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Rooney J, Rivera-de-Torre E, Li R, Mclean K, Price DR, Nisbet AJ, Laustsen AH, Jenkins TP, Hofmann A, Bakshi S, Zarkan A, Cantacessi C. Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions. Comput Struct Biotechnol J 2024; 23:1522-1533. [PMID: 38633385 PMCID: PMC11021794 DOI: 10.1016/j.csbj.2024.04.019] [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: 12/13/2023] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.
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Affiliation(s)
- James Rooney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ruizhe Li
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Kevin Mclean
- Moredun Research Institute, Penicuik Midlothian, United Kingdom
| | | | | | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Hofmann
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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2
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Mishra SK, Liu T, Wang H. Thousands of oscillating LncRNAs in the mouse testis. Comput Struct Biotechnol J 2024; 23:330-346. [PMID: 38205156 PMCID: PMC10776378 DOI: 10.1016/j.csbj.2023.11.046] [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: 09/20/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
The long noncoding RNAs (lncRNAs) are involved in numerous fundamental biological processes, including circadian regulation. Although recent studies have revealed insights into the functions of lncRNAs, how the lncRNAs regulate circadian rhythms still requires a deeper investigation. In this study, we generate two datasets of RNA-seq profiles of the mouse (Mus musculus) testis under light-dark (LD) cycle. The first dataset included 18,613 unannotated transcripts measured at 12 time points, each with duplicate samples, under LD conditions; while the second dataset included 21,414 unannotated transcripts measured at six time points, each with three replicates, under desynchronized and control conditions. We identified 5964 testicular lncRNAs in each dataset by BLASTing these transcripts against the known mouse lncRNAs from the NONCODE database. MetaCycle analyses were performed to identify 519, 475, and 494 rhythmically expressed mouse testicular lncRNAs in the 12-time-point dataset, the six-time-point control dataset, and the six-time-point desynchronized dataset, respectively. A comparison of the expression profiles of the lncRNAs under desynchronized and control conditions revealed that 427 rhythmically expressed lncRNAs from the control condition became arrhythmic under the desynchronized condition, suggesting a possible loss of rhythmicity. In contrast, 446 arrhythmic lncRNAs from the control condition became rhythmic under the desynchronized condition, suggesting a possible gain of rhythmicity. Interestingly, 48 lncRNAs were rhythmically expressed under both desynchronized and control conditions. These oscillating lncRNAs were divided into morning lncRNAs, evening lncRNAs, and night lncRNAs based on their time-course expression patterns. We interrogated the promoter regions of these rhythmically expressed mouse testicular lncRNAs to predict their possible regulation by the E-box, D-box, or RORE promoter motifs. GO and KEGG analyses were performed to identify the possible biological functions of these rhythmically expressed mouse testicular lncRNAs. Further, we conducted conservation analyses of the rhythmically expressed mouse testicular lncRNAs with lncRNAs from humans, rats, and zebrafish, and uncovered three mouse testicular lncRNAs conserved across these four species. Finally, we computationally predicted the conserved lncRNA-encoded peptides and their 3D structures from each of the four species. Taken together, our study revealed thousands of rhythmically expressed lncRNAs in the mouse testis, setting the stage for further computational and experimental validations.
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Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Taole Liu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
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3
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Li L, Fan B, Zhang Y, Zhao M, Kong Z, Wang F, Li M. Cannabidiol exposure during embryonic period caused serious malformation in embryos and inhibited the development of reproductive system in adult zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175315. [PMID: 39111451 DOI: 10.1016/j.scitotenv.2024.175315] [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: 04/08/2024] [Revised: 07/17/2024] [Accepted: 08/04/2024] [Indexed: 08/11/2024]
Abstract
Cannabidiol (CBD) is a non-psychoactive component of cannabis with potential applications in biomedicine, food, and cosmetics due to its analgesic, anti-inflammatory, and anticonvulsant properties. However, increasing reports of adverse CBD exposure events underscore the necessity of evaluating its toxicity. In this study, we investigated the developmental toxicity of CBD in zebrafish during the embryonic (0-4 dpf, days post fertilization) and early larval stages (5-7 dpf). The median lethal concentration of CBD in embryos/larvae is 793.28 μg/L. CBD exhibited concentration-dependent manner (ranging from 250 to 1500 μg/L) in inducing serious malformed somatotypes, like shorter body length, pericardial cysts, vitelline cysts, spinal curvature, and smaller eyes. However, no singular deformity predominates. The 5-month-old zebrafish treated with 100 and 200 μg/L of CBD during the embryonic and early larval stages produced fewer offspring with higher natural mortality and malformation rate. Gonadal growth and gamete development were inhibited. Transcriptomic and metabolomic analyses conducted with 400 μg/L CBD on embryos/larvae from 0 to 5 dpf suggested that CBD promoted the formation and transportation of extracellular matrix components on 1 dpf, promoting abnormal cell division and migration, probably resulting in random malformed somatotypes. It inhibited optical vesicle development and photoreceptors formation on 2 and 3 dpf, resulting in damaged sight and smaller eye size. CBD also induced an integrated stress response on 4 and 5 dpf, disrupting redox, protein, and cholesterol homeostasis, contributing to cellular damage, physiological dysfunction, embryonic death, and inhibited reproductive system and ability in adult zebrafish. At the tested concentrations, CBD exhibited developmental toxicity, lethal toxicity, and reproductive inhibition in zebrafish. These findings demonstrate that CBD threatens the model aquatic animal, highlighting the need for additional toxicological evaluations of CBD before its inclusion in dietary supplements, edible food, and other products.
