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Schnettler JD, Klein OJ, Kaminski TS, Colin PY, Hollfelder F. Ultrahigh-Throughput Directed Evolution of a Metal-Free α/β-Hydrolase with a Cys-His-Asp Triad into an Efficient Phosphotriesterase. J Am Chem Soc 2023; 145:1083-1096. [PMID: 36583539 PMCID: PMC9853848 DOI: 10.1021/jacs.2c10673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Finding new mechanistic solutions for biocatalytic challenges is key in the evolutionary adaptation of enzymes, as well as in devising new catalysts. The recent release of man-made substances into the environment provides a dynamic testing ground for observing biocatalytic innovation at play. Phosphate triesters, used as pesticides, have only recently been introduced into the environment, where they have no natural counterpart. Enzymes have rapidly evolved to hydrolyze phosphate triesters in response to this challenge, converging onto the same mechanistic solution, which requires bivalent cations as a cofactor for catalysis. In contrast, the previously identified metagenomic promiscuous hydrolase P91, a homologue of acetylcholinesterase, achieves slow phosphotriester hydrolysis mediated by a metal-independent Cys-His-Asp triad. Here, we probe the evolvability of this new catalytic motif by subjecting P91 to directed evolution. By combining a focused library approach with the ultrahigh throughput of droplet microfluidics, we increase P91's activity by a factor of ≈360 (to a kcat/KM of ≈7 × 105 M-1 s-1) in only two rounds of evolution, rivaling the catalytic efficiencies of naturally evolved, metal-dependent phosphotriesterases. Unlike its homologue acetylcholinesterase, P91 does not suffer suicide inhibition; instead, fast dephosphorylation rates make the formation of the covalent adduct rather than its hydrolysis rate-limiting. This step is improved by directed evolution, with intermediate formation accelerated by 2 orders of magnitude. Combining focused, combinatorial libraries with the ultrahigh throughput of droplet microfluidics can be leveraged to identify and enhance mechanistic strategies that have not reached high efficiency in nature, resulting in alternative reagents with novel catalytic machineries.
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Affiliation(s)
- J David Schnettler
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Oskar James Klein
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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Zhu M, He L, Liu J, Long Y, Shentu J, Lu L, Shen D. Dynamic processes in conjunction with microbial response to unveil the attenuation mechanisms of tris (2-chloroethyl) phosphate (TCEP) in non-sanitary landfill soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120666. [PMID: 36403879 DOI: 10.1016/j.envpol.2022.120666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/07/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
Although the environmental and health risks of chlorinated organophosphate esters (OPEs-Cl) have drawn much attention, its environmental behaviors have been insufficiently characterized. As a notable sink of this emerging contaminant, non-sanitary landfills, which may decompose/accumulate OPEs-Cl, is of particular concern. In the present study, the dynamic processes of the typical OPEs-Cl, tris(2-chloroethyl) phosphate (TCEP), in non-sanitary landfill soils were analyzed under anaerobic condition, and the microbial taxa involved in these processes were explored. Our results showed that TCEP could be simultaneously reduced by abiotic and biotic processes, as it was reduced by 73.9% and 65.5% over the 120-day experiment in landfill humus and subsoil, respectively. Notably, the degradation of TCEP was significantly (p < 0.05) enhanced under the stress of a high TCEP concentration (10 μg g-1), while its ecological consequences were found insignificant regarding the microbial diversity and community structure and the typical soil redox processes, including Fe(III)/SO42- reduction and methanogenesis, in both soils. The microbial diversity of subsoil was significantly lower, and acetate was an important factor in changing microbial communities in landfill soils. The microbes in the family Nocardioidaceae and genus Pseudomonas might contribute to in the degradation of TCEP in landfill humus and subsoil, respectively. The metabolism related to sulfur and sulfate respiration were significantly (p < 0.05) correlated with TCEP reduction, and Desulfosporosinus were found as a potentially functional microbial taxon in TCEP degradation in both soils. The results could advance our understanding of the environmental behavior of OPEs-Cl in landfill-like complex environments.
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Affiliation(s)
- Min Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310012, PR China; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Hangzhou, 310012, PR China
| | - Lisha He
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China
| | - Jiayi Liu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China
| | - Yuyang Long
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310012, PR China
| | - Jiali Shentu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310012, PR China
| | - Li Lu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310012, PR China
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, PR China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, PR China; Instrumental Analysis Center of Zhejiang Gongshang University, Hangzhou, 310012, PR China.
