1
|
Tian J, Li C, Dong Z, Yang Y, Xing J, Yu P, Xin Y, Xu F, Wang L, Mu Y, Guo X, Sun Q, Zhao G, Gu Y, Qin G, Jiang W. Inactivation of the antidiabetic drug acarbose by human intestinal microbial-mediated degradation. Nat Metab 2023; 5:896-909. [PMID: 37157031 DOI: 10.1038/s42255-023-00796-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
Drugs can be modified or degraded by the gut microbiota, which needs to be considered in personalized therapy. The clinical efficacy of the antidiabetic drug acarbose, an inhibitor of α-glucosidase, varies greatly among individuals for reasons that are largely unknown. Here we identify in the human gut acarbose-degrading bacteria, termed Klebsiella grimontii TD1, whose presence is associated with acarbose resistance in patients. Metagenomic analyses reveal that the abundance of K. grimontii TD1 is higher in patients with a weak response to acarbose and increases over time with acarbose treatment. In male diabetic mice, co-administration of K. grimontii TD1 reduces the hypoglycaemic effect of acarbose. Using induced transcriptome and protein profiling, we further identify an acarbose preferred glucosidase, Apg, in K. grimontii TD1, which can degrade acarbose into small molecules with loss of inhibitor function and is widely distributed in human intestinal microorganisms, especially in Klebsiella. Our results suggest that a comparatively large group of individuals could be at risk of acarbose resistance due to its degradation by intestinal bacteria, which may represent a clinically relevant example of non-antibiotic drug resistance.
Collapse
Affiliation(s)
- Jinzhong Tian
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, PR China
| | - Chong Li
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Zhixiang Dong
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yunpeng Yang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Jing Xing
- Lingang Laboratory, Shanghai, PR China
| | - Peijun Yu
- University of Chinese Academy of Sciences, Beijing, PR China
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, PR China
| | - Ying Xin
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Fengmei Xu
- Department of Endocrinology and Metabolism, Hebi Coal (group) Ltd. General Hospital, Hebi, PR China
| | - Lianwei Wang
- Department of Endocrinology and Metabolism, Zhumadian Central Hospital, Zhumadian, PR China
| | - Yahui Mu
- Department of Endocrinology and Metabolism, Huanghe Sanmenxia Hospital, Sanmenxia, PR China
| | - Xiangyang Guo
- Department of Endocrinology and Metabolism, Xinyang Central Hospital, Xinyang, PR China
| | - Qiang Sun
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, PR China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, PR China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, PR China.
| | - Guijun Qin
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China.
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, PR China.
| |
Collapse
|
2
|
Dimeric architecture of maltodextrin glucosidase (MalZ) provides insights into the substrate recognition and hydrolysis mechanism. Biochem Biophys Res Commun 2022; 586:49-54. [PMID: 34826700 DOI: 10.1016/j.bbrc.2021.11.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022]
Abstract
Maltodextrin glucosidase (MalZ) is a key enzyme in the maltose utilization pathway in Escherichia coli that liberates glucose from the reducing end of the short malto-oligosaccharides. Unlike other enzymes in the GH13_21 subfamily, the hydrolytic activity of MalZ is limited to maltodextrin rather than long starch substrates, forming various transglycosylation products in α-1,3, α-1,4 or α-1,6 linkages. The mechanism for the substrate binding and hydrolysis of this enzyme is not well understood yet. Here, we present the dimeric crystal structure of MalZ, with the N-domain generating a unique substrate binding groove. The N-domain bears CBM34 architecture and forms a part of the active site in the catalytic domain of the adjacent molecule. The groove found between the N-domain and catalytic domain from the adjacent molecule, shapes active sites suitable for short malto-oligosaccharides, but hinders long stretches of oligosaccharides. The conserved residue of E44 protrudes at subsite +2, elucidating the hydrolysis pattern of the substrate by the glucose unit from the reducing end. The structural analysis provides a molecular basis for the substrate specificity and the enzymatic property, and has potential industrial application for protein engineering.
Collapse
|
3
|
Wangpaiboon K, Laohawuttichai P, Kim SY, Mori T, Nakapong S, Pichyangkura R, Pongsawasdi P, Hakoshima T, Krusong K. A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1064-1076. [PMID: 34342279 DOI: 10.1107/s205979832100677x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
α-Glucosidase (EC 3.2.1.20) is a carbohydrate-hydrolyzing enzyme which generally cleaves α-1,4-glycosidic bonds of oligosaccharides and starch from the nonreducing ends. In this study, the novel α-glucosidase from Weissella cibaria BBK-1 (WcAG) was biochemically and structurally characterized. WcAG belongs to glycoside hydrolase family 13 (GH13) and to the neopullanase subfamily. It exhibits distinct hydrolytic activity towards the α-1,4 linkages of short-chain oligosaccharides from the reducing end. The enzyme prefers to hydrolyse maltotriose and acarbose, while it cannot hydrolyse cyclic oligosaccharides and polysaccharides. In addition, WcAG can cleave pullulan hydrolysates and strongly exhibits transglycosylation activity in the presence of maltose. Size-exclusion chromatography and X-ray crystal structures revealed that WcAG forms a homodimer in which the N-terminal domain of one monomer is orientated in proximity to the catalytic domain of another, creating the substrate-binding groove. Crystal structures of WcAG in complexes with maltose, maltotriose and acarbose revealed a remarkable enzyme active site with accessible +2, +1 and -1 subsites, along with an Arg-Glu gate (Arg176-Glu296) in front of the active site. The -2 and -3 subsites were blocked by Met119 and Asn120 from the N-terminal domain of a different subunit, resulting in an extremely restricted substrate preference.
