1
|
Chen R, Wang S, Sun Y, Li H, Wan S, Lin F, Xu H. Comparison of Glyphosate-Degradation Ability of Aldo-Keto Reductase (AKR4) Proteins in Maize, Soybean and Rice. Int J Mol Sci 2023; 24:ijms24043421. [PMID: 36834831 PMCID: PMC9966811 DOI: 10.3390/ijms24043421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Genes that participate in the degradation or isolation of glyphosate in plants are promising, for they endow crops with herbicide tolerance with a low glyphosate residue. Recently, the aldo-keto reductase (AKR4) gene in Echinochloa colona (EcAKR4) was identified as a naturally evolved glyphosate-metabolism enzyme. Here, we compared the glyphosate-degradation ability of theAKR4 proteins from maize, soybean and rice, which belong to a clade containing EcAKR4 in the phylogenetic tree, by incubation of glyphosate with AKR proteins both in vivo and in vitro. The results indicated that, except for OsALR1, the other proteins were characterized as glyphosate-metabolism enzymes, with ZmAKR4 ranked the highest activity, and OsAKR4-1 and OsAKR4-2 exhibiting the highest activity among the AKR4 family in rice. Moreover, OsAKR4-1 was confirmed to endow glyphosate-tolerance at the plant level. Our study provides information on the mechanism underlying the glyphosate-degradation ability of AKR proteins in crops, which enables the development of glyphosate-resistant crops with a low glyphosate residue, mediated by AKRs.
Collapse
Affiliation(s)
| | | | | | | | | | - Fei Lin
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
| | - Hanhong Xu
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
| |
Collapse
|
2
|
Li H, Yang Y, Hu Y, Chen CC, Huang JW, Min J, Dai L, Guo RT. Structural analysis and engineering of aldo-keto reductase from glyphosate-resistant Echinochloa colona. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129191. [PMID: 35739721 DOI: 10.1016/j.jhazmat.2022.129191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Glyphosate is a dominant organophosphate herbicide that inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) of the shikimate pathway. Glyphosate is extensively applied since manufactured, which has led to the emergence of various glyphosate-resistant crops and weeds. However, the molecular mechanism of many glyphosate-resistance machineries remains unclear. Recently, the upregulated expression of two homologous aldo-keto reductases (AKRs), designated as AKR4C16 and AKR4C17, were found to contribute to the glyphosate resistance in Echinochloa colona. This represents the first naturally evolved glyphosate-degrading machinery reported in plants. Here, we report the three-dimensional structure of these two AKR enzymes in complex with cofactor by performing X-ray crystallography. Furthermore, the binding-mode of glyphosate were elucidated in a ternary complex of AKR4C17. Based on the structural information and the previous study, we proposed a possible mechanism of action of AKR-mediated glyphosate degradation. In addition, a variant F291D of AKR4C17 that was constructed based on structure-based engineering showed a 70% increase in glyphosate degradation. In conclusion, these results demonstrate the structural features and glyphosate-binding mode of AKR4C17, which increases our understanding of the enzymatic mechanism of glyphosate bio-degradation and provides an important basis for the designation of AKR-based glyphosate-resistance for further applications.
Collapse
Affiliation(s)
- Hao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yumei Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.
| |
Collapse
|
3
|
Songsiriritthigul C, Narawongsanont R, Tantitadapitak C, Guan HH, Chen CJ. Structure-function study of AKR4C14, an aldo-keto reductase from Thai jasmine rice (Oryza sativa L. ssp. indica cv. KDML105). ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:472-483. [PMID: 32355043 DOI: 10.1107/s2059798320004313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 03/30/2020] [Indexed: 11/10/2022]
Abstract
Aldo-keto reductases (AKRs) are NADPH/NADP+-dependent oxidoreductase enzymes that metabolize an aldehyde/ketone to the corresponding alcohol. AKR4C14 from rice exhibits a much higher efficiency in metabolizing malondialdehyde (MDA) than do the Arabidopsis enzymes AKR4C8 and AKR4C9, despite sharing greater than 60% amino-acid sequence identity. This study confirms the role of rice AKR4C14 in the detoxification of methylglyoxal and MDA, and demonstrates that the endogenous contents of both aldehydes in transgenic Arabidopsis ectopically expressing AKR4C14 are significantly lower than their levels in the wild type. The apo structure of indica rice AKR4C14 was also determined in the absence of the cofactor, revealing the stabilized open conformation. This is the first crystal structure in AKR subfamily 4C from rice to be observed in the apo form (without bound NADP+). The refined AKR4C14 structure reveals a stabilized open conformation of loop B, suggesting the initial phase prior to cofactor binding. Based on the X-ray crystal structure, the substrate- and cofactor-binding pockets of AKR4C14 are formed by loops A, B, C and β1α1. Moreover, the residues Ser211 and Asn220 on loop B are proposed as the hinge residues that are responsible for conformational alteration while the cofactor binds. The open conformation of loop B is proposed to involve Phe216 pointing out from the cofactor-binding site and the opening of the safety belt. Structural comparison with other AKRs in subfamily 4C emphasizes the role of the substrate-channel wall, consisting of Trp24, Trp115, Tyr206, Phe216, Leu291 and Phe295, in substrate discrimination. In particular, Leu291 could contribute greatly to substrate selectivity, explaining the preference of AKR4C14 for its straight-chain aldehyde substrate.