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Gavira JA, Cámara-Artigas A, Neira JL, Torres de Pinedo JM, Sánchez P, Ortega E, Martinez-Rodríguez S. Structural insights into choline- O-sulfatase reveal the molecular determinants for ligand binding. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:669-682. [PMID: 35503214 PMCID: PMC9063841 DOI: 10.1107/s2059798322003709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022]
Abstract
The first structures of a choline-O-sulfatase bound to different ligands are reported. Choline-O-sulfatase (COSe; EC 3.1.6.6) is a member of the alkaline phosphatase (AP) superfamily, and its natural function is to hydrolyze choline-O-sulfate into choline and sulfate. Despite its natural function, the major interest in this enzyme resides in the landmark catalytic/substrate promiscuity of sulfatases, which has led to attention in the biotechnological field due to their potential in protein engineering. In this work, an in-depth structural analysis of wild-type Sinorhizobium (Ensifer) meliloti COSe (SmeCOSe) and its C54S active-site mutant is reported. The binding mode of this AP superfamily member to both products of the reaction (sulfate and choline) and to a substrate-like compound are shown for the first time. The structures further confirm the importance of the C-terminal extension of the enzyme in becoming part of the active site and participating in enzyme activity through dynamic intra-subunit and inter-subunit hydrogen bonds (Asn146A–Asp500B–Asn498B). These residues act as the ‘gatekeeper’ responsible for the open/closed conformations of the enzyme, in addition to assisting in ligand binding through the rearrangement of Leu499 (with a movement of approximately 5 Å). Trp129 and His145 clamp the quaternary ammonium moiety of choline and also connect the catalytic cleft to the C-terminus of an adjacent protomer. The structural information reported here contrasts with the proposed role of conformational dynamics in promoting the enzymatic catalytic proficiency of an enzyme.
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Awasthi MK. Engineered biochar: A multifunctional material for energy and environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 298:118831. [PMID: 35032603 DOI: 10.1016/j.envpol.2022.118831] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/14/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Biochar is a stable carbon-rich product loaded with upgraded properties obtained by thermal cracking of biomasses in an oxygen-free atmosphere. The pristine biochar is further modified to produce engineered biochar via various physical, mechanical, and chemical methods. The hasty advancement in engineered biochar synthesis via different technologies and their application in the field of energy and environment is a topical issue that required an up-to-date review. Therefore, this review deals with comprehensive and recent mechanistic approaches of engineered biochar synthesis and its further application in the field of energy and the environment. Synthesis and activation of engineered biochar via various methods has been deliberated in brief. Furthermore, this review systematically covered the impacts of engineered biochar amendment in the composting process, anaerobic digestion (AD), soil microbial community encouragement, and their enzymatic activities. Finally, this review provided a glimpse of the knowledge gaps and challenges associated with application of engineered biochar in various fields, which needs urgent attention in future research.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, PR China.
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Gabale U, Peña Palomino PA, Kim H, Chen W, Ressl S. The essential inner membrane protein YejM is a metalloenzyme. Sci Rep 2020; 10:17794. [PMID: 33082366 PMCID: PMC7576196 DOI: 10.1038/s41598-020-73660-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022] Open
Abstract
Recent recurrent outbreaks of Gram-negative bacteria show the critical need to target essential bacterial mechanisms to fight the increase of antibiotic resistance. Pathogenic Gram-negative bacteria have developed several strategies to protect themselves against the host immune response and antibiotics. One such strategy is to remodel the outer membrane where several genes are involved. yejM was discovered as an essential gene in E. coli and S. typhimurium that plays a critical role in their virulence by changing the outer membrane permeability. How the inner membrane protein YejM with its periplasmic domain changes membrane properties remains unknown. Despite overwhelming structural similarity between the periplasmic domains of two YejM homologues with hydrolases like arylsulfatases, no enzymatic activity has been previously reported for YejM. Our studies reveal an intact active site with bound metal ions in the structure of YejM periplasmic domain. Furthermore, we show that YejM has a phosphatase activity that is dependent on the presence of magnesium ions and is linked to its function of regulating outer membrane properties. Understanding the molecular mechanism by which YejM is involved in outer membrane remodeling will help to identify a new drug target in the fight against the increased antibiotic resistance.
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Affiliation(s)
- Uma Gabale
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA.
| | - Perla Arianna Peña Palomino
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - HyunAh Kim
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - Wenya Chen
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - Susanne Ressl
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA.
- Department of Neuroscience, The University of Texas At Austin, 100 E. 24th St., NHB 2.504, Austin, TX, 78712, USA.