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Affiliation(s)
- Lin Li
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Bei Fan
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, PR China
| | - Yifan Zhang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Mengying Zhao
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Zhiqiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Fengzhong Wang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Minmin Li
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, PR China.
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4
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Araújo MJ, Vazquez M, Rodriguez-Lorenzo L, Moreda-Piñeiro A, Fonseca E, Mallo N, Pinheiro I, Quarato M, Bigorra-Ferré E, Matos A, Barreiro-Felpeto A, Turkina MV, Suárez-Oubiña C, Bermejo-Barrera P, Cabaleiro S, Vasconcelos V, Espiña B, Campos A. Diving into the metabolic interactions of titanium dioxide nanoparticles in "Sparus aurata" and "Ruditapes philippinarum". ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124665. [PMID: 39116928 DOI: 10.1016/j.envpol.2024.124665] [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: 06/04/2024] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
The biological response to nanomaterials exposure depends on their properties, route of exposure, or model organism. Titanium dioxide nanoparticles (TiO2 NPs) are among the most used nanomaterials; however, concerns related to oxidative stress and metabolic effects resulting from their ingestion are rising. Therefore, in the present work, we addressed the metabolic effects of citrate-coated 45 nm TiO2 NPs combining bioaccumulation, tissue ultrastructure, and proteomics approaches on gilthead seabream, Sparus aurata and Japanese carpet shell, Ruditapes philippinarum. Sparus aurata was exposed through artificially contaminated feeds, while R. philippinarum was exposed using TiO2 NPs-doped microalgae solutions. The accumulation of titanium and TiO2 NPs in fish liver is associated with alterations in hepatic tissue structure, and alteration to the expression of proteins related to lipid and fatty acid metabolism, lipid breakdown for energy, lipid transport, and homeostasis. While cellular structure alterations and the expression of proteins were less affected than in gilthead seabream, atypical gill cilia and microvilli and alterations in metabolic-related proteins were also observed in the bivalve. Overall, the effects of TiO2 NPs exposure through feeding appear to stem from various interactions with cells, involving alterations in key metabolic proteins, and changes in cell membranes, their structures, and organelles. The possible appearance of metabolic disorders and the environmental risks to aquatic organisms posed by TiO2 NPs deserve further study.
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Affiliation(s)
- Mário Jorge Araújo
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - María Vazquez
- CETGA - Centro Tecnológico del Cluster de la Acuicultura, Punta de Couso s/n, 15965, Ribeira, A Coruña, Spain
| | - Laura Rodriguez-Lorenzo
- INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Antonio Moreda-Piñeiro
- GETEE - Trace Element, Spectroscopy and Speciation Group, Institute de Materiais iMATUS. Faculty of Chemistry, University of Santiago de Compostela, Av. das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Elza Fonseca
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Natalia Mallo
- CETGA - Centro Tecnológico del Cluster de la Acuicultura, Punta de Couso s/n, 15965, Ribeira, A Coruña, Spain
| | - Ivone Pinheiro
- INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Monica Quarato
- INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Elizabeth Bigorra-Ferré
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Ana Matos
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Aldo Barreiro-Felpeto
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Maria V Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Cristian Suárez-Oubiña
- GETEE - Trace Element, Spectroscopy and Speciation Group, Institute de Materiais iMATUS. Faculty of Chemistry, University of Santiago de Compostela, Av. das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Pilar Bermejo-Barrera
- GETEE - Trace Element, Spectroscopy and Speciation Group, Institute de Materiais iMATUS. Faculty of Chemistry, University of Santiago de Compostela, Av. das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Santiago Cabaleiro
- CETGA - Centro Tecnológico del Cluster de la Acuicultura, Punta de Couso s/n, 15965, Ribeira, A Coruña, Spain
| | - Vitor Vasconcelos
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; FCUP - Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Begoña Espiña
- INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Alexandre Campos
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
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5
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Zhi T, Ma A, Liu X, Chen Z, Li S, Jia Y. A multitissue transcriptomic analysis reveals a potential mechanism whereby Brevibacillus laterosporus S62-9 promotes broiler growth. Poult Sci 2024; 103:104050. [PMID: 39106700 PMCID: PMC11343061 DOI: 10.1016/j.psj.2024.104050] [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: 03/26/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 08/09/2024] Open
Abstract
Brevibacillus laterosporus S62-9 has been shown to improve broiler growth performance and immunity. In the present study, we aimed to evaluate the effects of B. laterosporus S62-9 on the immunity and lipid metabolism of broilers by means of transcriptomic analysis. A total of 160 1-day-old broilers were randomly allocated to a S62-9 group, the diet of which was supplemented with 106 CFU/g B. laterosporus S62-9 daily, and a control group, which was not. After 42 d of feeding, the broilers in the S62-9 group had higher body mass (7.2%) and feed conversion ratio (5.19%) than the control group. Supplementation with B. laterosporus S62-9 resulted in lower serum total cholesterol and low-density lipoprotein-cholesterol concentrations and higher high-density lipoprotein-cholesterol concentrations. An analysis of the fatty acid composition of the broiler's thigh muscles revealed that the proportions of the unsaturated fatty acids myristoleic acid (C14:1) and arachidonic acid (C20:1) were higher for birds in the S62-9 group. Transcriptomic analysis also showed an upregulation of immunity-related genes in the S62-9 group. Gene Ontology functional enrichment analysis showed that the mitogen-activated protein kinase pathway was enriched in the liver, the defense response was enriched in the duodenum, and immunoglobulin-related entries were enriched in the jejunum of the S62-9 group. Furthermore, the expression of key genes involved in unsaturated fatty acid synthesis (SCD, encoding stearoyl-CoA desaturase) and fatty acid metabolism (HACD2, encoding 3-hydroxyacyl-CoA dehydratase 2) was upregulated in the liver, and the expression of genes associated with fat biosynthesis and accumulation, such as PLIN1, encoding perilipin 1, and FABP4, encoding fatty acid binding protein 4, was upregulated in the ileum of the birds in the S62-9 group. In summary, supplementation with B. laterosporus S62-9 could improve immune defense and the fatty acid metabolism of broiler chickens, thereby enhancing their disease resistance and promoting growth and development.
