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Zhu C, Yang K, Li G, Li Y, Gao Z. Identification and Expression Analyses of Invertase Genes in Moso Bamboo Reveal Their Potential Drought Stress Functions. Front Genet 2021; 12:696300. [PMID: 34527019 PMCID: PMC8435750 DOI: 10.3389/fgene.2021.696300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/06/2021] [Indexed: 11/30/2022] Open
Abstract
Invertases (INVs) can irreversibly hydrolyze sucrose into fructose and glucose, which play principal roles in carbon metabolism and responses to various stresses in plants. However, little is known about the INV family in bamboos, especially their potential function in drought stress. In this study, 29 PeINVs were identified in moso bamboo (Phyllostachys edulis). They were clustered into alkaline/neutral invertase (NINV) and acid invertase (AINV) groups based on the gene structures, conserved motifs, and phylogenetic analysis results. The collinearity analysis showed nine segmental duplication pairs within PeINVs, and 25 pairs were detected between PeINVs and OsINVs. PeINVs may have undergone strong purification selection during evolution, and a variety of stress and phytohormone-related regulatory elements were found in the promoters of PeINVs. The tissue-specific expression analysis showed that PeINVs were differentially expressed in various moso bamboo tissues, which suggested that they showed functional diversity. Both the RNA-seq and quantitative real-time PCR results indicated that four PeINVs were significantly upregulated under drought stress. Co-expression network and Pearson’s correlation coefficient analyses showed that these PeINVs co-expressed positively with sugar and water transport genes (SWTGs), and the changes were consistent with sugar content. Overall, we speculate that the identified PeINVs are spatiotemporally expressed, which enables them to participate in moso bamboo growth and development. Furthermore, PeINVs, together with SWTGs, also seem to play vital roles in the response to drought stress. These results provide a comprehensive information resource for PeINVs, which will facilitate further study of the molecular mechanism underlying PeINVs involvement in the response to drought stress in moso bamboo.
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Affiliation(s)
- Chenglei Zhu
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.,Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo and Rattan Science and Technology, Beijing, China
| | - Kebin Yang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.,Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo and Rattan Science and Technology, Beijing, China
| | - Guangzhu Li
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.,Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo and Rattan Science and Technology, Beijing, China
| | - Ying Li
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.,Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo and Rattan Science and Technology, Beijing, China
| | - Zhimin Gao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.,Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo and Rattan Science and Technology, Beijing, China
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2
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Wang L, Zheng Y, Ding S, Zhang Q, Chen Y, Zhang J. Molecular cloning, structure, phylogeny and expression analysis of the invertase gene family in sugarcane. BMC PLANT BIOLOGY 2017; 17:109. [PMID: 28645264 PMCID: PMC5481874 DOI: 10.1186/s12870-017-1052-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 06/06/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism. RESULTS In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane. A comprehensive analysis of the invertase gene family was carried out, including gene structures, phylogenetic relationships, functional domains, conserved motifs of proteins. The results revealed that the 14 invertase members from sugarcane could be clustered into three subfamilies, including 6 neutral/alkaline invertases (ShN/AINVs), and 8 acid invertases (ShAINVs). Faster divergence occurred in acid INVs than in neutral/alkaline INVs after the split of sugarcane and sorghum. At least a one-time gene duplication event was observed to have occurred in the four groups of acid INVs, whereas ShN/AINV1 and ShN/AINV2 in the β8 lineage were revealed to be the most recently duplicated genes among their paralogous genes in the β group of N/AINVs. Furthermore, comprehensive expression analysis of these genes was performed in sugarcane seedlings subjected to five abiotic stresses (drought, low temperature, glucose, fructose, and sucrose) using Quantitative Real-time PCR. The results suggested a functional divergence of INVs and their potential role in response to the five different treatments. Enzymatic activity in sugarcane seedlings was detected under five abiotic stresses treatments, and showed that the activities of all INVs were significantly inhibited in response to five different abiotic stresses, and that the neutral/alkaline INVs played a more prominent role in abiotic stresses than the acid INVs. CONCLUSIONS In this study, we determined the INV gene family members of sugarcane by PCR cloning using sorghum as a reference, providing the first study of the INV gene family in sugarcane. Combining existing INV gene data from 7 plants with a comparative approach including a series of comprehensive analyses to isolate and identify INV gene family members proved to be highly successful. Moreover, the expression levels of INV genes and the variation of enzymatic activities associated with drought, low temperature, glucose, fructose, and sucrose are reported in sugarcane for the first time. The results offered useful foundation and framework for future research for understanding the physiological roles of INVs for sucrose accumulation in sugarcane.
