1
|
Gómez-Govea MA, Peña-Carillo KI, Ruiz-Ayma G, Guzmán-Velasco A, Flores AE, Ramírez-Ahuja MDL, Rodríguez-Sánchez IP. Unveiling the Microbiome Diversity in Telenomus (Hymenoptera: Scelionidae) Parasitoid Wasps. INSECTS 2024; 15:468. [PMID: 39057201 PMCID: PMC11277331 DOI: 10.3390/insects15070468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024]
Abstract
Bacterial symbionts in insects constitute a key factor for the survival of the host due to the benefits they provide. Parasitoid wasps are closely associated with viruses, bacteria, and fungi. However, the primary symbionts and their functions are not yet known. This study was undertaken to determine the gut microbiota of six species of the Telenomus genus: T. alecto (Crawford), T. sulculus Johnson, T. fariai Costa Lima, T. remus Nixon, T. podisi Ashmead, and T. lobatus Johnson & Bin. Wasp parasitoids were collected from their hosts in different locations in Mexico. DNA was extracted from gut collection, and sequencing of bacterial 16S rRNA was carried out in Illumina® MiSeq™. Among the six species of wasps, results showed that the most abundant phylum were Proteobacteria (82.3%), Actinobacteria (8.1%), and Firmicutes (7.8%). The most important genera were Delftia and Enterobacter. Seventeen bacteria species were found to be shared among the six species of wasps. The associate microbiota will help to understand the physiology of Telenomus to promote the use of these wasp parasitoids in the management of insect pests and as potential biomarkers to target new strategies to control pests.
Collapse
Affiliation(s)
- Mayra A. Gómez-Govea
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico;
| | - Kenzy I. Peña-Carillo
- Campo Experimental General Terán, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Km 31 Carretera Montemorelos-China, General Terán 67400, Mexico;
| | - Gabriel Ruiz-Ayma
- Laboratorio de Conservación de Vida Silvestre y Desarrollo Sustentable, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico; (G.R.-A.); (A.G.-V.)
| | - Antonio Guzmán-Velasco
- Laboratorio de Conservación de Vida Silvestre y Desarrollo Sustentable, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico; (G.R.-A.); (A.G.-V.)
| | - Adriana E. Flores
- Laboratorio de Entomología Médica, Departamento de Zoología de Invertebrados, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - María de Lourdes Ramírez-Ahuja
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico;
| | - Iram Pablo Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico;
| |
Collapse
|
2
|
Aldas-Vargas A, Poursat BAJ, Sutton NB. Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil. World J Microbiol Biotechnol 2022; 38:240. [PMID: 36261779 PMCID: PMC9581840 DOI: 10.1007/s11274-022-03426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
Abstract
Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.
Collapse
Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Baptiste A J Poursat
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
| |
Collapse
|
3
|
A Novel Alkaline Phosphatase/Phosphodiesterase, CamPhoD, from Marine Bacterium Cobetia amphilecti KMM 296. Mar Drugs 2019; 17:md17120657. [PMID: 31766749 PMCID: PMC6950083 DOI: 10.3390/md17120657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/24/2023] Open
Abstract
A novel extracellular alkaline phosphatase/phosphodiesterase from the structural protein family PhoD that encoded by the genome sequence of the marine bacterium Cobetia amphilecti KMM 296 (CamPhoD) has been expressed in Escherichia coli cells. The calculated molecular weight, the number of amino acids, and the isoelectric point (pI) of the mature protein’s subunit are equal to 54832.98 Da, 492, and 5.08, respectively. The salt-tolerant, bimetal-dependent enzyme CamPhoD has a molecular weight of approximately 110 kDa in its native state. CamPhoD is activated by Co2+, Mg2+, Ca2+, or Fe3+ at a concentration of 2 mM and exhibits maximum activity in the presence of both Co2+ and Fe3+ ions in the incubation medium at pH 9.2. The exogenous ions, such as Zn2+, Cu2+, and Mn2+, as well as chelating agents EDTA and EGTA, do not have an appreciable effect on the CamPhoD activity. The temperature optimum for the CamPhoD activity is 45 °C. The enzyme catalyzes the cleavage of phosphate mono- and diester bonds in nucleotides, releasing inorganic phosphorus from p-nitrophenyl phosphate (pNPP) and guanosine 5′-triphosphate (GTP), as determined by the Chen method, with rate approximately 150- and 250-fold higher than those of bis-pNPP and 5′-pNP-TMP, respectively. The Michaelis–Menten constant (Km), Vmax, and efficiency (kcat/Km) of CamPhoD were 4.2 mM, 0.203 mM/min, and 7988.6 S−1/mM; and 6.71 mM, 0.023 mM/min, and 1133.0 S−1/mM for pNPP and bis-pNPP as the chromogenic substrates, respectively. Among the 3D structures currently available, in this study we found only the low identical structure of the Bacillus subtilis enzyme as a homologous template for modeling CamPhoD, with a new architecture of the phosphatase active site containing Fe3+ and two Ca2+ ions. It is evident that the marine bacterial phosphatase/phosphidiesterase CamPhoD is a new structural member of the PhoD family.
