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Summer M, Tahir HM, Ali S, Nawaz S, Abaidullah R, Mumtaz S, Ali A, Gormani AH. Nanobiopesticides as an Alternative and Sustainable Solution to Tackle Pest Outbreaks. JOURNAL OF THE KANSAS ENTOMOLOGICAL SOCIETY 2024; 96. [DOI: 10.2317/0022-8567-96.4.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Affiliation(s)
- Muhammad Summer
- Department of Zoology, Government College University, Lahore, Pakistan
| | | | - Shaukat Ali
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Saira Nawaz
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Rimsha Abaidullah
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Shumaila Mumtaz
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Aamir Ali
- Department of Zoology, Government College University, Lahore, Pakistan
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Badiyal A, Mahajan R, Rana RS, Sood R, Walia A, Rana T, Manhas S, Jayswal DK. Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions. FRONTIERS IN PLANT SCIENCE 2024; 15:1280846. [PMID: 38584951 PMCID: PMC10995308 DOI: 10.3389/fpls.2024.1280846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/29/2024] [Indexed: 04/09/2024]
Abstract
The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.
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Affiliation(s)
- Anila Badiyal
- Department of Microbiology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Rishi Mahajan
- Department of Microbiology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Ranbir Singh Rana
- Centre for Geo-Informatics Research and Training, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Ruchi Sood
- Centre for Geo-Informatics Research and Training, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Abhishek Walia
- Department of Microbiology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Tanuja Rana
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Shilpa Manhas
- Lovely Professional University, Phagwara, Punjab, India
| | - D. K. Jayswal
- National Agricultural Higher Education Project, Indian Council of Agricultural Research, New Delhi, India
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Vermeire ML, Thiour-Mauprivez C, De Clerck C. Agroecological transition: towards a better understanding of the impact of ecology-based farming practices on soil microbial ecotoxicology. FEMS Microbiol Ecol 2024; 100:fiae031. [PMID: 38479782 PMCID: PMC10994205 DOI: 10.1093/femsec/fiae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/22/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Alternative farming systems have developed since the beginning of industrial agriculture. Organic, biodynamic, conservation farming, agroecology and permaculture, all share a grounding in ecological concepts and a belief that farmers should work with nature rather than damage it. As ecology-based agricultures rely greatly on soil organisms to perform the functions necessary for agricultural production, it is thus important to evaluate the performance of these systems through the lens of soil organisms, especially soil microbes. They provide numerous services to plants, including growth promotion, nutrient supply, tolerance to environmental stresses and protection against pathogens. An overwhelming majority of studies confirm that ecology-based agricultures are beneficial for soil microorganisms. However, three practices were identified as posing potential ecotoxicological risks: the recycling of organic waste products, plastic mulching, and pest and disease management with biopesticides. The first two because they can be a source of contaminants; the third because of potential impacts on non-target microorganisms. Consequently, developing strategies to allow a safe recycling of the increasingly growing organic matter stocks produced in cities and factories, and the assessment of the ecotoxicological impact of biopesticides on non-target soil microorganisms, represent two challenges that ecology-based agricultural systems will have to face in the future.
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Affiliation(s)
- Marie-Liesse Vermeire
- CIRAD, UPR Recyclage et Risque, Dakar 18524, Sénégal
- Recyclage et Risque, Univ Montpellier, CIRAD, Montpellier 34398, France
| | - Clémence Thiour-Mauprivez
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, Dijon 21000, France
| | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech, Liege University, 2 Passage des Déportés, 5030 Gembloux, Belgium
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Chaudhary V, Kumar M, Chauhan C, Sirohi U, Srivastav AL, Rani L. Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120326. [PMID: 38387349 DOI: 10.1016/j.jenvman.2024.120326] [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: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.
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Affiliation(s)
- Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar-Pradesh, India
| | - Mukesh Kumar
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Chetan Chauhan
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Ujjwal Sirohi
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Lal Srivastav
- Chitkara University School of Engineering and Technology, Chitkara University, Himachal Pradesh, India.