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Affiliation(s)
- Liming Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 35002 China
| | - Yuexia Zheng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 35002 China
| | - Shihui Ding
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 35002 China
| | - Youqiang Chen
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 35002 China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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3
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Nakamichi Y, Oiki S, Mikami B, Murata K, Hashimoto W. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115. Protein J 2016; 35:300-9. [PMID: 27402448 DOI: 10.1007/s10930-016-9673-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst.
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Affiliation(s)
- Yusuke Nakamichi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Sayoko Oiki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Kousaku Murata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka, 572-8508, Japan
| | - Wataru Hashimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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4
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Takase R, Maruyama Y, Oiki S, Mikami B, Murata K, Hashimoto W. Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity. Proteins 2016; 84:934-47. [PMID: 27028675 DOI: 10.1002/prot.25042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 03/08/2016] [Accepted: 03/17/2016] [Indexed: 11/11/2022]
Abstract
Short-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccharide metabolism is 2-keto-3-deoxy-d-gluconate (KDG). Recently, two short and long loops in Sphingomonas KDG-producing SDR enzymes (NADPH-dependent A1-R and NADH-dependent A1-R') involved in alginate metabolism were shown to be crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes-KduD from Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes (SpyDhuD)-prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH and NADH. Both enzymes reduce 2,5-diketo-3-deoxy-d-gluconate to produce KDG. Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with NADH were determined at high resolution (approximately 1.6 Å) by X-ray crystallography. Both PcaKduD and SpyDhuD consist of a three-layered structure, α/β/α, with a coenzyme-binding site in the Rossmann fold; similar to enzymes A1-R and A1-R', both arrange the two short and long loops close to the coenzyme-binding site. The primary structures of the two loops in PcaKduD and SpyDhuD were similar to those in A1-R' but not A1-R. Charge neutrality and moderate space at the binding site of the nucleoside ribose 2' coenzyme region were determined to be structurally crucial for dual-coenzyme specificity in PcaKduD by structural comparison of the NADH- and NADPH-specific SDR enzymes. The corresponding site in SpyDhuD was negatively charged and spatially shallow. This is the first reported study on structural determinants in SDR family KduD related to dual-coenzyme specificity. Proteins 2016; 84:934-947. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryuichi Takase
- Laboratory of Basic and Applied Molecular Biotechnology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Yukie Maruyama
- Laboratory of Basic and Applied Molecular Biotechnology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Sayoko Oiki
- Laboratory of Basic and Applied Molecular Biotechnology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Kousaku Murata
- Laboratory of Basic and Applied Molecular Biotechnology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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5
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Draft Genome Sequence of a Deep-Sea Bacterium, Bacillus niacini Strain JAM F8, Involved in the Degradation of Glycosaminoglycans. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00983-14. [PMID: 25278530 PMCID: PMC4183874 DOI: 10.1128/genomea.00983-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Bacillus niacini JAM F8, which was newly isolated from deep-sea sediment at a depth of 2,759 m from the Izu-Ogasawara Trench. An array of genes related to degradation of glycosaminoglycans in this bacterium was identified by whole-genome analysis.
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6
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Raghavan V, Lowe EC, Townsend GE, Bolam DN, Groisman EA. Tuning transcription of nutrient utilization genes to catabolic rate promotes growth in a gut bacterium. Mol Microbiol 2014; 93:1010-25. [PMID: 25041429 DOI: 10.1111/mmi.12714] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 01/30/2023]
Abstract
Cells respond to nutrient availability by expressing nutrient catabolic genes. We report that the regulator controlling utilization of chondroitin sulphate (CS) in the mammalian gut symbiont Bacteroides thetaiotaomicron is activated by an intermediate in CS breakdown rather than CS itself. We determine that the rate-determining enzyme in CS breakdown is responsible for degrading this intermediate and establish that the levels of the enzyme increase 100-fold, whereas those of the regulator remain constant upon exposure to CS. Because enzyme and regulator compete for the intermediate, B. thetaiotaomicron tunes transcription of CS utilization genes to CS catabolic rate. This tuning results in a transient increase in CS utilization transcripts upon exposure to excess CS. Constitutive expression of the rate-determining enzyme hindered activation of CS utilization genes and growth on CS. An analogous mechanism regulates heparin utilization genes, suggesting that the identified strategy aids B. thetaiotaomicron in the competitive gut environment.