Collapse
Affiliation(s)
- Chomphunuch Songsiriritthigul
- Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Rawint Narawongsanont
- Department of Biochemistry, Faculty of Science, Kasetsart University, Pahonyothin Road, Bangkok 10903, Thailand
| | - Chonticha Tantitadapitak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Pahonyothin Road, Bangkok 10903, Thailand
| | - Hong Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Chun Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| |
Collapse
|
4
|
Zhang S, Li Y, Shi C, Guo F, He C, Cao Z, Hu J, Cui C, Liu H. Induced-fit adsorption of diol-based porous organic polymers for tetracycline removal. CHEMOSPHERE 2018; 212:937-945. [PMID: 30286550 DOI: 10.1016/j.chemosphere.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/24/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Adsorption is recognized as one of the most efficient approaches for antibiotics removal from water. Inspired by the enzyme-substrate interaction model, we proposed induced-fit adsorption (IFA) model, and rationally designed and fabricated diol-based porous organic polymers (POPs) as adsorbents for tetracycline (TC) removal. For 2,3-naphthalenediol-based POP (NTdiol-POP), the preferable geometry of diol-groups contributed to the high binding energy with TC species and flexible methylene linkages between neighboring rigid naphthalene rings gave rise to precisely matching between TC species and adsorbents, that is, the induced-fit conformation change. As a result, NTdiol-POP exhibited a high saturated adsorption capacity of 155.8 mg g-1. More importantly, NTdiol-POP exhibited excellent TC removal efficiencies in both concentrated solution (96% for 4 p.p.m) and trace level solution (97% for 250 p.p.b).
Collapse
Affiliation(s)
| | - Yankai Li
- School of Chemistry and Molecular Engineering, China
| | - Chunhong Shi
- Shanghai Songjiang Institute for Food and Drug Control, 28 Middle Zhongshan Road, Shanghai, 201600, China
| | - Fangyuan Guo
- School of Chemistry and Molecular Engineering, China
| | - Congze He
- School of Materials Science and Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zan Cao
- Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, China
| | - Jun Hu
- School of Chemistry and Molecular Engineering, China.
| | - Changzheng Cui
- Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, China.
| | - Honglai Liu
- School of Chemistry and Molecular Engineering, China
| |
Collapse
|
5
|
Paidimuddala B, Mohapatra SB, Gummadi SN, Manoj N. Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis. FEBS J 2018; 285:4445-4464. [PMID: 30269423 DOI: 10.1111/febs.14667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/13/2018] [Accepted: 09/26/2018] [Indexed: 11/30/2022]
Abstract
Aldose reductases (ARs) belonging to the aldo-keto reductase (AKR) superfamily catalyze the conversion of carbonyl substrates into their respective alcohols. Here we report the crystal structures of the yeast Debaryomyces nepalensis xylose reductase (DnXR, AKR2B10) in the apo form and as a ternary complex with a novel NADP-DTT adduct. Xylose reductase, a key enzyme in the conversion of xylose to xylitol, has several industrial applications. The enzyme displayed the highest catalytic efficiency for l-threose (138 ± 7 mm-1 ·s-1 ) followed by d-erythrose (30 ± 3 mm-1 ·s-1 ). The crystal structure of the complex reveals a covalent linkage between the C4N atom of the nicotinamide ring of the cosubstrate and the S1 sulfur atom of DTT and provides the first structural evidence for a protein mediated NADP-low-molecular-mass thiol adduct. We hypothesize that the formation of the adduct is facilitated by an in-crystallo Michael addition of the DTT thiolate to the specific conformation of bound NADPH in the active site of DnXR. The interactions between DTT, a four-carbon sugar alcohol analog, and the enzyme are representative of a near-cognate product ternary complex and provide significant insights into the structural basis of aldose binding and specificity and the catalytic mechanism of ARs. DATABASE: Structural data are available in the PDB under the accession numbers 5ZCI and 5ZCM.
Collapse
Affiliation(s)
- Bhaskar Paidimuddala
- Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Samar B Mohapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| |
Collapse
|