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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Sodnikar K, Kaegi R, Christl I, Schroth MH, Sander M. Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:2067-2080. [PMID: 37870439 DOI: 10.1039/d3em00294b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Assessing ecological risks associated with the use of genetically modified RNA interference crops demands an understanding of the fate of crop-released insecticidal double-stranded RNA (dsRNA) molecules in soils. We studied the adsorption of one dsRNA and two double-stranded DNA as model nucleic acids (NAs) during transport through sand- and iron oxide-coated sand (IOCS)-filled columns over a range of solution pH and ionic compositions. Consistent with NA-sand electrostatic repulsion, we observed only slight retention of NAs in sand columns. Conversely, pronounced NA retention in IOCS columns is consistent with strong and irreversible NA adsorption involving electrostatic attraction to and inner-sphere complex formation of NAs with iron oxide coatings. Adsorption of NAs to iron oxides revealed a fast and a slow kinetic adsorption regime, possibly caused by the excluded-area effect. Adsorption of NAs to sand and IOCS increased in the presence of dissolved Mg2+ and with increasing ionic strength, reflecting cation-bridging and screening of repulsive electrostatics, respectively. The co-solute phosphate and a pre-adsorbed dissolved organic matter isolate competitively suppressed dsRNA adsorption to IOCS. Similar adsorption characteristics of dsRNA and similarly sized DNA suggest that existing information on DNA adsorption to soil particles helps in predicting adsorption and fate of dsRNA molecules in soils.
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Affiliation(s)
- Katharina Sodnikar
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Ralf Kaegi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Iso Christl
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Martin Herbert Schroth
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
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Chatterjee A, Zhang K, Parker KM. Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16086-16096. [PMID: 37811805 DOI: 10.1021/acs.est.3c05019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Hough J, Howard JD, Brown S, Portwood DE, Kilby PM, Dickman MJ. Strategies for the production of dsRNA biocontrols as alternatives to chemical pesticides. Front Bioeng Biotechnol 2022; 10:980592. [PMID: 36299286 PMCID: PMC9588923 DOI: 10.3389/fbioe.2022.980592] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Current crop pest control strategies rely on insecticidal and fungicidal sprays, plant genetic resistance, transgenes and agricultural practices. However, many insects, plant viruses, and fungi have no current means of control or have developed resistance against traditional pesticides. dsRNA is emerging as a novel sustainable method of plant protection as an alternative to traditional chemical pesticides. The successful commercialisation of dsRNA based biocontrols for effective pest management strategies requires the economical production of large quantities of dsRNA combined with suitable delivery methods to ensure RNAi efficacy against the target pest. A number of methods exist for the production and delivery of dsRNA based biocontrols and here we review alternative methods currently employed and emerging new approaches for their production. Additionally, we highlight potential challenges that will need to be addressed prior to widespread adoption of dsRNA biocontrols as novel sustainable alternatives to traditional chemical pesticides.
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Affiliation(s)
- James Hough
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
| | - John D Howard
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
| | - Stephen Brown
- Sheffield RNAi Screening Facility, School of Biosciences, University of Sheffield, Sheffield, United Kingtom
| | - David E Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
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Un Jan Contreras S, Gardner CM. Environmental fate and behaviour of antibiotic resistance genes and small interference RNAs released from genetically modified crops. J Appl Microbiol 2022; 133:2877-2892. [PMID: 35892194 DOI: 10.1111/jam.15741] [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: 03/30/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
Abstract
Rising global populations have amplified food scarcity across the world and ushered in the development of genetically modified (GM) crops to overcome these challenges. Cultivation of major crops such as corn and soy has favoured GM crops over conventional varieties to meet crop production and resilience needs. Modern GM crops containing small interference RNA molecules and antibiotic resistance genes have become increasingly common in the United States. However, the use of these crops remains controversial due to the uncertainty regarding the unintended release of its genetic material into the environment and possible downstream effects on human and environmental health. DNA or RNA transgenes may be exuded from crop tissues during cultivation or released during plant decomposition and adsorbed by soil. This can contribute to the persistence and bioavailability in soil or water environment and possible uptake by soil microbial communities and further passing of this information to neighbouring bacteria, disrupting microbial ecosystem services such as nutrient cycling and soil fertility. In this review, transgene mechanisms of action, uses in crops, and knowledge regarding their environmental fate and impact to microbes are evaluated. This aims to encapsulate the current knowledge and promote further research regarding unintended effects transgenes may cause.