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Affiliation(s)
- Varsha Raghavan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63105, USA
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7
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Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glöckner FO, Golyshina OV, Golyshin PN, Teeling H. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader. Environ Microbiol 2014; 16:2525-37. [PMID: 24428220 PMCID: PMC4257568 DOI: 10.1111/1462-2920.12393] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 01/05/2014] [Indexed: 11/28/2022]
Abstract
Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX-2(T) from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4B(T) from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.
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Affiliation(s)
- Johannes Werner
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, Bremen, Germany
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8
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Jongkees SAK, Yoo H, Withers SG. Mechanistic investigations of unsaturated glucuronyl hydrolase from Clostridium perfringens. J Biol Chem 2014; 289:11385-11395. [PMID: 24573682 DOI: 10.1074/jbc.m113.545293] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Experiments were carried out to probe the details of the hydration-initiated hydrolysis catalyzed by the Clostridium perfringens unsaturated glucuronyl hydrolase of glycoside hydrolase family 88 in the CAZy classification system. Direct (1)H NMR monitoring of the enzymatic reaction detected no accumulated reaction intermediates in solution, suggesting that rearrangement of the initial hydration product occurs on-enzyme. An attempt at mechanism-based trapping of on-enzyme intermediates using a 1,1-difluoro-substrate was unsuccessful because the probe was too deactivated to be turned over by the enzyme. Kinetic isotope effects arising from deuterium-for-hydrogen substitution at carbons 1 and 4 provide evidence for separate first-irreversible and overall rate-determining steps in the hydration reaction, with two potential mechanisms proposed to explain these results. Based on the positioning of catalytic residues in the enzyme active site, the lack of efficient turnover of a 2-deoxy-2-fluoro-substrate, and several unsuccessful attempts at confirmation of a simpler mechanism involving a covalent glycosyl-enzyme intermediate, the most plausible mechanism is one involving an intermediate bearing an epoxide on carbons 1 and 2.
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Affiliation(s)
- Seino A K Jongkees
- Departments of Chemistry and Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Hayoung Yoo
- Departments of Chemistry and Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Departments of Chemistry and Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
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9
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Abstract
Over the sixty years since Koshland initially formulated the classical mechanisms for retaining and inverting glycosidases, researchers have assembled a large body of supporting evidence and have documented variations of these mechanisms. Recently, however, researchers have uncovered a number of completely distinct mechanisms for enzymatic cleavage of glycosides involving elimination and/or hydration steps. In family GH4 and GH109 glycosidases, the reaction proceeds via transient NAD(+)-mediated oxidation at C3, thereby acidifying the proton at C2 and allowing for elimination across the C1-C2 bond. Subsequent Michael-type addition of water followed by reduction at C3 generates the hydrolyzed product. Enzymes employing this mechanism can hydrolyze thioglycosides as well as both anomers of activated substrates. Sialidases employ a conventional retaining mechanism in which a tyrosine functions as the nucleophile, but in some cases researchers have observed off-path elimination end products. These reactions occur via the normal covalent intermediate, but instead of an attack by water on the anomeric center, the catalytic acid/base residue abstracts an adjacent proton. These enzymes can also catalyze hydration of the enol ether via the reverse pathway. Reactions of α-(1,4)-glucan lyases also proceed through a covalent intermediate with subsequent abstraction of an adjacent proton to give elimination. However, in this case, the departing carboxylate "nucleophile" serves as the base in a concerted but asynchronous syn-elimination process. These enzymes perform only elimination reactions. Polysaccharide lyases, which act on uronic acid-containing substrates, also catalyze only elimination reactions. Substrate binding neutralizes the charge on the carboxylate, which allows for abstraction of the proton on C5 and leads to an elimination reaction via an E1cb mechanism. These enzymes can also cleave thioglycosides, albeit slowly. The unsaturated product of polysaccharide lyases can then serve as a substrate for a hydration reaction carried out by unsaturated glucuronyl hydrolases. This hydration is initiated by protonation at C4 and proceeds in a Markovnikov fashion rather than undergoing a Michael-type addition, giving a hemiketal at C5. This hemiketal then undergoes a rearrangement that results in cleavage of the anomeric bond. These enzymes can also hydrolyze thioglycosides efficiently and slowly turn over substrates with inverted anomeric configuration. The mechanisms discussed in this Account proceed through transition states that involve either positive or negative charges, unlike the exclusively cationic transition states of the classical Koshland retaining and inverting glycosidases. In addition, the distribution of this charge throughout the substrate can vary substantially. The nature of these mechanisms and their transition states means that any inhibitors or inactivators of these unusual enzymes probably differ from those presently used for Koshland retaining or inverting glycosidases.