Collapse
|
4
|
Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
| |
Collapse
|
5
|
An atypical phosphodiesterase capable of degrading haloalkyl phosphate diesters from Sphingobium sp. strain TCM1. Sci Rep 2017; 7:2842. [PMID: 28588250 PMCID: PMC5460133 DOI: 10.1038/s41598-017-03142-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/20/2017] [Indexed: 11/17/2022] Open
Abstract
Sphingobium sp. strain TCM1 can degrade tris(2-chloroethyl) phosphate (TCEP) to inorganic phosphate and 2-chloroethanol. A phosphotriesterase (PTE), phosphodiesterase (PDE) and phosphomonoesterase (PME) are believed to be involved in the degradation of TCEP. The PTE and PME that respectively catalyze the first and third steps of TCEP degradation in TCM1 have been identified. However, no information has been reported on a PDE catalyzing the second step. In this study, we identified, purified, and characterized a PDE capable of hydrolyzing haloalkyl phosphate diesters. The final preparation of the enzyme had a specific activity of 29 µmol min−1 mg−1 with bis(p-nitrophenyl) phosphate (BpNPP) as the substrate. It also possessed low PME activity with p-nitrophenyl phosphate (pNPP) as substrate. The catalytic efficiency (kcat/Km) with BpNPP was significantly higher than that with pNPP, indicating that the enzyme prefers the organophosphorus diester to the monoester. The enzyme degraded bis(2,3-dibromopropyl) phosphate, bis(1,3-dichloro-2-propyl) phosphate and bis(2-chloroethyl) phosphate, suggesting that it is involved in the metabolism of haloalkyl organophosphorus triesters. The primary structure of the PDE from TCM1 is distinct from those of typical PDE family members and the enzyme belongs to the polymerase and histidinol phosphatase superfamily.
Collapse
|
6
|
de Almeida LG, de Moraes LAB, Trigo JR, Omoto C, Cônsoli FL. The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation. PLoS One 2017; 12:e0174754. [PMID: 28358907 PMCID: PMC5373613 DOI: 10.1371/journal.pone.0174754] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 03/14/2017] [Indexed: 11/18/2022] Open
Abstract
The exploration of new niches for microorganisms capable of degrading recalcitrant molecules is still required. We hypothesized the gut microbiota associated with insect-resistant lines carry pesticide degrading bacteria, and predicted they carry bacteria selected to degrade pesticides they were resistant to. We isolated and accessed the pesticide-degrading capacity of gut bacteria from the gut of fifth instars of Spodoptera frugiperda strains resistant to lambda-cyhalothrin, deltamethrin, chlorpyrifos ethyl, spinosad and lufenuron, using insecticide-selective media. Sixteen isolates belonging to 10 phylotypes were obtained, from which four were also associated with the susceptible strain. However, growth of gut bacteria associated with larvae from the susceptible strain was not obtained in any of the insecticide-based selective media tested. Growth of isolates was affected by the concentration of insecticides in the media, and all grew well up to 40 μg/ml. The insecticide-degrading capacity of selected isolates was assessed by GC or LC-MS/MS analyses. In conclusion, resistant strains of S. frugiperda are an excellent reservoir of insecticide-degrading bacteria with bioremediation potential. Moreover, gut-associated bacteria are subjected to the selection pressure imposed by insecticides on their hosts and may influence the metabolization of pesticides in insects.