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Affiliation(s)
- Sandra Un Jan Contreras
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
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Chatterjee A, Zhang K, Rao Y, Sharma N, Giammar DE, Parker KM. Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3564-3574. [PMID: 35226478 DOI: 10.1021/acs.est.1c08468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yue Rao
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Sharma
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel E Giammar
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Liu J, Liang YS, Hu T, Zeng H, Gao R, Wang L, Xiao YH. Environmental fate of Bt proteins in soil: Transport, adsorption/desorption and degradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 226:112805. [PMID: 34592526 DOI: 10.1016/j.ecoenv.2021.112805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/05/2021] [Accepted: 09/16/2021] [Indexed: 05/26/2023]
Abstract
During the production and application of Bacillus thuringiensis (Bt) transgenic crops, large doses of insecticidal Bt toxic proteins are expressed continuously. The multi-interfacial behaviors of Bt proteins entering the environment in multi-media affects their states of existence transformation, transport and fate as well as biological and ecological impacts. Because both soil matrix and organisms will be exposed to Bt proteins to a certain extent, knowledge of the multi-interfacial behaviors and affecting factors of Bt proteins are vital not only for understanding the source-sink distribution mechanisms, predicting their bio-availability, but also for exploring the soil safety and environmental problems caused by the interaction between Bt proteins and soil matrix. This review summarized and analyzed various internal and external factors that affect the adsorption/ desorption and degradation of Bt proteins in the environment, so as to understand the multi-interfacial behaviors of Bt proteins. In addition, the reasons of concentration changes of Bt proteins in soil are discussed. This review will also discuss the existing knowledge of the combined effects of Bt proteins and other pollutants in environment. Finally, discussing the factors that should be considered when assessing the environmental risk of Bt proteins, thus to further improve the understanding of the environmental fate of Bt proteins.
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Affiliation(s)
- Jiao Liu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha 410128, PR China
| | - Yun-Shan Liang
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha 410128, PR China; College of Bioscience and Biotechnology, Hunan Agricultural University and Hunan Engineering Laboratory for Pollution Control and Waste Utilization in Swine Production, Changsha 410128, PR China.
| | - Teng Hu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha 410128, PR China
| | - Hong Zeng
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha 410128, PR China
| | - Rong Gao
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha 410128, PR China; College of Bioscience and Biotechnology, Hunan Agricultural University and Hunan Engineering Laboratory for Pollution Control and Waste Utilization in Swine Production, Changsha 410128, PR China
| | - Li Wang
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha 410128, PR China
| | - Yun-Hua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University and Hunan Engineering Laboratory for Pollution Control and Waste Utilization in Swine Production, Changsha 410128, PR China
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Raffa CM, Chiampo F. Bioremediation of Agricultural Soils Polluted with Pesticides: A Review. Bioengineering (Basel) 2021; 8:bioengineering8070092. [PMID: 34356199 PMCID: PMC8301097 DOI: 10.3390/bioengineering8070092] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/12/2021] [Accepted: 06/23/2021] [Indexed: 01/06/2023] Open
Abstract
Pesticides are chemical compounds used to eliminate pests; among them, herbicides are compounds particularly toxic to weeds, and this property is exploited to protect the crops from unwanted plants. Pesticides are used to protect and maximize the yield and quality of crops. The excessive use of these chemicals and their persistence in the environment have generated serious problems, namely pollution of soil, water, and, to a lower extent, air, causing harmful effects to the ecosystem and along the food chain. About soil pollution, the residual concentration of pesticides is often over the limits allowed by the regulations. Where this occurs, the challenge is to reduce the amount of these chemicals and obtain agricultural soils suitable for growing ecofriendly crops. The microbial metabolism of indigenous microorganisms can be exploited for degradation since bioremediation is an ecofriendly, cost-effective, rather efficient method compared to the physical and chemical ones. Several biodegradation techniques are available, based on bacterial, fungal, or enzymatic degradation. The removal efficiencies of these processes depend on the type of pollutant and the chemical and physical conditions of the soil. The regulation on the use of pesticides is strictly connected to their environmental impacts. Nowadays, every country can adopt regulations to restrict the consumption of pesticides, prohibit the most harmful ones, and define the admissible concentrations in the soil. However, this variability implies that each country has a different perception of the toxicology of these compounds, inducing different market values of the grown crops. This review aims to give a picture of the bioremediation of soils polluted with commercial pesticides, considering the features that characterize the main and most used ones, namely their classification and their toxicity, together with some elements of legislation into force around the world.