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Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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10
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Collén PN, Jeudy A, Sassi JF, Groisillier A, Czjzek M, Coutinho PM, Helbert W. A novel unsaturated β-glucuronyl hydrolase involved in ulvan degradation unveils the versatility of stereochemistry requirements in family GH105. J Biol Chem 2014; 289:6199-211. [PMID: 24407291 DOI: 10.1074/jbc.m113.537480] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.
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Affiliation(s)
- Pi Nyvall Collén
- From the CNRS, Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 "Marine Plants and Biomolecules," Station Biologique, F-29682 Roscoff Cedex, France
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11
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Nakamichi Y, Mikami B, Murata K, Hashimoto W. Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin. J Biol Chem 2014; 289:4787-97. [PMID: 24403065 DOI: 10.1074/jbc.m113.522573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in β-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by x-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and Bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35-Å resolution. In comparison with structures of streptococcal and Bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.
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Affiliation(s)
- Yusuke Nakamichi
- From the Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, and
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12
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Jongkees SAK, Yoo H, Withers SG. Mechanistic Insights from Substrate Preference in Unsaturated Glucuronyl Hydrolase. Chembiochem 2013; 15:124-34. [PMID: 24227702 DOI: 10.1002/cbic.201300547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Seino A K Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1 (Canada)
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13
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Zhou P, Chen Z, Yan Q, Yang S, Hilgenfeld R, Jiang Z. The structure of a glycoside hydrolase family 81 endo-β-1,3-glucanase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2027-38. [PMID: 24100321 DOI: 10.1107/s090744491301799x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 06/29/2013] [Indexed: 11/11/2022]
Abstract
Endo-β-1,3-glucanases catalyze the hydrolysis of β-1,3-glycosidic linkages in glucans. They are also responsible for rather diverse physiological functions such as carbon utilization, cell-wall organization and pathogen defence. Glycoside hydrolase (GH) family 81 mainly consists of β-1,3-glucanases from fungi, higher plants and bacteria. A novel GH family 81 β-1,3-glucanase gene (RmLam81A) from Rhizomucor miehei was expressed in Escherichia coli. Purified RmLam81A was crystallized and the structure was determined in two crystal forms (form I-free and form II-Se) at 2.3 and 2.0 Å resolution, respectively. Here, the crystal structure of a member of GH family 81 is reported for the first time. The structure of RmLam81A is greatly different from all endo-β-1,3-glucanase structures available in the Protein Data Bank. The overall structure of the RmLam81A monomer consists of an N-terminal β-sandwich domain, a C-terminal (α/α)6 domain and an additional domain between them. Glu553 and Glu557 are proposed to serve as the proton donor and basic catalyst, respectively, in a single-displacement mechanism. In addition, Tyr386, Tyr482 and Ser554 possibly contribute to both the position or the ionization state of the basic catalyst Glu557. The first crystal structure of a GH family 81 member will be helpful in the study of the GH family 81 proteins and endo-β-1,3-glucanases.