Collapse
Affiliation(s)
- Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pasunee Laohawuttichai
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sun Yong Kim
- Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Mori
- Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192, Japan
| | - Santhana Nakapong
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192, Japan
| | - Kuakarun Krusong
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
4
|
Sakaguchi M, Mukaeda H, Kume A, Toyoda Y, Sakoh T, Kawakita M. Evaluation of the roles of hydrophobic residues in the N-terminal region of archaeal trehalase in its folding. Appl Microbiol Biotechnol 2021; 105:3181-3194. [PMID: 33791835 DOI: 10.1007/s00253-021-11237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/01/2021] [Accepted: 03/14/2021] [Indexed: 11/30/2022]
Abstract
Thermoplasma trehalase Tvn1315 is predicted to be composed of a β-sandwich domain (BD) and a catalytic domain (CD) based on the structure of the bacterial GH15 family glucoamylase (GA). Tvn1315 as well as Tvn1315 (Δ5), in which the 5 N-terminal amino acids are deleted, could be expressed in Escherichia coli as active enzymes, but deletion of 10 residues (Δ10) led to inclusion body formation. To further investigate the role of the N-terminal region of BD, we constructed five mutants of Δ5, in which each of the 5th to 10th residues of the N-terminus of Tvn1315 was mutated to Ala. Every mutant protein could be recovered in soluble form, but only a small fraction of the Y9A mutant was recovered in the soluble fraction. The Y9A mutant recovered in soluble form had similar specific activity to the other proteins. Subsequent mutation analysis at the 9th position of Tvn1315 in Δ5 revealed that aromatic as well as bulky hydrophobic residues could function properly, but residues with hydroxy groups impaired the solubility. Similar results were obtained with mutants based on untruncated Tvn1315. When the predicted BD, Δ5BD, Δ10BD, and BD mutants were expressed, the Δ10BD protein formed inclusion bodies, and the BD mutants behaved similarly to the Δ5 and full-length enzyme mutants. These results suggest that the hydrophobic region is involved in the solubilization of BD during the folding process. Taken together, these results indicate that the solubility of CD depends on BD folding. KEY POINTS: • N-terminal hydrophobic region of the BD is involved in the protein folding. • The N-terminal hydrophobic region of the BD is also involved in the BD folding. • BD is able to weakly interact with the insoluble β-glucan.
Collapse
Affiliation(s)
- Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan.
| | - Hinako Mukaeda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Anna Kume
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yukiko Toyoda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Takumi Sakoh
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masao Kawakita
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| |
Collapse
|
5
|
Banerjee A, Levy Y, Mitra P. Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database. J Proteome Res 2019; 18:1402-1410. [PMID: 30735617 DOI: 10.1021/acs.jproteome.9b00048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in vitro experimentations. In the absence of any benchmark database documenting SPDs, we curate a data set containing SPDs that lead to both folded conformations and unfolded state. We differentiate these SPD instances with the help of simple structural and physicochemical features and eventually classify the foldability resulting out of SPDs using a Random Forest classifier and an Elliptic Envelope based outlier detector. Adhering to leave one out cross validation, the accuracy of the Random Forest classifier and the Elliptic Envelope is of 99.4% and 98.1%, respectively. The newly defined database and the delineation of SPD instances based on its resulting foldability provide a head start toward finding a solution to the given problem.
Collapse
Affiliation(s)
| | - Yaakov Levy
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 76100 , Israel
| | | |
Collapse
|
6
|
Jain N, Knowles TJ, Lund PA, Chaudhuri TK. Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:941-951. [PMID: 29864530 DOI: 10.1016/j.bbapap.2018.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/02/2018] [Accepted: 05/28/2018] [Indexed: 10/14/2022]
Abstract
The isolated apical domain of GroEL consisting of residues 191-345 (known as "minichaperone") binds and assists the folding of a wide variety of client proteins without GroES and ATP, but the mechanism of its action is still unknown. In order to probe into the matter, we have examined minichaperone-mediated folding of a large aggregation prone protein Maltodextrin-glucosidase (MalZ). The key objective was to identify whether MalZ exists free in solution, or remains bound to, or cycling on and off the minichaperone during the refolding process. When GroES was introduced during refolding process, production of the native MalZ was inhibited. We also observed the same findings with a trap mutant of GroEL, which stably captures a predominantly non-native MalZ released from minichaperone during refolding process, but does not release it. Tryptophan and ANS fluorescence measurements indicated that refolded MalZ has the same structure as the native MalZ, but that its structure when bound to minichaperone is different. Surface plasmon resonance measurements provide an estimate for the equilibrium dissociation constant KD for the MalZ-minichaperone complex of 0.21 ± 0.04 μM, which are significantly higher than for most GroEL clients. This showed that minichaperone interacts loosely with MalZ to allow the protein to change its conformation and fold while bound during the refolding process. These observations suggest that the minichaperone works by carrying out repeated cycles of binding aggregation-prone protein MalZ in a relatively compact conformation and in a partially folded but active state, and releasing them to attempt to fold in solution.
Collapse
Affiliation(s)
- Neha Jain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India; Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK
| | - Timothy J Knowles
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK
| | - Peter A Lund
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK.
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India.
| |
Collapse
|
7
|
Sardis MF, Tsirigotaki A, Chatzi KE, Portaliou AG, Gouridis G, Karamanou S, Economou A. Preprotein Conformational Dynamics Drive Bivalent Translocase Docking and Secretion. Structure 2017. [DOI: 10.1016/j.str.2017.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|