165 02 Praha, Czech Republic
| | - Kateřina Káňová
- Regional Centre for Applied and Molecular Oncology, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Roman Hrstka
- Regional Centre for Applied and Molecular Oncology, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Charles University, Hlavova 2030, 128 43 Praha 2, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the CAS, Rozvojová 135, 165 02 Praha, Czech Republic
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29
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Zhang H, Ravcheev DA, Hu D, Zhang F, Gong X, Hao L, Cao M, Rodionov DA, Wang C, Feng Y. Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections. Microbiologyopen 2015; 4:983-1000. [PMID: 26540018 PMCID: PMC4694137 DOI: 10.1002/mbo3.307] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/21/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
Bacterial pathogens can exploit metabolic pathways to facilitate their successful infection cycles, but little is known about roles of d‐galactosamine (GalN)/N‐acetyl‐d‐galactosamine (GalNAc) catabolism pathway in bacterial pathogenesis. Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons. We delineated two new paralogous AgaR regulators for the GalN/GalNAc catabolism pathway. The electrophoretic mobility shift assays experiment demonstrated that AgaR2 (AgaR1) binds the predicted palindromes, and the combined in vivo data from reverse transcription quantitative polymerase chain reaction and RNA‐seq suggested that AgaR2 (not AgaR1) can effectively repress the transcription of the target genes. Removal of agaR2 (not agaR1) from Streptococcus suis 05ZYH33 augments significantly the abilities of both adherence to Hep‐2 cells and anti‐phagocytosis against RAW264.7 macrophage. As anticipated, the dysfunction in AgaR2‐mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets. Our finding discovered two novel regulators specific for GalN/GalNAc catabolism and assigned them distinct roles into bacterial infections. To the best of our knowledge, it might represent a first paradigm that links the GalN/GalNAc catabolism pathway to bacterial pathogenesis.
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Affiliation(s)
- Huimin Zhang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4360, Luxembourg
| | - Dan Hu
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Fengyu Zhang
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Xiufang Gong
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Lina Hao
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Min Cao
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Changjun Wang
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
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Griepentrog M, Bodé S, Boeckx P, Hagedorn F, Heim A, Schmidt MWI. Nitrogen deposition promotes the production of new fungal residues but retards the decomposition of old residues in forest soil fractions. Glob Chang Biol 2014; 20:327-340. [PMID: 23996910 DOI: 10.1111/gcb.12374] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Abstract
Atmospheric nitrogen (N) deposition has frequently been observed to increase soil carbon (C) storage in forests, but the underlying mechanisms still remain unclear. Changes in microbial community composition and substrate use are hypothesized to be one of the key mechanisms affected by N inputs. Here, we investigated the effects of N deposition on amino sugars, which are used as biomarkers for fungal- and bacterial-derived microbial residues in soil. We made use of a 4-year combined CO2 enrichment and N deposition experiment in model forest ecosystems, providing a distinct (13) C signal for 'new' and 'old' C in soil organic matter and microbial residues measured in density and particle-size fractions of soils. Our hypothesis was that N deposition decreases the amount of fungal residues in soils, with the new microbial residues being more strongly affected than old residues. The soil fractionation showed that organic matter and microbial residues are mainly stabilized by association with soil minerals in the heavy and fine fractions. Moreover, the bacterial residues are relatively enriched at mineral surfaces compared to fungal residues. The (13) C tracing indicated a greater formation of fungal residues compared to bacterial residues after 4 years of experiment. In contradiction to our hypotheses, N deposition significantly increased the amount of new fungal residues in bulk soil and decreased the decomposition of old microbial residues associated with soil minerals. The preservation of old microbial residues could be due to decreased N limitation of microorganisms and therefore a reduced dependence on organic N sources. This mechanism might be especially important in fine heavy fractions with low C/N ratios, where microbial residues are effectively protected from decomposition by association with soil minerals.
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Affiliation(s)
- Marco Griepentrog
- Department of Geography, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
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Romo AJ, Liu HW. Mechanisms and structures of vitamin B(6)-dependent enzymes involved in deoxy sugar biosynthesis. Biochim Biophys Acta 2011; 1814:1534-47. [PMID: 21315852 PMCID: PMC3115481 DOI: 10.1016/j.bbapap.2011.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/08/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
PLP is well-regarded for its role as a coenzyme in a number of diverse enzymatic reactions. Transamination, deoxygenation, and aldol reactions mediated by PLP-dependent enzymes enliven and enrich deoxy sugar biosynthesis, endowing these compounds with unique structures and contributing to their roles as determinants of biological activity in many natural products. The importance of deoxy aminosugars in natural product biosynthesis has spurred several recent structural investigations of sugar aminotransferases. The structure of a PMP-dependent enzyme catalyzing the C-3 deoxygenation reaction in the biosynthesis of ascarylose was also determined. These studies, and the crystal structures they have provided, offer a wealth of new insights regarding the enzymology of PLP/PMP-dependent enzymes in deoxy sugar biosynthesis. In this review, we consider these recent achievements in the structural biology of deoxy sugar biosynthetic enzymes and the important implications they hold for understanding enzyme catalysis and natural product biosynthesis in general. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Anthony J. Romo
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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32
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Abstract
The (1)H-(15)N coupling constants of a suite of organic-soluble amino sugar derivatives have been measured by one-dimensional and two-dimensional (1)H/(15)N heteronuclear single quantum, multiple bond correlation (HSQMBC), and the values so obtained are compared with those measured by analysis of (1)H spectra of (15)N-labeled amino sugar derivatives. A number of bicyclic amino sugar models have been studied, including methyl 2- (and 3-)amino-4,6-O-benzylidene-2- (and 3-)deoxy-alpha-D-hexopyranosides in chair or skew conformations, and methyl 2,6-anhydro-3-deoxy-3-phthalimido-alpha-d-mannopyranoside in a locked, almost classical boat conformation. The magnitudes of the vicinal (1)H-(15)N coupling constants (3)J(HCCN) have been correlated with (1)H/(15)N dihedral angles phi computed for the favored conformations by molecular dynamics with molecular mechanics energy minimization. Non-linear regression of the coupling constants on the dihedral angles has yielded a Karplus equation: (3)J(HCCN)=3.1 cos(2) phi-0.6 cos phi+0.4. The coefficients of the terms in this equation have been compared with those reported for 15 other pairs of nuclei, and the coefficient of the important cos(2)phi term found to be numerically smallest for (3)J(HCCN).
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Affiliation(s)
- Bruce Coxon
- National Institute of Child Health and Human Development, 31 Center Drive, MSC 2423, National Institutes of Health, Bethesda, MD 20892, USA.
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