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Affiliation(s)
- Peng Zhou
- Department of Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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14
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Nakamichi Y, Maruyama Y, Mikami B, Hashimoto W, Murata K. Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups. J Biol Chem 2011; 286:6262-71. [PMID: 21147778 PMCID: PMC3057837 DOI: 10.1074/jbc.m110.182618] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/23/2010] [Indexed: 11/06/2022] Open
Abstract
Pathogenic Streptococcus agalactiae produces polysaccharide lyases and unsaturated glucuronyl hydrolase (UGL), which are prerequisite for complete degradation of mammalian extracellular matrices, including glycosaminoglycans such as chondroitin and hyaluronan. Unlike the Bacillus enzyme, streptococcal UGLs prefer sulfated glycosaminoglycans. Here, we show the loop flexibility for substrate binding and structural determinants for recognition of glycosaminoglycan sulfate groups in S. agalactiae UGL (SagUGL). UGL also degraded unsaturated heparin disaccharides; this indicates that the enzyme released unsaturated iduronic and glucuronic acids from substrates. We determined the crystal structures of SagUGL wild-type enzyme and both substrate-free and substrate-bound D175N mutants by x-ray crystallography and noted that the loop over the active cleft exhibits flexible motion for substrate binding. Several residues in the active cleft bind to the substrate, unsaturated chondroitin disaccharide with a sulfate group at the C-6 position of GalNAc residue. The sulfate group is hydrogen-bonded to Ser-365 and Ser-368 and close to Lys-370. As compared with wild-type enzyme, S365H, S368G, and K370I mutants exhibited higher Michaelis constants toward the substrate. The conversion of SagUGL to Bacillus sp. GL1 UGL-like enzyme via site-directed mutagenesis demonstrated that Ser-365 and Lys-370 are essential for direct binding and for electrostatic interaction, respectively, for recognition of the sulfate group by SagUGL. Molecular conversion was also achieved in SagUGL Arg-236 with an affinity for the sulfate group at the C-4 position of the GalNAc residue. These residues binding to sulfate groups are frequently conserved in pathogenic bacterial UGLs, suggesting that the motif "R-//-SXX(S)XK" (where the hyphen and slash marks in the motif indicate the presence of over 100 residues in the enzyme and parentheses indicate that Ser-368 makes little contribution to enzyme activity) is crucial for degradation of sulfated glycosaminoglycans.
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Affiliation(s)
- Yusuke Nakamichi
- From the Laboratories of Basic and Applied Molecular Biotechnology and
| | - Yukie Maruyama
- From the Laboratories of Basic and Applied Molecular Biotechnology and
| | - Bunzo Mikami
- Applied Structural Biology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wataru Hashimoto
- From the Laboratories of Basic and Applied Molecular Biotechnology and
| | - Kousaku Murata
- From the Laboratories of Basic and Applied Molecular Biotechnology and
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15
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Maruyama Y, Nakamichi Y, Itoh T, Mikami B, Hashimoto W, Murata K. Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. J Biol Chem 2009; 284:18059-69. [PMID: 19416976 PMCID: PMC2709336 DOI: 10.1074/jbc.m109.005660] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 04/08/2009] [Indexed: 11/06/2022] Open
Abstract
Unsaturated glucuronyl hydrolase (UGL) categorized into the glycoside hydrolase family 88 catalyzes the hydrolytic release of an unsaturated glucuronic acid from glycosaminoglycan disaccharides, which are produced from mammalian extracellular matrices through the beta-elimination reaction of polysaccharide lyases. Here, we show enzyme characteristics of pathogenic streptococcal UGLs and structural determinants for the enzyme substrate specificity. The putative genes for UGL and phosphotransferase system for amino sugar, a component of glycosaminoglycans, are assembled into a cluster in the genome of pyogenic and hemolytic streptococci such as Streptococcus agalactiae, Streptococcus pneumoniae, and Streptococcus pyogenes, which produce extracellular hyaluronate lyase as a virulent factor. The UGLs of these three streptococci were overexpressed in Escherichia coli cells, purified, and characterized. Streptococcal UGLs degraded unsaturated hyaluronate and chondroitin disaccharides most efficiently at approximately pH 5.5 and 37 degrees C. Distinct from Bacillus sp. GL1 UGL, streptococcal UGLs preferred sulfated substrates. DNA microarray and Western blotting indicated that the enzyme was constitutively expressed in S. agalactiae cells, although the expression level increased in the presence of glycosaminoglycan. The crystal structure of S. agalactiae UGL (SagUGL) was determined at 1.75 A resolution by x-ray crystallography. SagUGL adopts alpha(6)/alpha(6)-barrel structure as a basic scaffold similar to Bacillus UGL, but the arrangement of amino acid residues in the active site differs between the two. SagUGL Arg-236 was found to be one of the residues involved in its activity for the sulfated substrate through structural comparison and site-directed mutagenesis. This is the first report on the structure and function of streptococcal UGLs.