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Zhang K, Hodge J, Chatterjee A, Moon TS, Parker KM. Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8045-8053. [PMID: 34033461 DOI: 10.1021/acs.est.1c01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phosphodiester bonds in the backbones of double-stranded (ds)RNA and single-stranded (ss)RNA are known to undergo alkaline hydrolysis. Consequently, dsRNA agents used in emerging RNA interference (RNAi) products have been assumed to exhibit low chemical persistence in solutions. However, the impact of the duplex structure of dsRNA on alkaline hydrolysis has not yet been evaluated. In this study, we demonstrated that dsRNA undergoes orders-of-magnitude slower alkaline hydrolysis than ssRNA. Furthermore, we observed that dsRNA remains intact for multiple months at neutral pH, challenging the assumption that dsRNA is chemically unstable. In systems enabling both enzymatic degradation and alkaline hydrolysis of dsRNA, we found that increasing pH effectively attenuated enzymatic degradation without inducing alkaline hydrolysis that was observed for ssRNA. Overall, our findings demonstrated, for the first time, that key degradation pathways of dsRNA significantly differ from those of ssRNA. Consideration of the unique properties of dsRNA will enable greater control of dsRNA stability during the application of emerging RNAi technology and more accurate assessment of its fate in environmental and biological systems, as well as provide insights into broader application areas including dsRNA isolation, detection and inactivation of dsRNA viruses, and prebiotic molecular evolution.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph Hodge
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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14
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Fenibo EO, Ijoma GN, Matambo T. Biopesticides in Sustainable Agriculture: A Critical Sustainable Development Driver Governed by Green Chemistry Principles. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.619058] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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15
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Gu J, Ye R, Xu Y, Yin Y, Li S, Chen H. A historical overview of analysis systems for Bacillus thuringiensis (Bt) Cry proteins. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Sodnikar K, Parker KM, Stump SR, ThomasArrigo LK, Sander M. Adsorption of double-stranded ribonucleic acids (dsRNA) to iron (oxyhydr-)oxide surfaces: comparative analysis of model dsRNA molecules and deoxyribonucleic acids (DNA). ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:605-620. [PMID: 33723564 DOI: 10.1039/d1em00010a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Double-stranded ribonucleic acid (dsRNA) molecules are novel plant-incorporated protectants expressed in genetically modified RNA interference (RNAi) crops. Ecological risk assessment (ERA) of RNAi crops requires a heretofore-missing detailed understanding of dsRNA adsorption in soils, a key fate process. Herein, we systematically study the adsorption of a model dsRNA molecule and of two double-stranded deoxyribonucleic acid (DNA) molecules of varying lengths to three soil iron (oxyhydr-)oxides - goethite, lepidocrocite, and hematite - over a range of solution pH (4.5-10), ionic strength (I = 10-100 mM NaCl) and composition (0.5, 1, and 3 mM MgCl2) and in the absence and presence of phosphate (0.05-5 mM) as co-adsorbate. We hypothesized comparable adsorption characteristics of dsRNA and DNA based on their structural similarities. Consistently, the three nucleic acids (NAs) showed high adsorption affinities to the iron (oxyhydr-)oxides with decreasing adsorption in the order goethite, lepidocrocite, and hematite, likely reflecting a decrease in the hydroxyl group density and positive charges of the oxide surfaces in the same order. NA adsorption also decreased with increasing solution pH, consistent with weakening of NA electrostatic attraction to and inner-sphere complex formation with the iron (oxyhydr-)oxides surfaces as pH increased. Adsorbed NA concentrations increased with increasing I and in the presence of Mg2+, consistent with adsorbed NA molecules adopting more compact conformations. Strong NA-phosphate adsorption competition demonstrates that co-adsorbates need consideration in assessing dsRNA fate in soils. Comparable adsorption characteristics of dsRNA and DNA molecules to iron (oxyhydr-)oxides imply that information on DNA adsorption to soil particle surfaces can inform dsRNA ERA.