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Affiliation(s)
- Tongxin Zhi
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China
| | - Aijin Ma
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China
| | - Xiangfei Liu
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China
| | - Zhou Chen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China
| | - Siting Li
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China
| | - Yingmin Jia
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
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6
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Rahmat NL, Zifruddin AN, Yusoff NS, Sulaiman S, Zainal Abidin CMR, Othman NW, Nor Muhammad NA, Hassan M. Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana. Comput Biol Chem 2024; 112:108176. [PMID: 39181100 DOI: 10.1016/j.compbiolchem.2024.108176] [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: 03/26/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
Metisa plana is a widespread insect pest infesting oil palm plantations in Malaysia. Farnesyl acetate (FA), a juvenile hormone analogue, has been reported to exert in vitro and in vivo insecticidal activity against other insect pests. However, the insecticidal mechanism of FA on M. plana remains unclear. Therefore, this study aims to elucidate responsive genes in M. plana in response to FA treatment. The RNA-sequencing reads of FA-treated M. plana were de novo-assembled with existing raw reads from non-treated third instar larvae, and 55,807 transcripts were functionally annotated to multiple protein databases. Several insecticide detoxification-related genes were differentially regulated among the 321 differentially expressed transcripts. Cytochrome P450 monooxygenase, carboxylesterase, and ATP-binding cassette protein were upregulated, while peptidoglycan recognition protein was downregulated. Innate immune response genes, such as glutathione S-transferases, acetylcholinesterase, and heat shock protein, were also identified in the transcriptome. The findings signify that changes occurred in the insect's receptor and signaling, metabolic detoxification of insecticides, and immune responses upon FA treatment on M. plana. This valuable information on FA toxicity may be used to formulate more effective biorational insecticides for better M. plana pest management strategies in oil palm plantations.
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Affiliation(s)
- Nur Lina Rahmat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Anis Nadyra Zifruddin
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Nur Syamimi Yusoff
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Suhaila Sulaiman
- Bioinformatics Unit, FGV R&D Sdn. Bhd., FGV Innovation Centre, PT23417 Lengkuk Teknologi,Bandar Enstek, Nilai, Negeri Sembilan 71760, Malaysia
| | | | - Nurul Wahida Othman
- Centre for Insect Systematics, Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia; Bioinformatics and Molecular Simulations Group, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia; Systems and Synthetic Biology Group, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
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7
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Rey-Campos M, Saco A, Novoa B, Figueras A. Transcriptomic and functional analysis of the antiviral response of mussels after a poly I:C stimulation. FISH & SHELLFISH IMMUNOLOGY 2024; 153:109867. [PMID: 39214263 DOI: 10.1016/j.fsi.2024.109867] [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: 02/09/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
The study of mussels (Mytilus galloprovincialis) has grown in importance in recent years due to their high economic value and resistance to pathogens. Because of the biological characteristics revealed by mussel genome sequencing, this species is a valuable research model. The high genomic variability and diversity, particularly in immune genes, may be responsible for their resistance to pathogens found in seawater and continuously filtered and internalized by them. These facts, combined with the lack of proven mussel susceptibility to viruses in comparison to other bivalves such as oysters, result in a lack of studies on mussel antiviral response. We used RNA-seq to examine the genomic response of mussel hemocytes after they were exposed to poly I:C, simulating immune cell contact with viral dsRNA. Apoptosis and the molecular axis IRFs/STING-IFI44/IRGC1 were identified as the two main pathways in charge of the response but we also found a modulation of lncRNAs. Finally, in order to obtain new information about the response of mussels to putative natural challenges, we used VHSV virus (Viral Hemorrhagic Septicemia Virus) to run some functional analysis and confirm poly I:C's activity as an immunomodulator in a VHSV waterborne stimulation. Both, poly I:C as well as an injury stimulus (filtered sea water injection) accelerated the viral clearance by hemocytes and altered the expression of several immune genes, including IL-17, IRF1 and viperin.