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Affiliation(s)
- Yukie Maruyama
- From the Laboratory of Basic and Applied Molecular Biotechnology, and
| | - Yusuke Nakamichi
- From the Laboratory of Basic and Applied Molecular Biotechnology, and
| | - Takafumi Itoh
- From the Laboratory of Basic and Applied Molecular Biotechnology, and
| | - Bunzo Mikami
- the Laboratory of Applied Structural Biology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wataru Hashimoto
- From the Laboratory of Basic and Applied Molecular Biotechnology, and
| | - Kousaku Murata
- From the Laboratory of Basic and Applied Molecular Biotechnology, and
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16
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Abstract
The pectic enzymes are a diverse group of enzymes that collectively degrade pectin, a mixture of highly heterogeneous and branched polysaccharides rich in D: -galacturonic acids forming a major component of the primary cell wall of plants. This review covers key enzymes that function to deconstruct the "ramified region" of pectin. The enzymes include glycoside hydrolases and polysaccharide lyases that degrade complex pectic domains consisting of rhamnogalacturonans, xylogalacturonans, and other heterogeneous polymers. The chemical nature of the pectic substrates for the enzymes is presented. The biochemical properties of the enzymes, the mechanisms of enzyme actions, and related structures and functions, are described. Applications of these enzymes in fruit juice processing and in the production of bioactive compounds, as well as their technological relevance to the deconstruction of cell wall structures for biomass conversion are discussed.
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Affiliation(s)
- Dominic Wong
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA.
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17
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Crystal Structure of YihS in Complex with d-Mannose: Structural Annotation of Escherichia coli and Salmonella enterica yihS-encoded Proteins to an Aldose–Ketose Isomerase. J Mol Biol 2008; 377:1443-59. [DOI: 10.1016/j.jmb.2008.01.090] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/20/2022]
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18
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Bocock PN, Morse AM, Dervinis C, Davis JM. Evolution and diversity of invertase genes in Populus trichocarpa. PLANTA 2008; 227:565-76. [PMID: 17938954 DOI: 10.1007/s00425-007-0639-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 09/27/2007] [Indexed: 05/21/2023]
Abstract
Invertase (EC 3.2.1.26) plays a key role in carbon utilization as it catalyzes the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families thought to have distinct evolutionary origins and can be distinguished by their pH optima for activity: acid invertases and neutral/alkaline invertases. The acid invertases apparently originated in eubacteria and are targeted to the cell wall and vacuole, while neutral/alkaline invertases apparently originated in cyanobacteria and function in the cytosol. The recently sequenced genome of Populus trichocharpa (Torr. and Gray) allowed us to identify the genes encoding invertase in this woody perennial. Here we describe the identification of eight acid invertase genes; three of which belong to the vacuolar targeted group (PtVIN1-3), and five of which belong to the cell wall targeted group (PtCIN1-5). Similarly, we report the identification of 16 neutral/alkaline invertase genes (PtNIN1-16). Expression analyses using whole genome microarrays and RT-PCR reveal evidence for expression of all invertase family members. An examination of the micro-syntenic regions surrounding the poplar invertase genes reveals extensive colinearity with Arabidopsis invertases. We also find evidence for expression of a novel intronless vacuolar invertase (PtVIN1), which apparently arose from a processed PtVIN2 transcript that re-inserted into the genome. To our knowledge, this is the first intronless invertase found in plants. This work increases the understanding of the role this family plays in carbon allocation and partitioning in forest trees as well as its evolutionary development.
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Affiliation(s)
- Philip N Bocock
- Plant Molecular and Cellular Biology Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA
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19
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Crystal Structure of Glycoside Hydrolase Family 78 α-L-Rhamnosidase from Bacillus sp. GL1. J Mol Biol 2007; 374:384-98. [DOI: 10.1016/j.jmb.2007.09.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 08/31/2007] [Accepted: 09/04/2007] [Indexed: 11/21/2022]
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20
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Itoh T, Hashimoto W, Mikami B, Murata K. Crystal Structure of Unsaturated Glucuronyl Hydrolase Complexed with Substrate. J Biol Chem 2006; 281:29807-16. [PMID: 16893885 DOI: 10.1074/jbc.m604975200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Unsaturated glucuronyl hydrolase (UGL), which is a member of glycoside hydrolase family GH-88, is a bacterial enzyme that degrades mammalian glycosaminoglycans and bacterial biofilms. The enzyme, which acts on unsaturated oligosaccharides with an alpha-glycoside bond produced by microbial polysaccharide lyases responsible for bacterial invasion of host cells, was believed to release 4-deoxy-l-threo-5-hexosulose-uronate (unsaturated glucuronic acid, or DeltaGlcA) and saccharide with a new nonreducing terminus by hydrolyzing the glycosidic bond. We detail the crystal structures of wild-type inactive mutant UGL of Bacillus sp. GL1 and its complex with a substrate (unsaturated chondroitin disaccharide), identify active site residues, and postulate a reaction mechanism catalyzed by UGL that triggers the hydration of the vinyl ether group in DeltaGlcA, based on the structural analysis of the enzyme-substrate complex and biochemical analysis. The proposed catalytic mechanism of UGL is a novel case among known glycosidases. Under the proposed mechanism, Asp-149 acts as a general acid and base catalyst to protonate the DeltaGlcA C4 atom and to deprotonate the water molecule. The deprotonated water molecule attacks the DeltaGlcA C5 atom to yield unstable hemiketal; this is followed by spontaneous conversion to an aldehyde (4-deoxy-l-threo-5-hexosulose-uronate) and saccharide through hemiacetal formation and cleavage of the glycosidic bond. UGL is the first clarified alpha(6)/alpha(6)-barrel enzyme using aspartic acid as the general acid/base catalyst.