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Zhang J, Liu ZH, Zhong SS, Wang H, Caidan B, Yin H, Dang Z. Strategy for effective inhibition of arylsulfatase/β-glucuronidase to prevent deconjugation of sulfate and glucuronide conjugates in wastewater during sample collection and storage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:135536. [PMID: 31759726 DOI: 10.1016/j.scitotenv.2019.135536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 05/20/2023]
Abstract
Arylsulfatase and β-glucuronidase are two important enzymes that are responsible for deconjugation of estrogen conjugates. It is important to keep estrogen conjugates intact during sample collection and storage, while the effective inhibition conditions for arylsulfatase and β-glucuronidase remain unknown. To elucidate these conditions, inhibition experiments were performed by adding several inhibitors or by introducing extreme pH conditions. This work confirms that arylsulfatase and β-glucuronidase can tolerate some extremes, including high concentrations of mercury dichloride, ethanol, and EDTA, while low pH (<3) or high pH (>11) can effectively inhibit their activities. The high tolerance of arylsulfatase and β-glucuronidase for mercury dichloride explains why estrogen conjugates in wastewater samples were deconjugated, even in the extremely unfavorable condition with a high concentration of mercury dichloride. Although low pH (<3) can effectively inhibit arylsulfatase/β-glucuronidase, deconjugation of sulfate conjugates by acid hydrolysis readily occurs; thus, a high pH of 11 is an appropriate storage condition for the effective inhibition of arylsulfatase/β-glucuronidase. This appropriate storage condition was confirmed and validated with diluted and sterilized activated sludge samples in which arylsulfatase/β-glucuronidase inhibition was effective for 48 h at room temperature and with a high pH of 11. The developed appropriate storage condition for effective inhibition of arylsulfatase/β-glucuronidase has wide application potential not only for estrogen conjugates but also for all conjugates of other organic micropollutants.
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Affiliation(s)
- Jun Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Ze-Hua Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China; Key Lab Pollution Control & Ecosystem Restoration in Industry Cluster, Ministry of Education, Guangzhou 510006, Guangdong, China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, Guangdong, China; Guangdong Provincial Engineering and Technology Research Center for Environment Risk Prevention and Emergency Disposal, South China University of Technology, Guangzhou 510006, Guangdong, China.
| | - Shu-Shu Zhong
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Hao Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Bamu Caidan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
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7
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Breton-Deval L, Sanchez-Flores A, Juárez K, Vera-Estrella R. Integrative study of microbial community dynamics and water quality along The Apatlaco River. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113158. [PMID: 31521989 DOI: 10.1016/j.envpol.2019.113158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 08/21/2019] [Accepted: 09/01/2019] [Indexed: 06/10/2023]
Abstract
The increasing demand for clean water resources for human consumption, is raising concerning about the sustainable worldwide provisioning. In Mexico, rivers near to high-density urbanizations are subject to irrational exploitation where polluted water is a risk for human health. Therefore, the aims of this study are to analyze water quality parameters and bacterial community dynamics to understand the relation between them, in the Apatlaco river, which presents a clear environmental perturbance. Parameters such as total coliforms, chemical oxygen demand, harness, ammonium, nitrite, nitrate, total Kjeldahl nitrogen, dissolved oxygen, total phosphorus, total dissolved solids, and temperature were analyzed in 17 sampling points along the river. The high pollution level was registered in the sampling point 10 with 480 mg/L chemical oxygen demand, 7 mg/L nitrite, 34 mg/L nitrate, 2 mg/L dissolved oxygen, and 299 mg/L of total dissolved solids. From these sites, we selected four samples for DNA extraction and performed a metagenomic analysis using a whole metagenome shotgun approach, to compare the microbial communities between polluted and non-polluted sites. In general, Proteobacteria was the most representative phylum in all sites. However, the clean water reference point was enriched with microorganism from the Limnohabitans genus, a planktonic bacterium widespread in freshwater ecosystems. Nevertheless, in the polluted sampled sites, we found a high abundance of potential opportunistic pathogen genera such as Acinetobacter, Arcobacter, and Myroides, among others. This suggests that in addition to water contamination, an imminent human health risk due to pathogenic bacteria can potentially affect a population of ∼1.6 million people dwelling nearby. These results will contribute to the knowledge regarding anthropogenic pollution on the microbial population dynamic and how they affect human health and life quality.
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Affiliation(s)
- Luz Breton-Deval
- Cátedras-Conacyt, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico.
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juárez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
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