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Affiliation(s)
- Magalí Rey-Campos
- Institute of Marine Research (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Amaro Saco
- Institute of Marine Research (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Beatriz Novoa
- Institute of Marine Research (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain.
| | - Antonio Figueras
- Institute of Marine Research (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain.
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8
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Maini Rekdal V, Villalobos-Escobedo JM, Rodriguez-Valeron N, Olaizola Garcia M, Prado Vásquez D, Rosales A, Sörensen PM, Baidoo EEK, Calheiros de Carvalho A, Riley R, Lipzen A, He G, Yan M, Haridas S, Daum C, Yoshinaga Y, Ng V, Grigoriev IV, Munk R, Wijaya CH, Nuraida L, Damayanti I, Cruz-Morales P, Keasling JD. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nat Microbiol 2024; 9:2666-2683. [PMID: 39209985 DOI: 10.1038/s41564-024-01799-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Miller Institute for Basic Research in Science, University of California Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - José Manuel Villalobos-Escobedo
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Tecnológico de Monterrey, Institute for Obesity Research, Monterrey, Nuevo León, Mexico
| | - Nabila Rodriguez-Valeron
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
- Basque Culinary Center, Mondragon Universitatea, Donostia, Gipuzkoa, Spain
| | | | - Diego Prado Vásquez
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
| | - Alexander Rosales
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Pia M Sörensen
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Calheiros de Carvalho
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rasmus Munk
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
| | - Christofora Hanny Wijaya
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Lilis Nuraida
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Isty Damayanti
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
- California Institute of Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
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9
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Tao X, Xu Z, Tian H, He J, Wang G, Tao X. Differential proteins from EVs identification based on tandem mass tags analysis and effect of Treg-derived EVs on T-lymphocytes in COPD patients. Respir Res 2024; 25:349. [PMID: 39342213 PMCID: PMC11439212 DOI: 10.1186/s12931-024-02980-2] [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: 07/10/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a widespread respiratory disease. This study examines extracellular vesicles (EVs) and proteins contained in EVs in COPD. METHODS Blood samples were collected from 40 COPD patients and 10 health controls. Cytokines including IFN-γ, TNF-α, IL-1β, IL-6, IL-8, and IL-17, were measured by ELISA. Small EVs samples were extracted from plasma and identified by transmission electron microscope (TEM), nanoparticle tracking analysis (NTA), and Western blot. Protein components contained in EVs were analyzed by Tandem Mass Tags (TMT) to identify differential proteins. Treg-derived EV was extracted and added to isolated CD8+, Treg, and Th17 subsets to assess its effect on T-lymphocytes. RESULTS ELISA revealed higher levels of all cytokines and flow cytometry suggested a higher proportion of Treg and Th17 cells in COPD patients. After identification, TMT analysis identified 207 unique protein components, including five potential COPD biomarkers: BTRC, TRIM28, CD209, NCOA3, and SSR3. Flow cytometry revealed that Treg-derived EVs inhibited differentiation into CD8+, CD4+, and Th17 cells. CONCLUSION The study shows that cytokines, T-lymphocyte subsets differences in COPD and Treg-derived EVs influence T-lymphocyte differentiation. Identified biomarkers may assist in understanding COPD pathogenesis, prognosis, and therapy. The study contributes to COPD biomarker research.
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Affiliation(s)
- Xuefang Tao
- Department of Respiratory Medicine, The Affiliated Hospital of ShaoXing University, No. 999 Zhongxing South Road, Yuecheng District, Shaoxing, Zhejiang, 312000, China
| | - Zhisong Xu
- Department of Respiratory Medicine, The Affiliated Hospital of ShaoXing University, No. 999 Zhongxing South Road, Yuecheng District, Shaoxing, Zhejiang, 312000, China
| | - Hai Tian
- Department of Basic Medicine, Medical College, Shaoxing University, No. 900 Chengnan Avenue, Yuecheng District, Shaoxing, Zhejiang, 312000, China
| | - Jingfeng He
- Department of Respiratory Medicine, The Affiliated Hospital of ShaoXing University, No. 999 Zhongxing South Road, Yuecheng District, Shaoxing, Zhejiang, 312000, China
| | - Guowen Wang
- Department of Respiratory Medicine, The Affiliated Hospital of ShaoXing University, No. 999 Zhongxing South Road, Yuecheng District, Shaoxing, Zhejiang, 312000, China
| | - Xuexia Tao
- Phase I Clinical Research Center, Hangzhou First People's Hospital of West Lake University, No. 261 Huansha Road, Hangzhou, Zhejiang, 310006, China.