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Affiliation(s)
- Takafumi Itoh
- Division of Applied Life Sciences and Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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21
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Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem Biophys Res Commun 2006; 347:1021-9. [PMID: 16870154 DOI: 10.1016/j.bbrc.2006.07.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 07/05/2006] [Indexed: 11/30/2022]
Abstract
Bacillus subtilis strain 168 YteR has been identified as a novel enzyme "unsaturated rhamnogalacturonyl hydrolase" classified in glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) produced from plant cell wall RG type-I treated with RG lyases, releasing unsaturated galacturonic acid (DeltaGalA) from the substrate. The most likely candidate catalytic residue is Asp-143. Here, we show the structure of D143N in complex with unsaturated RG disaccharide (substrate) determined at 1.9A resolution by X-ray crystallography. This structural feature directly contributes to the postulation of the enzyme reaction mechanism. YteR triggers the hydration of vinyl ether group in DeltaGalA, but not of glycoside bond, by using Asp-143 as a general acid and base catalyst. Asp-143 donates proton to the double bond of DeltaGalA as an acid catalyst and also deprotonates a water molecule as a base catalyst. Deprotonated water molecule attacks the C5 atom of DeltaGalA.
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Affiliation(s)
- Takafumi Itoh
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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22
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Itoh T, Hashimoto W, Mikami B, Murata K. Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1. Biochem Biophys Res Commun 2006; 344:253-62. [PMID: 16630576 DOI: 10.1016/j.bbrc.2006.03.141] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2006] [Accepted: 03/20/2006] [Indexed: 11/20/2022]
Abstract
Bacterial unsaturated glucuronyl hydrolases (UGLs) together with polysaccharide lyases are responsible for the complete depolymerization of mammalian extracellular matrix glycosaminoglycans. UGL acts on various oligosaccharides containing unsaturated glucuronic acid (DeltaGlcA) at the nonreducing terminus and releases DeltaGlcA through hydrolysis. In this study, we demonstrate the substrate recognition mechanism of the UGL of Bacillus sp. GL1 by determining the X-ray crystallographic structure of its substrate-enzyme complexes. The tetrasaccharide-enzyme complex demonstrated that at least four subsites are present in the active pocket. Although several amino acid residues are crucial for substrate binding, the enzyme strongly recognizes DeltaGlcA at subsite -1 through the formation of hydrogen bonds and stacking interactions, and prefers N-acetyl-d-galactosamine and glucose rather than N-acetyl-d-glucosamine as a residue accommodated in subsite +1, due to the steric hindrance.
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Affiliation(s)
- Takafumi Itoh
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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23
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Zhang R, Minh T, Lezondra L, Korolev S, Moy S, Collart F, Joachimiak A. 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins 2006; 60:561-5. [PMID: 15906318 PMCID: PMC2792013 DOI: 10.1002/prot.20410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- R. Zhang
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - T. Minh
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
- College of Chemistry, University of California at Berkeley, Berkeley, CA
| | - L. Lezondra
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - S. Korolev
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - S.F. Moy
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - F. Collart
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
| | - A. Joachimiak
- Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory
- Correspondence to: Andrzej Joachimiak, Structural Biology Center, Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, 9700 South Cass Ave., Bldg. 202, Argonne, IL 60439.