Collapse
Affiliation(s)
- Luis Gustavo de Almeida
- Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Departamento de Entomologia e Acarologia, Piracicaba, São Paulo, Brasil
| | - Luiz Alberto Beraldo de Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras, Departamento de Química, Ribeirão Preto, São Paulo, Brasil
| | - José Roberto Trigo
- Universidade Estadual de Campinas, Instituo de Biologia, Departamento de Biologia Animal, Campinas, São Paulo, Brasil
| | - Celso Omoto
- Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Departamento de Entomologia e Acarologia, Piracicaba, São Paulo, Brasil
| | - Fernando Luis Cônsoli
- Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Departamento de Entomologia e Acarologia, Piracicaba, São Paulo, Brasil
- * E-mail:
| |
Collapse
|
7
|
Brown ME, Mukhopadhyay A, Keasling JD. Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol. ACS Synth Biol 2016; 5:1485-1496. [PMID: 27403844 DOI: 10.1021/acssynbio.6b00115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report an engineered strain of Escherichia coli that catabolizes the carbonaceous component of the extremely toxic chemical warfare agent sarin. Enzymatic decomposition of sarin generates isopropanol waste that, with this engineered strain, is then transformed into acetyl-CoA by enzymatic conversion with a key reaction performed by the acetone carboxylase complex (ACX). We engineered the heterologous expression of the ACX complex from Xanthobacter autotrophicus PY2 to match the naturally occurring subunit stoichiometry and purified the recombinant complex from E. coli for biochemical analysis. Incorporating this ACX complex and enzymes from diverse organisms, we introduced an isopropanol degradation pathway in E. coli, optimized induction conditions, and decoupled enzyme expression to probe pathway bottlenecks. Our engineered E. coli consumed 65% of isopropanol compared to no-cell controls and was able to grow on isopropanol as a sole carbon source. In the process, reconstitution of this large ACX complex (370 kDa) in a system naïve to its structural and mechanistic requirements allowed us to study this otherwise cryptic enzyme in more detail than would have been possible in the less genetically tractable native Xanthobacter system.
Collapse
Affiliation(s)
- Margaret E. Brown
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Aindrila Mukhopadhyay
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jay D. Keasling
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle, DK2970-Hørsholm, Denmark
| |
Collapse
|
8
|
Involvement of phosphoesterases in tributyl phosphate degradation in Sphingobium sp. strain RSMS. Appl Microbiol Biotechnol 2015; 100:461-8. [DOI: 10.1007/s00253-015-6979-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/20/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
|
9
|
Singh DN, Gupta A, Singh VS, Mishra R, Kateriya S, Tripathi AK. Identification and characterization of a novel phosphodiesterase from the metagenome of an Indian coalbed. PLoS One 2015; 10:e0118075. [PMID: 25658120 PMCID: PMC4320098 DOI: 10.1371/journal.pone.0118075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/05/2015] [Indexed: 11/21/2022] Open
Abstract
Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25°C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn2+ was required for the activity of PdeM, but addition of metals (Mn2+ or Fe3+) did not induce oligomerization. Further increase in concentration of Mn2+ upto 3 mM, increased α-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases.