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10
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Nien TS, Chan TH, Li YY, Liu TS, Shiau YJ, Ho MY. Two cyanobacterial species exhibit stress responses when grown together in visible light or far-red light. mSphere 2024; 9:e0025124. [PMID: 39120135 PMCID: PMC11423583 DOI: 10.1128/msphere.00251-24] [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: 03/25/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Although most cyanobacteria grow in visible light (VL; λ = 400-700 nm), some cyanobacteria can also use far-red light (FRL; λ = 700-800 nm) for oxygenic photosynthesis by performing far-red light photoacclimation. These two types of cyanobacteria can be found in the same environment. However, how they respond to each other remains unknown. Here, we reveal that coculture stresses FRL-using Chlorogloeopsis fritschii PCC 9212 and VL-using Synechocystis sp. PCC 6803. No significant growth difference was found in Synechocystis sp. PCC 6803 between the coculture and the monoculture. Conversely, the growth of Chlorogloeopsis fritschii PCC 9212 was suppressed in VL under coculture. According to transcriptomic analysis, Chlorogloeopsis fritschii PCC 9212 in coculture shows low transcript levels of metabolic activities and high transcript levels of ion transporters, with the differences being more noticeable in VL than in FRL. The transcript levels of stress responses in coculture were likewise higher than in monoculture in Synechocystis sp. PCC 6803 under FRL. The low transcript level of metabolic activities in coculture or the inhibition of cyanobacterial growth indicates a possible negative interaction between these two cyanobacterial strains.IMPORTANCEThe interaction between two cyanobacterial species is the primary focus of this study. One species harvests visible light, while the other can harvest far-red and visible light. Prior research on cyanobacteria interaction concentrated on its interactions with algal, coral, and fungal species. Interactions between cyanobacterial species were, nevertheless, rarely discussed. Thus, we characterized the interaction between two cyanobacterial species, one capable of photosynthesis using far-red light and the other not. Through experimental and bioinformatic approaches, we demonstrate that when one cyanobacterium thrives under optimal light conditions, it stresses the remaining cyanobacterial species. We contribute to an ecological understanding of these two kinds of cyanobacteria distribution patterns. Cyanobacteria that utilize far-red light probably disperse in environments with limited visible light to avoid competition with other cyanobacteria. From a biotechnological standpoint, this study suggests that the simultaneous cultivation of two cyanobacterial species in large-scale cultivation facilities may reduce the overall biomass yield.
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Affiliation(s)
- Ting-Shuo Nien
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Ying-Yang Li
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Ting-So Liu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yo-Jin Shiau
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Ming-Yang Ho
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
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11
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Abdel-Glil MY, Solle J, Wibberg D, Neubauer H, Sprague LD. Chromosome-level genome assembly of Tritrichomonas foetus, the causative agent of Bovine Trichomonosis. Sci Data 2024; 11:1030. [PMID: 39304666 PMCID: PMC11415386 DOI: 10.1038/s41597-024-03818-8] [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: 06/27/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024] Open
Abstract
Tritrichomonas foetus is a parasitic protist responsible for bovine trichomonosis, a reproductive disease associated with significant economic burden to the livestock industry throughout the world. Here, we present a chromosome-level reference genome of T. foetus -KV-1 (ATCC 30924) using short-read (Illumina Miseq), long-read (Oxford Nanopore) and chromatin-linked (Hi-C) sequencing. This is the first chromosome-level genome of a parasitic protist of the order Tritrichomonadida and the second within the Parabasalia lineage, after Trichomonas vaginalis, the human-associated causative agent of the sexually transmitted infection in humans. Our constructed genome is 148 Mb in size, with a N50 length of the scaffolds of 22.9 Mb. The contigs are anchored in five super-scaffolds, corresponding to the expected five chromosomes of the species and covering 78% of the genome assembly. We predict 41,341 protein-coding genes, of which 95.10% have been functionally annotated. This high-quality genome assembly serves as a valuable reference genome for T. foetus to support future studies in functional genomics, genetic conservation and taxonomy.
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Affiliation(s)
- Mostafa Y Abdel-Glil
- Friedrich-Loeffler-Institut, Institut für Bakterielle Infektionen und Zoonosen (IBIZ), Naumburger Str. 96a, 07743, Jena, Germany.
- Jena University Hospital - Friedrich Schiller University, Institute for Infectious Diseases and Infection Control, Jena, Germany.
| | - Johannes Solle
- Friedrich-Loeffler-Institut, Institut für Bakterielle Infektionen und Zoonosen (IBIZ), Naumburger Str. 96a, 07743, Jena, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615, Bielefeld, Germany
- ELIXIR DE Administration Office, Institute of Bio- and Geosciences IBG-5, Forschungszentrum Jülich GmbH - Branch office Bielefeld, Universitätsstraße 27, D-33615, Bielefeld, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institut für Bakterielle Infektionen und Zoonosen (IBIZ), Naumburger Str. 96a, 07743, Jena, Germany
| | - Lisa D Sprague
- Friedrich-Loeffler-Institut, Institut für Bakterielle Infektionen und Zoonosen (IBIZ), Naumburger Str. 96a, 07743, Jena, Germany.
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12
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Zhou J, Hu X, Zhang N, Chu Y, Wang J, Cui X, Zhang Y, Han R, Liu C, Yang S, Li J. Proteomic Analysis Reveals Differential Protein Expression in Placental Tissues of Early-Onset Preeclampsia Patients. J Proteome Res 2024. [PMID: 39287518 DOI: 10.1021/acs.jproteome.4c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Preeclampsia, a significant cause of maternal and perinatal morbidity and mortality, remains poorly understood, in terms of its pathogenesis. This study aims to uncover novel and effective biomarkers for preeclampsia by conducting a comparative analysis of differential proteins in placentas from early onset preeclampsia (EOPE) and normal pregnancies. Utilizing tandem mass tag (TMT)-based quantitative proteomics, we identified differentially expressed proteins in placental tissues from 15 EOPE patients and 15 normal pregnant women. These proteins were subsequently validated by using parallel reaction monitoring (PRM). Our analysis revealed a total of 59 differentially expressed proteins, with 25 up-regulated and 34 down-regulated proteins in EOPE placental tissues compared to those from normal pregnancies. Validation through PRM confirmed the differential expression of 6 proteins. Our findings suggest these 6 proteins could play crucial roles in the pathogenesis of EOPE, highlighting the potential involvement of the estrogen signaling pathway and dilated cardiomyopathy (DCM) pathway in the development of preeclampsia. The data were deposited with the ProteomeXchange Consortium via the iProX partner repository with the identifier PXD055025.
