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Xu N, Kahn TW, Jacob T, Liu Y. Graphical models for identifying pore-forming proteins. Proteins 2024; 92:975-983. [PMID: 38618860 DOI: 10.1002/prot.26687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Pore-forming toxins (PFTs) are proteins that form lesions in biological membranes. Better understanding of the structure and function of these proteins will be beneficial in a number of biotechnological applications, including the development of new pest control methods in agriculture. When searching for new pore formers, existing sequence homology-based methods fail to discover truly novel proteins with low sequence identity to known proteins. Search methodologies based on protein structures would help us move beyond this limitation. As the number of known structures for PFTs is very limited, it's quite challenging to identify new proteins having similar structures using computational approaches like deep learning. In this article, we therefore propose a sample-efficient graphical model, where a protein structure graph is first constructed according to consensus secondary structures. A semi-Markov conditional random fields model is then developed to perform protein sequence segmentation. We demonstrate that our method is able to distinguish structurally similar proteins even in the absence of sequence similarity (pairwise sequence identity < 0.4)-a feat not achievable by traditional approaches like HMMs. To extract proteins of interest from a genome-wide protein database for further study, we also develop an efficient framework for UniRef50 with 43 million proteins.
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Affiliation(s)
- Nan Xu
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Theodore W Kahn
- BASF Corporation, Research Triangle Park, North Carolina, USA
| | - Theju Jacob
- BASF Corporation, Research Triangle Park, North Carolina, USA
| | - Yan Liu
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
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2
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Yao H, Gao S, Sun T, Zhou G, Lu C, Gao B, Chen W, Liang Y. Transcriptomic analysis of the defense response in "Cabernet Sauvignon" grape leaf induced by Apolygus lucorum feeding. PLANT DIRECT 2024; 8:e590. [PMID: 38779180 PMCID: PMC11108798 DOI: 10.1002/pld3.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/14/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
To investigate the molecular mechanism of the defense response of "Cabernet Sauvignon" grapes to feeding by Apolygus lucorum, high-throughput sequencing technology was used to analyze the transcriptome of grape leaves under three different treatments: feeding by A. lucorum, puncture injury, and an untreated control. The research findings indicated that the differentially expressed genes were primarily enriched in three aspects: cellular composition, molecular function, and biological process. These genes were found to be involved in 42 metabolic pathways, particularly in plant hormone signaling metabolism, plant-pathogen interaction, MAPK signaling pathway, and other metabolic pathways associated with plant-induced insect resistance. Feeding by A. lucorum stimulated and upregulated a significant number of genes related to jasmonic acid and calcium ion pathways, suggesting their crucial role in the defense molecular mechanism of "Cabernet Sauvignon" grapes. The consistency between the gene expression and transcriptome sequencing results further supports these findings. This study provides a reference for the further exploration of the defense response in "Cabernet Sauvignon" grapes by elucidating the expression of relevant genes during feeding by A. lucorum.
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Affiliation(s)
- Heng Yao
- College of Agronomy and BiotechnologyHebei Normal University of Science and TechnologyChangliHebeiChina
- Hebei Key Laboratory of Crop Stress Biology (in Preparation)ChangliHebeiChina
| | - Suhong Gao
- College of Agronomy and BiotechnologyHebei Normal University of Science and TechnologyChangliHebeiChina
- Hebei Key Laboratory of Crop Stress Biology (in Preparation)ChangliHebeiChina
| | - Tianhua Sun
- College of ForestryHebei Agricultural UniversityBaodingHebeiChina
| | - Guona Zhou
- College of ForestryHebei Agricultural UniversityBaodingHebeiChina
| | - Changkuan Lu
- College of Agronomy and BiotechnologyHebei Normal University of Science and TechnologyChangliHebeiChina
| | - Baojia Gao
- College of ForestryHebei Agricultural UniversityBaodingHebeiChina
| | - Wenshu Chen
- College of Agronomy and BiotechnologyHebei Normal University of Science and TechnologyChangliHebeiChina
- Hebei Key Laboratory of Crop Stress Biology (in Preparation)ChangliHebeiChina
| | - Yiming Liang
- College of Agronomy and BiotechnologyHebei Normal University of Science and TechnologyChangliHebeiChina
- Hebei Key Laboratory of Crop Stress Biology (in Preparation)ChangliHebeiChina
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3
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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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Yadav J, Jasrotia P, Jaglan MS, Sareen S, Kashyap PL, Kumar S, Yadav SS, Singh G, Singh GP. Unravelling the novel genetic diversity and marker-trait associations of corn leaf aphid resistance in wheat using microsatellite markers. PLoS One 2024; 19:e0289527. [PMID: 38386640 PMCID: PMC10883527 DOI: 10.1371/journal.pone.0289527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/17/2023] [Indexed: 02/24/2024] Open