Collapse
Affiliation(s)
- Durgesh Narain Singh
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi—221005, Uttar Pradesh, India
| | - Ankush Gupta
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi—221005, Uttar Pradesh, India
| | - Vijay Shankar Singh
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi—221005, Uttar Pradesh, India
| | - Rajeev Mishra
- Bioinformatics programme, Mahila Maha Vidyalaya, Banaras Hindu University, Varanasi—221005, Uttar Pradesh, India
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
| | - Anil Kumar Tripathi
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi—221005, Uttar Pradesh, India
- * E-mail:
| |
Collapse
|
10
|
Itoh H, Navarro R, Takeshita K, Tago K, Hayatsu M, Hori T, Kikuchi Y. Bacterial population succession and adaptation affected by insecticide application and soil spraying history. Front Microbiol 2014; 5:457. [PMID: 25221549 PMCID: PMC4148734 DOI: 10.3389/fmicb.2014.00457] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/12/2014] [Indexed: 12/16/2022] Open
Abstract
Although microbial communities have varying degrees of exposure to environmental stresses such as chemical pollution, little is known on how these communities respond to environmental disturbances and how past disturbance history affects these community-level responses. To comprehensively understand the effect of organophosphorus insecticide application on microbiota in soils with or without insecticide-spraying history, we investigated the microbial succession in response to the addition of fenitrothion [O,O-dimethyl O-(3-methyl-p-nitrophenyl) phosphorothioate, abbreviated as MEP] by culture-dependent experiments and deep sequencing of 16S rRNA genes. Despite similar microbial composition at the initial stage, microbial response to MEP application was remarkably different between soils with and without MEP-spraying history. MEP-degrading microbes more rapidly increased in the soils with MEP-spraying history, suggesting that MEP-degrading bacteria might already exist at a certain level and could quickly respond to MEP re-treatment in the soil. Culture-dependent and -independent evaluations revealed that MEP-degrading Burkholderia bacteria are predominant in soils after MEP application, limited members of which might play a pivotal role in MEP-degradation in soils. Notably, deep sequencing also revealed that some methylotrophs dramatically increased after MEP application, strongly suggesting that these bacteria play a role in the consumption and removal of methanol, a harmful derivative from MEP-degradation, for better growth of MEP-degrading bacteria. This comprehensive study demonstrated the succession and adaptation processes of microbial communities under MEP application, which were critically affected by past experience of insecticide-spraying.
Collapse
Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Sapporo, Japan
| | - Ronald Navarro
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Japan
| | - Kazutaka Takeshita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Sapporo, Japan
| | - Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan
| | - Tomoyuki Hori
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Sapporo, Japan
| |
Collapse
|
11
|
Iyer R, Iken B, Damania A. A comparison of organophosphate degradation genes and bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:787-798. [PMID: 24249287 DOI: 10.1111/1758-2229.12095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 08/11/2013] [Accepted: 08/13/2013] [Indexed: 06/02/2023]
Abstract
Organophosphates (OPs) form the bulk of pesticides that are currently in use around the world accounting for more than 30% of the world market. They also form the core for many nerve-based warfare agents including sarin and soman. The widespread use and the resultant build-up of OP pesticides and chemical nerve agents has led to the development of major health problems due to their extremely toxic interaction with any biological system that encounters them. Growing concern over the accumulation of OP compounds in our food products, in the soils from which they are harvested and in wastewater run-off has fuelled a growing interest in microbial biotechnology that provides cheap, efficient OP detoxification to supplement expensive chemical methods. In this article, we review the current state of knowledge of OP pesticide and chemical agent degradation and attempt to clarify confusion over identification and nomenclature of two major families of OP-degrading enzymes through a comparison of their structure and function. The isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation of OP pesticides and chemical nerve agents are discussed as well as the achievements and technological advancements made towards the bioremediation of such compounds.