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Affiliation(s)
- Jun Zhou
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Xiaoyu Hu
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Ning Zhang
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Yijing Chu
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Junhuan Wang
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Xuena Cui
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Yan Zhang
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Rendong Han
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Chong Liu
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Shengmei Yang
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
| | - Jing Li
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao 266003, Shandong, China
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13
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Manjarrez LF, de María N, Vélez MD, Cabezas JA, Mancha JA, Ramos P, Pizarro A, Blanco-Urdillo E, López-Hinojosa M, Cobo-Simón I, Guevara MÁ, Díaz-Sala MC, Cervera MT. Comparative Stem Transcriptome Analysis Reveals Pathways Associated with Drought Tolerance in Maritime Pine Grafts. Int J Mol Sci 2024; 25:9926. [PMID: 39337414 PMCID: PMC11432578 DOI: 10.3390/ijms25189926] [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: 08/21/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
The maritime pine (Pinus pinaster Ait.) is a highly valuable Mediterranean conifer. However, recurrent drought events threaten its propagation and conservation. P. pinaster populations exhibit remarkable differences in drought tolerance. To explore these differences, we analyzed stem transcriptional profiles of grafts combining genotypes with contrasting drought responses under well-watered and water-stress regimes. Our analysis underscored that P. pinaster drought tolerance is mainly associated with constitutively expressed genes, which vary based on genotype provenance. However, we identified key genes encoding proteins involved in water stress response, abscisic acid signaling, and growth control including a PHD chromatin regulator, a histone deubiquitinase, the ABI5-binding protein 3, and transcription factors from Myb-related, DOF NAC and LHY families. Additionally, we identified that drought-tolerant rootstock could enhance the drought tolerance of sensitive scions by regulating the accumulation of transcripts involved in carbon mobilization, osmolyte biosynthesis, flavonoid and terpenoid metabolism, and reactive oxygen species scavenging. These included genes encoding galactinol synthase, CBL-interacting serine/threonine protein kinase 5, BEL1-like homeodomain protein, dihydroflavonol 4-reductase, and 1-deoxy-D-xylulose-5-phosphate. Our results revealed several hub genes that could help us to understand the molecular and physiological response to drought of conifers. Based on all the above, grafting with selected drought-tolerant rootstocks is a promising method for propagating elite recalcitrant conifer species, such as P. pinaster.
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Affiliation(s)
- Lorenzo Federico Manjarrez
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - Nuria de María
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - María Dolores Vélez
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - José Antonio Cabezas
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - José Antonio Mancha
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - Paula Ramos
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - Alberto Pizarro
- Departamento de Ciencias de la Vida, Universidad de Alcalá (UAH), 28805 Alcalá de Henares, Spain
| | - Endika Blanco-Urdillo
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - Miriam López-Hinojosa
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - Irene Cobo-Simón
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - María Ángeles Guevara
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
| | - María Carmen Díaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá (UAH), 28805 Alcalá de Henares, Spain
| | - María Teresa Cervera
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Consejo Superior de Investigaciones Científicas (INIA-CSIC), 28040 Madrid, Spain
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14
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Schamann A, Soukup ST, Geisen R, Kulling S, Schmidt-Heydt M. Comparative analysis of the genomes and aflatoxin production patterns of three species within the Aspergillus section Flavi reveals an undescribed chemotype and habitat-specific genetic traits. Commun Biol 2024; 7:1134. [PMID: 39271769 PMCID: PMC11399119 DOI: 10.1038/s42003-024-06738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/14/2024] [Indexed: 09/15/2024] Open
Abstract
Aflatoxins are the most dangerous mycotoxins for food safety. They are mainly produced by Aspergillus flavus, A. parasiticus, and A. minisclerotigenes. The latter, an understudied species, was the main culprit for outbreaks of fatal aflatoxicosis in Kenya in the past. To determine specific genetic characteristics of these Aspergillus species, their genomes are comparatively analyzed. Differences reflecting the typical habitat are reported, such as an increased number of carbohydrate-active enzymes, including enzymes for lignin degradation, in the genomes of A. minisclerotigenes and A. parasiticus. Further, variations within the aflatoxin gene clusters are described, which are related to different chemotypes of aflatoxin biosynthesis. These include a substitution within the aflL gene of the A. parasiticus isolate, which leads to the translation of a stop codon, thereby switching off the production of the group 1 aflatoxins B1 and G1. In addition, we demonstrate that the inability of the A. minisclerotigenes isolates to produce group G aflatoxins is associated with a 2.2 kb deletion within the aflF and aflU genes. These findings reveal a relatively high genetic homology among the three Aspergillus species investigated. However, they also demonstrate consequential genetic differences that have an important impact on risk-assessment and food safety.