Abstract
The study was conducted to identify novel simple sequence repeat (SSR) markers associated with resistance to corn aphid (CLA), Rhopalosiphum maidis L. in 48 selected bread wheat (Triticum aestivum L.) and wild wheat (Aegilops spp. & T. dicoccoides) genotypes during two consecutive cropping seasons (2018-19 and 2019-20). A total of 51 polymorphic markers containing 143 alleles were used for the analysis. The frequency of the major allele ranged from 0.552 (Xgwm113) to 0.938 (Xcfd45, Xgwm194 and Xgwm526), with a mean of 0.731. Gene diversity ranged from 0.116 (Xgwm526) to 0.489 (Xgwm113), with a mean of 0.354. The polymorphic information content (PIC) value for the SSR markers ranged from 0.107 (Xgwm526) to 0.370 (Xgwm113) with a mean of 0.282. The results of the STRUCTURE analysis revealed the presence of four main subgroups in the populations. Analysis of molecular variance (AMOVA) showed that the between-group difference was around 37 per cent of the total variation contributed to the diversity by the whole germplasm, while 63 per cent of the variation was attributed between individuals within the group. A general linear model (GLM) was used to identify marker-trait associations, which detected a total of 23 and 27 significant new marker-trait associations (MTAs) at the p < 0.01 significance level during the 2018-19 and 2019-20 crop seasons, respectively. The findings of this study have important implications for the identification of molecular markers associated with CLA resistance. These markers can increase the accuracy and efficiency of aphid-resistant germplasm selection, ultimately facilitating the transfer of resistance traits to desirable wheat genotypes.
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Affiliation(s)
- Jayant Yadav
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Poonam Jasrotia
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | | | - Sindhu Sareen
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Prem Lal Kashyap
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Sudheer Kumar
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | | | - Gyanendra Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Gyanendra Pratap Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
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Bulle M, Sheri V, Aileni M, Zhang B. Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3448. [PMID: 37836188 PMCID: PMC10574609 DOI: 10.3390/plants12193448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
The world population's growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering.
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Affiliation(s)
- Mallesham Bulle
- Agri Biotech Foundation, Agricultural University Campus, Rajendranagar, Hyderabad 500030, India
| | - Vijay Sheri
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
| | - Mahender Aileni
- Department of Biotechnology, Telangana University, Dichpally, Nizamabad 503322, India;
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
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Abu El-Ghiet UM, Moustafa SA, Ayashi MM, El-Sakhawy MA, Ateya AAES, Waggiallah HA. Characterization of Bacillus thuringiensis isolated from soils in the Jazan region of Saudi Arabia, and their efficacy against Spodoptera littoralis and Aedes aegypti larvae. Saudi J Biol Sci 2023; 30:103721. [PMID: 37457233 PMCID: PMC10344810 DOI: 10.1016/j.sjbs.2023.103721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
Pest control in Saudi Arabia depends on applying chemical insecticides, which have many undesirable considerations and impacts on the environment. Therefore, the aim of this study was to isolate Bacillus thuringiensis from different rhizosphere soil samples in the Jazan region for the biological control of Spodoptera littoralis and Aedes aegypti larvae. The samples were collected from the rhizosphere of different plants located in eight agricultural areas in Jazan, Saudi Arabia. Out of 100 bacterial isolates, four bacterial isolates belonging to Bacillus species were selected namely JZ1, JZ2, JZ3, and JZ4, and identified using classical bacteriological and molecular identification using 16S rRNA. JZ1 and JZ2 isolates were identified as Bacillus thuringiensis. SDS-PAGE analysis and the detection of the Cry1 gene were used to describe the two isolates JZ1 and JZ2 in comparison to Bacillus thuringiensis reference strain Kurstaki HD1 (BTSK) were revealed that slightly different from each other due to the place of their isolation and namely Khlab JZ1 and Ayash JZ2. The EC50 of JZ1 and JZ2 isolates, BTSK, and the commercial biopesticide DiPEL 6.4 DF against the second-instar larvae of Aedes aegypti were 207, 932, 400, and 500 ppm respectively, while EC50 against first-instar larvae of Spodoptera littoralis were 193.93, 589.7, 265.108, and 342.9, ppm respectively. Isolate JZ1 recorded the highest mortality while JZ2 isolate gave the lowest mortality. It can be concluded that the local isolate of JZ1 and JZ2 can be developed for bio formulations to be used in Spodoptera littoralis and Aedes aegypti biological control programs.