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Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J Mol Biol 2006; 360:573-85. [PMID: 16781735 DOI: 10.1016/j.jmb.2006.04.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 04/18/2006] [Accepted: 04/20/2006] [Indexed: 11/19/2022]
Abstract
YteR, a hypothetical protein with unknown functions, is derived from Bacillus subtilis strain 168 and has an overall structure similar to that of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits little amino acid sequence identity with UGL. UGL releases unsaturated glucuronic acid from glycosaminoglycan treated with glycosaminoglycan lyases. The amino acid sequence of YteR shows a significant homology (26% identity) with the hypothetical protein YesR also from B. subtilis strain 168. To clarify the intrinsic functions of YteR and YesR, both proteins were overexpressed in Escherichia coli, purified, and characterized. Based on their gene arrangements in genome and enzyme properties, YteR and YesR were found to constitute a novel enzyme activity, "unsaturated rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and releases an unsaturated galacturonic acid. The crystal structure of YteR complexed with unsaturated chondroitin disaccharide (UGL substrate) was obtained and compared to the structure of UGL complexed with the same disaccharide. The UGL substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively. The most likely candidate catalytic residues for general acid/base are Asp143 in YteR and Asp135 in YesR. This is supported by three-dimensional structural and site-directed mutagenesis studies. These findings provide molecular insights into novel enzyme catalysis and sequential reaction mechanisms involved in RG-I depolymerization by bacteria.
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Affiliation(s)
- Takafumi Itoh
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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25
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Ji X, Van den Ende W, Van Laere A, Cheng S, Bennett J. Structure, evolution, and expression of the two invertase gene families of rice. J Mol Evol 2005; 60:615-34. [PMID: 15983871 DOI: 10.1007/s00239-004-0242-1] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2004] [Accepted: 12/07/2004] [Indexed: 01/08/2023]
Abstract
Invertases catalyze the irreversible hydrolysis of sucrose to glucose and fructose. Plants contain two unrelated families of these enzymes: acid forms that derive from periplasmic invertases of eubacteria and are found in cell wall and vacuole, and neutral/alkaline forms evolved from the cytosolic invertases of cyanobacteria. Genomes of rice (Oryza sativa) and thale cress (Arabidopsis thaliana) contain multiple genes encoding these two families. Here for rice we identify the member genes of a cell-wall group (designated OsCIN1-9), a vacuolar group (OsVIN1-2), and two ancient neutral/alkaline groups: alpha (OsNIN1-4) and beta (OsNIN5-8). In Arabidopsis these groups contain six, two, four and five members, respectively. It is believed that the vacuolar group evolved from the cell-wall group. We provide evidence that the N-terminal signal peptide that directs cell-wall invertases co-translationally into the endoplasmic reticulum for secretion was replaced in the vacuolar group by a sequence similar to the complex N-terminal motif that targets alkaline phosphatase post-translationally to the vacuolar membrane of yeast. Since the last common ancestor of Arabidopsis and rice, the two invertase families evolved equally rapidly via gene duplication and gene loss, but the acid invertase family underwent approximately 10 events of intron loss compared with a single event of intron gain in the neutral/alkaline invertase family. Transcripts were detected for all rice invertase genes except OsCIN9. The acid invertase genes showed greater spatial and temporal diversity of expression than the neutral/alkaline genes.
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Affiliation(s)
- Xuemei Ji
- Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, Metro Manila, Philippines
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26
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Hashimoto W, Yamasaki M, Itoh T, Momma K, Mikami B, Murata K. Super-channel in bacteria: Structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules. J Biosci Bioeng 2004; 98:399-413. [PMID: 16233728 DOI: 10.1016/s1389-1723(05)00304-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Accepted: 09/27/2004] [Indexed: 11/22/2022]
Abstract
Cells of Sphingomonas sp. A1 directly incorporate a macromolecule, alginate, into the cytoplasm through a biosystem, super-channel, consisting of a pit on the cell surface, alginate-binding proteins in the periplasm, and an ATP-binding cassette transporter in the inner membrane. The alginate is finally depolymerized into constituent monosaccharides by polysaccharide lyases present in the cytoplasm. The fundamental frame of the biosystem for alginate transport, and the functions of the pit, binding proteins, and ABC transporter have already been reviewed together with those of alginate-depolymerization processes [Hashimoto et al., J. Biosci. Bioeng., 87, 123-136 (1999)]. In this review, we have attempted to demonstrate the three-dimensional structure and evolution features of the super-channel, and alginate-depolymerization processes by using information obtained mainly through genomics, proteomics, and X-ray crystallography.
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Affiliation(s)
- Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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