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Affiliation(s)
- Alexandra Schamann
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Sebastian T Soukup
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Rolf Geisen
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Sabine Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Markus Schmidt-Heydt
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany.
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15
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Pereira S, Oliveira IB, Sousa ML, Gonçalves C, Preto M, Turkina MV, Vasconcelos V, Campos A, Almeida JR. Antifouling activity and ecotoxicological profile of the cyanobacterial oxadiazine nocuolin A. CHEMOSPHERE 2024; 365:143318. [PMID: 39271082 DOI: 10.1016/j.chemosphere.2024.143318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024]
Abstract
Pursuing effective and biocompatible natural compounds to supplant current biocidal antifouling (AF) technologies remains crucial and challenging. Among natural products hosts, cyanobacteria are recognized as producers of bioactive secondary metabolites that are underexplored in terms of anti-biofilm and AF potential. Nocuolin A, a natural oxadiazine previously isolated and known to be produced by different cyanobacterial strains, has demonstrated bioactive potential, particularly against tumor cell lines. Considering this potential and its exquisite chemical structure, here nocuolin A was investigated as a potential natural AF agent through an integrative approach including AF bioactivity testing across distinct levels of biological organization, mode of action assessment, ecotoxicity evaluation, and ecological risk predictions. Nocuolin A was found to inhibit the settlement of mussel (Mytilus galloprovincialis) plantigrades (EC50 = 3.905 μM) while showing no toxicity to this biofouling species (LC50 > 100 μM). Additionally, while exhibiting no inhibitory activity against the growth of five marine biofilm-forming bacterial strains, it significantly suppressed the growth of the marine biofilm-forming diatom Navicula sp. (EC50 = 1.561 μM), and had a lethal effect on this diatom species (>3.1 μM). The AF targets of nocuolin A on mussel plantigrades revealed no correlation with acetylcholinesterase and tyrosinase metabolic processes; however, proteins involved in oxidative stress, muscle regulation, and energy production were highlighted. The results also provide insights into the ecological risk of nocuolin A, including its ecotoxicity against Artemia salina nauplii (LC50 = 2.480 μM), Amphibalanus amphitrite nauplii (LC50 = 0.0162 μM), and Danio rerio embryos (LC50 = 0.0584 μM). When matching these results with simulated environmental values, nocuolin A was deemed a considerable threat to the ecosystems. While this research highlights the AF activity of nocuolin A, it also emphasizes the potential adverse environmental impact when applied in preventive coatings.
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Affiliation(s)
- Sandra Pereira
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal; Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Isabel B Oliveira
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Maria Lígia Sousa
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Catarina Gonçalves
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal; Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Marco Preto
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Maria V Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden.
| | - Vitor Vasconcelos
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal; Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Alexandre Campos
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Joana R Almeida
- CIIMAR- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
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16
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Low ETL, Chan KL, Zaki NM, Taranenko E, Ordway JM, Wischmeyer C, Buntjer J, Halim MAA, Sanusi NSNM, Nagappan J, Rosli R, Bondar E, Amiruddin N, Sarpan N, Ting NC, Chan PL, Ong-Abdullah M, Marjuni M, Mustaffa S, Abdullah N, Azizi N, Bacher B, Lakey N, Tatarinova TV, Manaf MAA, Sambanthamurti R, Singh R. Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae. G3 (BETHESDA, MD.) 2024; 14:jkae135. [PMID: 38918881 PMCID: PMC11373658 DOI: 10.1093/g3journal/jkae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 04/18/2023] [Accepted: 05/16/2024] [Indexed: 06/27/2024]
Abstract
Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.
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Affiliation(s)
- Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Noorhariza Mohd Zaki
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | | | - Jared M Ordway
- Orion Genomics, 3730 Foundry Way, St. Louis, MO 63110, USA
| | | | - Jaap Buntjer
- Orion Genomics, 3730 Foundry Way, St. Louis, MO 63110, USA
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Jayanthi Nagappan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eugeniya Bondar
- Biology Department, University of La Verne, La Verne, CA 91750, USA
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Ngoot-Chin Ting
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Marhalil Marjuni
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Suzana Mustaffa
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norziha Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Blaire Bacher
- Orion Genomics, 3730 Foundry Way, St. Louis, MO 63110, USA
| | - Nathan Lakey
- Orion Genomics, 3730 Foundry Way, St. Louis, MO 63110, USA
| | | | - Mohamad Arif Abd Manaf
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Ravigadevi Sambanthamurti
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
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Dittmann MA, Buczkowski G, Scharf M, Harpur BA. Comparative transcriptomics and phylostratigraphy of Argentine ant odorant receptors. PLoS One 2024; 19:e0307604. [PMID: 39226298 PMCID: PMC11371221 DOI: 10.1371/journal.pone.0307604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 07/09/2024] [Indexed: 09/05/2024] Open
Abstract
Nestmate recognition in ants is regulated through the detection of cuticular hydrocarbons by odorant receptors (ORs) in the antennae. These ORs are crucial for maintaining colony cohesion that allows invasive ant species to dominate colonized environments. In the invasive Argentine ant, Linepithema humile, ORs regulating nestmate recognition are thought to be present in a clade of nine-exon odorant receptors, but the identity of the specific genes remains unknown. We sought to narrow down the list of candidate genes using transcriptomics and phylostratigraphy. Comparative transcriptomic analyses were conducted on the antennae, head, thorax, and legs of Argentine ant workers. We have identified a set of twenty-one nine-exon odorant receptors enriched in the antennae compared to the other tissues, allowing for downstream verification of whether they can detect Argentine ant cuticular hydrocarbons. Further investigation of these ORs could allow us to further understand the mechanisms underlying nestmate recognition and colony cohesion in ants.