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Affiliation(s)
- Katharina Sodnikar
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Simona R Stump
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
| | - Laurel K ThomasArrigo
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, DUSYS, IBP, Universitätsstrasse 16, CHN H50.3, 8092 Zurich, Switzerland.
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17
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Li Y, Wang M, Zhang Y, Koopal LK, Tan W. Goethite effects on transport and activity of lysozyme with humic acid in quartz sand. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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18
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Papadopoulou N, Devos Y, Álvarez-Alfageme F, Lanzoni A, Waigmann E. Risk Assessment Considerations for Genetically Modified RNAi Plants: EFSA's Activities and Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:445. [PMID: 32373145 PMCID: PMC7186845 DOI: 10.3389/fpls.2020.00445] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/25/2020] [Indexed: 05/18/2023]
Abstract
Genetically modified plants (GMPs) intended for market release can be designed to induce "gene silencing" through RNA interference (RNAi). The European Food Safety Authority (EFSA) and other international risk assessment bodies/regulatory agencies have taken several actions to determine whether the existing risk assessment approaches for GMPs are appropriate for the risk assessment of RNAi-based GMPs or require complementary or alternative approaches. To our knowledge, at the international level, no dedicated guidelines have been developed for the risk assessment and regulation of RNAi-based GMPs, confirming that existing science-based risk assessment approaches for GMPs are generally considered suitable for RNAi-based GMPs. However, some specificities have been identified for the risk assessment of RNAi-based GMPs. Here, we report on some of these specificities as identified and addressed by the EFSA GMO Panel for the molecular characterisation, food/feed safety assessment and environmental risk assessment of RNAi-based GMPs, using the DvSnf7 dsRNA-expressing maize MON87411 as a case study.