Collapse
Affiliation(s)
- Rupa Iyer
- College of Technology, University of Houston, 300 Technology Building Houston, TX 77204-4021, USA
| | | | | |
Collapse
|
12
|
Duncan KE, Perez-Ibarra BM, Jenneman G, Harris JB, Webb R, Sublette K. The effect of corrosion inhibitors on microbial communities associated with corrosion in a model flow cell system. Appl Microbiol Biotechnol 2013; 98:907-18. [DOI: 10.1007/s00253-013-4906-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/05/2013] [Accepted: 04/06/2013] [Indexed: 10/26/2022]
|
13
|
Abstract
Molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP substrate by phosphodiesterase 4B (PDE4B). PDE4B is a member of the PDE superfamily of enzymes that play crucial roles in cellular signal transduction. We have determined a two-dimensional potential of mean force (PMF) for the coupled phosphoryl bond cleavage and proton transfer through a general acid catalysis mechanism in PDE4B. The results indicate that the ring-opening process takes place through an S(N)2 reaction mechanism, followed by a proton transfer to stabilize the leaving group. The computed free energy of activation for the PDE4B-catalyzed cAMP hydrolysis is about 13 kcal·mol(-1) and an overall reaction free energy is about -17 kcal·mol(-1), both in accord with experimental results. In comparison with the uncatalyzed reaction in water, the enzyme PDE4B provides a strong stabilization of the transition state, lowering the free energy barrier by 14 kcal·mol(-1). We found that the proton transfer from the general acid residue His234 to the O3' oxyanion of the ribosyl leaving group lags behind the nucleophilic attack, resulting in a shallow minimum on the free energy surface. A key contributing factor to transition state stabilization is the elongation of the distance between the divalent metal ions Zn(2+) and Mg(2+) in the active site as the reaction proceeds from the Michaelis complex to the transition state.
Collapse
Affiliation(s)
- Kin-Yiu Wong
- Department of Chemistry, Digital Technology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | | |
Collapse
|
14
|
Marner WD, Shaikh AS, Muller SJ, Keasling JD. Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support. Biotechnol Prog 2009; 25:417-23. [PMID: 19334285 PMCID: PMC11245164 DOI: 10.1002/btpr.136] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Enzymes and other biomolecules are often immobilized in a matrix to improve their stability or to improve their ability to be reused. Performing a polycondensation reaction in the presence of a biomolecule of interest relies on random entrapment events during polymerization and may not ensure efficient, homogeneous, or complete biomolecule encapsulation. To overcome these limitations, we have developed a method of incorporating autosilification activity into proteins without affecting enzymatic functionality. The unmodified R5 silaffin peptide from Cylindrotheca fusiformis is capable of initiating silica polycondensation in vitro at ambient temperatures and pressures in aqueous solution. In this study, translational fusion proteins between R5 and various functional proteins (phosphodiesterase, organophosphate hydrolase, and green fluorescent protein) were produced in Escherichia coli. Each of the fusion proteins initiated silica polycondensation, and enzymatic activity (or fluorescence) was retained in the resulting silica spheres. Under certain circumstances, the enzymatically-active biosilica displayed improved stability relative to free enzyme at elevated temperatures.
Collapse
Affiliation(s)
- Wesley D. Marner
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | - Afshan S. Shaikh
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | - Susan J. Muller
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | - Jay D. Keasling
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
- Synthetic Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| |
Collapse
|
15
|
Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni. BMC Genomics 2007; 8:110. [PMID: 17470265 PMCID: PMC1868759 DOI: 10.1186/1471-2164-8-110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 04/30/2007] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Previous studies have sought to identify a link between the distribution of variable genes amongst isolates of Campylobacter jejuni and particular host preferences. The genomic sequence data available currently was obtained using only isolates from human or chicken hosts. In order to identify variable genes present in isolates from alternative host species, five subtractions between C. jejuni isolates from different sources (rabbit, cattle, wild bird) were carried out, designed to assess genomic variability within and between common multilocus sequence type (MLST) clonal complexes (ST-21, ST-42, ST-45 and ST-61). RESULTS The vast majority (97%) of the 195 subtracted sequences identified had a best BLASTX match with a Campylobacter protein. However, there was considerable variation within and between the four clonal complexes included in the subtractions. The distributions of eight variable sequences, including four with putative roles in the use of alternative terminal electron acceptors, amongst a panel of C. jejuni isolates representing diverse sources and STs, were determined. CONCLUSION There was a clear correlation between clonal complex and the distribution of the metabolic genes. In contrast, there was no evidence to support the hypothesis that the distribution of such genes may be related to host preference. The other variable genes studied were also generally distributed according to MLST type. Thus, we found little evidence for widespread horizontal gene transfer between clonal complexes involving these genes.