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Affiliation(s)
| | - Salah A. Moustafa
- Biology Department, Faculty of Science, Jazan University, Saudi Arabia
- Agriculture Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Mousa M. Ayashi
- Biology Department, Faculty of Science, Jazan University, Saudi Arabia
| | - Mohamed A. El-Sakhawy
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Medicinal and Aromatic Plants, Desert Research Center, Cairo, Egypt
| | - Abeer Ali El-Sherbiny Ateya
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hisham Ali Waggiallah
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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Yáñez O, Alegría-Arcos M, Suardiaz R, Morales-Quintana L, Castro RI, Palma-Olate J, Galarza C, Catagua-González Á, Rojas-Pérez V, Urra G, Hernández-Rodríguez EW, Bustos D. Calcium-Alginate-Chitosan Nanoparticle as a Potential Solution for Pesticide Removal, a Computational Approach. Polymers (Basel) 2023; 15:3020. [PMID: 37514411 PMCID: PMC10383139 DOI: 10.3390/polym15143020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Pesticides have a significant negative impact on the environment, non-target organisms, and human health. To address these issues, sustainable pest management practices and government regulations are necessary. However, biotechnology can provide additional solutions, such as the use of polyelectrolyte complexes to encapsulate and remove pesticides from water sources. We introduce a computational methodology to evaluate the capture capabilities of Calcium-Alginate-Chitosan (CAC) nanoparticles for a broad range of pesticides. By employing ensemble-docking and molecular dynamics simulations, we investigate the intermolecular interactions and absorption/adsorption characteristics between the CAC nanoparticles and selected pesticides. Our findings reveal that charged pesticide molecules exhibit more than double capture rates compared to neutral counterparts, owing to their stronger affinity for the CAC nanoparticles. Non-covalent interactions, such as van der Waals forces, π-π stacking, and hydrogen bonds, are identified as key factors which stabilized the capture and physisorption of pesticides. Density profile analysis confirms the localization of pesticides adsorbed onto the surface or absorbed into the polymer matrix, depending on their chemical nature. The mobility and diffusion behavior of captured compounds within the nanoparticle matrix is assessed using mean square displacement and diffusion coefficients. Compounds with high capture levels exhibit limited mobility, indicative of effective absorption and adsorption. Intermolecular interaction analysis highlights the significance of hydrogen bonds and electrostatic interactions in the pesticide-polymer association. Notably, two promising candidates, an antibiotic derived from tetracycline and a rodenticide, demonstrate a strong affinity for CAC nanoparticles. This computational methodology offers a reliable and efficient screening approach for identifying effective pesticide capture agents, contributing to the development of eco-friendly strategies for pesticide removal.
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Affiliation(s)
- Osvaldo Yáñez
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago 7500000, Chile
| | - Melissa Alegría-Arcos
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago 7500000, Chile
| | - Reynier Suardiaz
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3400000, Chile
| | - Ricardo I Castro
- Multidisciplinary Agroindustry Research Laboratory, Carrera de Ingeniería en Construcción, Instituto de Ciencias Químicas Aplicadas, Universidad Autónoma de Chile, Talca 3400000, Chile
| | | | - Christian Galarza
- Escuela Superior Politécnica del Litoral, Guayaquil EC090903, Ecuador
| | | | - Víctor Rojas-Pérez
- Doctorado en Biotecnología Traslacional, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca 3480094, Chile
| | - Gabriela Urra
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
| | - Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
- Unidad de Bioinformática Clínica, Centro Oncológico, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
| | - Daniel Bustos
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca 3460000, Chile
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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: 10] [Impact Index Per Article: 5.0] [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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