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Affiliation(s)
- Nikoletta Papadopoulou
- Genetically Modified Organisms Unit, Department of Scientific Evaluation of Regulated Products Development, European Food Safety Authority, Parma, Italy
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19
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Zhang K, Wei J, Huff Hartz KE, Lydy MJ, Moon TS, Sander M, Parker KM. Analysis of RNA Interference (RNAi) Biopesticides: Double-Stranded RNA (dsRNA) Extraction from Agricultural Soils and Quantification by RT-qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4893-4902. [PMID: 32212649 DOI: 10.1021/acs.est.9b07781] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Double-stranded RNA (dsRNA) molecules are used as a novel class of biopesticides. To enable assessments of the ecological risk associated with their release to receiving environments, we developed an approach to quantify dsRNA in agricultural soils using quantitative reverse transcription-polymerase chain reaction (RT-qPCR). To allow quantification of dsRNA adsorbed to particles, we also developed a protocol to transfer dsRNA from particles to the extraction buffer by changing particle surface charge and adding constituents to compete with dsRNA for adsorption sites. Our approach could quantify dsRNA amounts as low as 0.003 ngdsRNA/gsoil. This approach is the first available field-applicable approach able to quantify dsRNA biopesticides down to environmentally relevant concentrations. We applied this approach to investigate dsRNA dissipation (including dilution, degradation, and adsorption) in two agricultural soils. When we applied a low amount of dsRNA (1 ngdsRNA/gsoil) to the soils, we observed that a greater fraction of dsRNA was adsorbed to and extractable from soil particles in a silty clay loam soil than in a fine sandy loam soil. In both soils, dsRNA dissipated on the timescale of hours. Overall, these results demonstrate that our approach can be applied to assess the environmental fate of dsRNA biopesticides at concentrations relevant to their release to soils.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jingmiao Wei
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kara E Huff Hartz
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Michael J Lydy
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael Sander
- Department of Environmental Systems Science (DUSYS), ETH Zurich, 8092 Zurich, Switzerland
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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20
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Darsan Singh JK, Mat Jalaluddin NS, Sanan-Mishra N, Harikrishna JA. Genetic modification in Malaysia and India: current regulatory framework and the special case of non-transformative RNAi in agriculture. PLANT CELL REPORTS 2019; 38:1449-1463. [PMID: 31350570 DOI: 10.1007/s00299-019-02446-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/09/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Recent developments in modern biotechnology such as the use of RNA interference (RNAi) have broadened the scope of crop genetic modification. RNAi strategies have led to significant achievements in crop protection against biotic and abiotic stresses, modification of plant traits, and yield improvement. As RNAi-derived varieties of crops become more useful in the field, it is important to examine the capacity of current regulatory systems to deal with such varieties, and to determine if changes are needed to improve the existing frameworks. We review the biosafety frameworks from the perspective of developing countries that are increasingly involved in modern biotechnology research, including RNAi applications, and make some recommendations. Malaysia and India have approved laws regulating living modified organisms and products thereof, highlighting that the use of any genetically modified step requires regulatory scrutiny. In view of production methods for exogenously applied double-stranded RNAs and potential risks from the resulting double-stranded RNA-based products, we argue that a process-based system may be inappropriate for the non-transformative RNAi technology. We here propose that the current legislation needs rewording to take account of the non-transgenic RNAi technology, and discuss the best alternative for regulatory systems in India and Malaysia in comparison with the existing frameworks in other countries.
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Affiliation(s)
- Jasdeep Kaur Darsan Singh
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, University of Malaya, Jalan Universiti, 50603, Kuala Lumpur, Malaysia
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Jalan Universiti, 50603, Kuala Lumpur, Malaysia
| | - Nurzatil Sharleeza Mat Jalaluddin
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, University of Malaya, Jalan Universiti, 50603, Kuala Lumpur, Malaysia
| | - Neeti Sanan-Mishra
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, University of Malaya, Jalan Universiti, 50603, Kuala Lumpur, Malaysia.
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Jalan Universiti, 50603, Kuala Lumpur, Malaysia.
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21
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Qiao J, Du Y, Yu J, Guo J. MicroRNAs as Potential Biomarkers of Insecticide Exposure: A Review. Chem Res Toxicol 2019; 32:2169-2181. [PMID: 31625722 DOI: 10.1021/acs.chemrestox.9b00236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Insecticides are key weapons for the control of pests. Large scale use of insecticides is harmful to the ecosystem, which is made up of a wide range of species and environments. MicroRNAs (miRNAs) are a class of endogenous single-stranded noncoding small RNAs in length of 20-24 nucleotides (nt), which extensively regulate expression of genes at transcriptional and post-transcriptional levels. The current research on miRNA-induced insecticide resistance reveals that dysregulated miRNAs cause significant changes in detoxification genes, particularly cytochrome P450s. Meanwhile, insecticide-induced changes in miRNAs are related to the decline of honeybees and threatened the development of zebrafish and other animals. Additionally, miRNAs are involved in insecticide-induced cytotoxicity, and dysregulated miRNAs are associated with human occupational and environmental exposure to insecticides. Therefore, miRNAs are valuable novel biomarkers of insecticide exposure, and they are potential factors to explain the toxicological effects of insecticides.