Collapse
|
16
|
de la Peña Mattozzi M, Tehara SK, Hong T, Keasling JD. Mineralization of paraoxon and its use as a sole C and P source by a rationally designed catabolic pathway in Pseudomonas putida. Appl Environ Microbiol 2006; 72:6699-706. [PMID: 17021221 PMCID: PMC1610300 DOI: 10.1128/aem.00907-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Organophosphate compounds, which are widely used as pesticides and chemical warfare agents, are cholinesterase inhibitors. These synthetic compounds are resistant to natural degradation and threaten the environment. We constructed a strain of Pseudomonas putida that can efficiently degrade a model organophosphate, paraoxon, and use it as a carbon, energy, and phosphorus source. This strain was engineered with the pnp operon from Pseudomonas sp. strain ENV2030, which encodes enzymes that transform p-nitrophenol into beta-ketoadipate, and with a synthetic operon encoding an organophosphate hydrolase (encoded by opd) from Flavobacterium sp. strain ATCC 27551, a phosphodiesterase (encoded by pde) from Delftia acidovorans, and an alkaline phosphatase (encoded by phoA) from Pseudomonas aeruginosa HN854 under control of a constitutive promoter. The engineered strain can efficiently mineralize up to 1 mM (275 mg/liter) paraoxon within 48 h, using paraoxon as the sole carbon and phosphorus source and an inoculum optical density at 600 nm of 0.03. Because the organism can utilize paraoxon as a sole carbon, energy, and phosphorus source and because one of the intermediates in the pathway (p-nitrophenol) is toxic at high concentrations, there is no need for selection pressure to maintain the heterologous pathway.
Collapse
|
17
|
Abstract
Synthetic organophosphorus compounds are used as pesticides, plasticizers, air fuel ingredients and chemical warfare agents. Organophosphorus compounds are the most widely used insecticides, accounting for an estimated 34% of world-wide insecticide sales. Contamination of soil from pesticides as a result of their bulk handling at the farmyard or following application in the field or accidental release may lead occasionally to contamination of surface and ground water. Several reports suggest that a wide range of water and terrestrial ecosystems may be contaminated with organophosphorus compounds. These compounds possess high mammalian toxicity and it is therefore essential to remove them from the environments. In addition, about 200,000 metric tons of nerve (chemical warfare) agents have to be destroyed world-wide under Chemical Weapons Convention (1993). Bioremediation can offer an efficient and cheap option for decontamination of polluted ecosystems and destruction of nerve agents. The first micro-organism that could degrade organophosphorus compounds was isolated in 1973 and identified as Flavobacterium sp. Since then several bacterial and a few fungal species have been isolated which can degrade a wide range of organophosphorus compounds in liquid cultures and soil systems. The biochemistry of organophosphorus compound degradation by most of the bacteria seems to be identical, in which a structurally similar enzyme called organophosphate hydrolase or phosphotriesterase catalyzes the first step of the degradation. organophosphate hydrolase encoding gene opd (organophosphate degrading) gene has been isolated from geographically different regions and taxonomically different species. This gene has been sequenced, cloned in different organisms, and altered for better activity and stability. Recently, genes with similar function but different sequences have also been isolated and characterized. Engineered microorganisms have been tested for their ability to degrade different organophosphorus pollutants, including nerve agents. In this article, we review and propose pathways for degradation of some organophosphorus compounds by microorganisms. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are discussed. The major achievements and technological advancements towards bioremediation of organophosphorus compounds, limitations of available technologies and future challenge are also discussed.