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Affiliation(s)
- Jiakai Qiao
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| | - Yuting Du
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| | - Junjie Yu
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
| | - Jiangfeng Guo
- College of Life Sciences and Medicine , Zhejiang Sci-Tech University , Hangzhou , Zhejiang 310018 , China
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22
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Parker KM, Barragán Borrero V, van Leeuwen DM, Lever MA, Mateescu B, Sander M. Environmental Fate of RNA Interference Pesticides: Adsorption and Degradation of Double-Stranded RNA Molecules in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3027-3036. [PMID: 30681839 DOI: 10.1021/acs.est.8b05576] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Double-stranded RNA (dsRNA) pesticides are a new generation of crop protectants that interfere with protein expression in targeted pest insects by a cellular mechanism called RNA interference (RNAi). The ecological risk assessment of these emerging pesticides necessitates an understanding of the fate of dsRNA molecules in receiving environments, among which agricultural soils are most important. We herein present an experimental approach using phosphorus-32 (32P)-radiolabeled dsRNA that allows studying key fate processes of dsRNA in soils with unprecedented sensitivity. This approach resolves previous analytical challenges in quantifying unlabeled dsRNA and its degradation products in soils. We demonstrate that 32P-dsRNA and its degradation products are quantifiable at concentrations as low as a few nanograms of dsRNA per gram of soil by both Cerenkov counting (to quantify total 32P-activity) and by polyacrylamide gel electrophoresis followed by phosphorimaging (to detect intact 32P-dsRNA and its 32P-containing degradation products). We show that dsRNA molecules added to soil suspensions undergo adsorption to soil particle surfaces, degradation in solution, and potential uptake by soil microorganisms. The results of this work on dsRNA adsorption and degradation advance a process-based understanding of the fate of dsRNA in soils and will inform ecological risk assessments of emerging dsRNA pesticides.
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Affiliation(s)
- Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering , Washington University in St. Louis , St. Louis , Missouri 63130 , United States
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
| | - Verónica Barragán Borrero
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Daniël M van Leeuwen
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
| | - Bogdan Mateescu
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
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23
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Qiao Z, Ye Y, Chang PH, Thirunarayanan D, Wigginton KR. Nucleic Acid Photolysis by UV 254 and the Impact of Virus Encapsidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10408-10415. [PMID: 30106282 DOI: 10.1021/acs.est.8b02308] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Determining the influence of higher order structure on UVC photolysis will help inform predictions of nucleic acid fate and microorganism inactivation. We measured the direct UV254 photolysis kinetics of four model viral genomes composed of single-stranded and double-stranded RNA (ssRNA and dsRNA, respectively), as well as single-stranded and double-stranded DNA (ssDNA and dsDNA, respectively), in ultrapure water, in phosphate buffered saline (PBS), and encapsidated in their native virus particles. The photolysis rate constants of naked nucleic acids measured by qPCR (RT-qPCR for RNA) and normalized by the number of bases measured in a particular sequence exhibited the following trend: ssDNA > ssRNA ≈ dsDNA > dsRNA. In PBS, naked ssRNA bases reacted, on average, 24× faster than the dsRNA bases, whereas naked ssDNA bases reacted 4.3× faster than dsDNA bases. Endogenous indirect photolysis involving 1O2 and ·OH was ruled out as a major contributing factor in the reactions. A comparison of our measured rate constants with rate constants reported in the literature shows a general agreement among the nucleic acid UV254 direct photolysis kinetics. Our results underscore the high resistance of dsRNA to UVC photolysis and demonstrate the role that nucleic acid structure and solution chemistry play in photoreactivity.
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Affiliation(s)
- Zhong Qiao
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Yinyin Ye
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Pin Hsuan Chang
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Devibaghya Thirunarayanan
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
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