Collapse
Affiliation(s)
- Brajesh K Singh
- Environmental Sciences, Macaulay Institute, Craigiebuckler, Aberdeen, UK.
| | | |
Collapse
|
18
|
Han J, Sun L, Dong X, Cai Z, Sun X, Yang H, Wang Y, Song W. Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potential biocontrol agent against various plant pathogens. Syst Appl Microbiol 2005; 28:66-76. [PMID: 15709367 DOI: 10.1016/j.syapm.2004.09.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A novel, plant growth-promoting bacterium Delftia tsuruhatensis, strain HR4, was isolated from the rhizoplane of rice (Oryza sativa L., cv. Yueguang) in North China. In vitro antagonistic assay showed this strain could suppress the growth of various plant pathogens effectively, especially the three main rice pathogens (Xanthomonas oryzae pv. oryzae, Rhizoctonia solani and Pyricularia oryzae Cavara). Treated with strain HR4 culture, rice blast, rice bacterial blight and rice sheath blight for cv. Yuefu and cv. Nonghu 6 were evidently controlled in the greenhouse. Strain HR4 also showed a high nitrogen-fixing activity in N-free Döbereiner culture medium. The acetylene reduction activity and 15N2-fixing activity (N2FA) were 13.06 C2H4 nmolml(-1) h(-1) and 2.052 15Na.e.%, respectively. The nif gene was located in the chromosome of this strain. Based on phenotypic, physiological, biochemical and phylogenetic studies, strain HR4 could be classified as a member of D. tsuruhatensis. However, comparisons of characteristics with other known species of the genus Delftia suggested that strain HR4 was a novel dizotrophic PGPB strain.
Collapse
MESH Headings
- Antibiosis
- Base Composition
- China
- Chromosomes, Bacterial/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Delftia/chemistry
- Delftia/cytology
- Delftia/genetics
- Delftia/physiology
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Genes, Bacterial/genetics
- Genes, Fungal
- Genes, rRNA
- Magnaporthe/drug effects
- Magnaporthe/growth & development
- Molecular Sequence Data
- Nitrogen Fixation/genetics
- Oryza/microbiology
- Phylogeny
- Plant Diseases/microbiology
- Plant Growth Regulators/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rhizoctonia/drug effects
- Rhizoctonia/growth & development
- Sequence Analysis, DNA
- Soil Microbiology
- Xanthomonas/drug effects
- Xanthomonas/growth & development
Collapse
Affiliation(s)
- Jigang Han
- College of Life Sciences, Capital Normal University, No.105, Xisanhuan Beilu, Beijing 100037, PR China
| | | | | | | | | | | | | | | |
Collapse
|
19
|
McLoughlin SY, Jackson C, Liu JW, Ollis DL. Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source. Appl Environ Microbiol 2004; 70:404-12. [PMID: 14711669 PMCID: PMC321290 DOI: 10.1128/aem.70.1.404-412.2004] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphotriesterases catalyze the hydrolytic detoxification of phosphotriester pesticides and chemical warfare nerve agents with various efficiencies. The directed evolution of phosphotriesterases to enhance the breakdown of poor substrates is desirable for the purposes of bioremediation. A limiting factor in the identification of phosphotriesterase mutants with increased activity is the ability to effectively screen large mutant libraries. To this end, we have investigated the possibility of coupling phosphotriesterase activity to cell growth by using methyl paraoxon as the sole phosphorus source. The catabolism of paraoxon to phosphate would occur via the stepwise enzymatic hydrolysis of paraoxon to dimethyl phosphate, methyl phosphate, and then phosphate. The Escherichia coli strain DH10B expressing the phosphotriesterase from Agrobacterium radiobacter P230 (OpdA) is unable to grow when paraoxon is used as the sole phosphorus source. Enterobacter aerogenes is an organism capable of growing when dimethyl phosphate is the sole phosphorus source. The enzyme responsible for hydrolyzing dimethyl phosphate has been previously characterized as a nonspecific phosphohydrolase. We isolated and characterized the genes encoding the phosphohydrolase operon. The operon was identified from a shotgun clone that enabled E. coli to grow when dimethyl phosphate is the sole phosphorus source. E. coli coexpressing the phosphohydrolase and OpdA grew when paraoxon was the sole phosphorus source. By constructing a short degradative pathway, we have enabled E. coli to use phosphotriesters as a sole source of phosphorus.
Collapse
Affiliation(s)
- Sean Yu McLoughlin
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | | | | | | |
Collapse
|