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Affiliation(s)
- Mathew A. Dittmann
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Grzegorz Buczkowski
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Michael Scharf
- University of Florida, Gainesville, FL, United States of America
| | - Brock A. Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
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18
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Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC, Torres MP. Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J 2024; 123:2790-2806. [PMID: 38297834 PMCID: PMC11393682 DOI: 10.1016/j.bpj.2024.01.029] [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: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the β-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of β hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial β-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.
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Affiliation(s)
- Vardhan Satalkar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Gemechis D Degaga
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Wei Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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Vanamamalai VK, Priyanka E, Kannaki TR, Sharma S. Integrative study of chicken lung transcriptome to understand the host immune response during Newcastle disease virus challenge. Front Cell Infect Microbiol 2024; 14:1368887. [PMID: 39290979 PMCID: PMC11405381 DOI: 10.3389/fcimb.2024.1368887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 08/01/2024] [Indexed: 09/19/2024] Open
Abstract
Introduction Newcastle disease is one of the significant issues in the poultry industry, having catastrophic effects worldwide. The lung is one of the essential organs which harbours Bronchus-associated lymphoid tissue and plays a vital role in the immune response. Leghorn and Fayoumi breeds are known to have differences in resistance to Newcastle disease. Along with genes and long non-coding RNAs (lncRNAs) are also known to regulate various biological pathways through gene regulation. Methods This study analysed the lung transcriptome data and identified the role of genes and long non-coding RNAs in differential immune resistance. The computational pipeline, FHSpipe, as used in our previous studies on analysis of harderian gland and trachea transcriptome was used to identify genes and lncRNAs. This was followed by differential expression analysis, functional annotation of genes and lncRNAs, identification of transcription factors, microRNAs and finally validation using qRT-PCR. Results and discussion A total of 8219 novel lncRNAs were identified. Of them, 1263 lncRNAs and 281 genes were differentially expressed. About 66 genes were annotated with either an immune-related GO term or pathway, and 12 were annotated with both. In challenge and breed-based analysis, most of these genes were upregulated in Fayoumi compared to Leghorn, and in timepoint-based analysis, Leghorn challenge chicken showed downregulation between time points. A similar trend was observed in the expression of lncRNAs. Co-expression analysis has revealed several lncRNAs co-expressing with immune genes with a positive correlation. Several genes annotated with non-immune pathways, including metabolism, signal transduction, transport of small molecules, extracellular matrix organization, developmental biology and cellular processes, were also impacted. With this, we can understand that Fayoumi chicken showed upregulated immune genes and positive cis-lncRNAs during both the non-challenged and NDV-challenge conditions, even without viral transcripts in the tissue. This finding shows that these immune-annotated genes and coexpressing cis-lncRNAs play a significant role in Fayoumi being comparatively resistant to NDV compared to Leghorn. Our study affirms and expands upon the outcomes of previous studies and highlights the crucial role of lncRNAs during the immune response to NDV. Conclusion This analysis clearly shows the differences in the gene expression patterns and lncRNA co-expression with the genes between Leghorn and Fayoumi, indicating that the lncRNAs and co-expressing genes might potentially have a role in differentiating these breeds. We hypothesise that these genes and lncRNAs play a vital role in the higher resistance of Fayoumi to NDV than Leghorn. This study can pave the way for future studies to unravel the biological mechanism behind the regulation of immune-related genes.
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Affiliation(s)
- Venkata Krishna Vanamamalai
- Bioinformatics Laboratory, DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, Haryana, India
| | - E Priyanka
- Laboratory of Avian Health and Pathology, ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India
| | - T R Kannaki
- Laboratory of Avian Health and Pathology, ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India
| | - Shailesh Sharma
- Bioinformatics Laboratory, DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, Haryana, India
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20
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Chen Y, Tang X, Fei Z, Giovannoni JJ. Fruit ripening and postharvest changes in very early-harvested tomatoes. HORTICULTURE RESEARCH 2024; 11:uhae199. [PMID: 39263630 PMCID: PMC11387008 DOI: 10.1093/hr/uhae199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/10/2024] [Indexed: 09/13/2024]
Abstract
It is well known that if a fruit is harvested extremely early its development and function are interrupted, and it may never attain full maturity and optimal quality. Reports revealing insights regarding the alterations of maturation, ripening and postharvest quality in very early picked fruits are rare. We examined the effects of early harvesting on tomatoes by characterizing different accessions at the molecular, physiological, and biochemical levels. We found that even very early-harvested fruits could achieve postharvest maturation and ripening though with some defects in pigment and cuticle formation, and seeds from very early-harvested fruits could still germinate and develop as normal and healthy plants. One critical regulator of tomato cuticle integrity, SlCER1-2, was shown to contribute to cuticle defects in very early-harvested fruits. Very early fruit harvest still allowing ripening and seed development indicate that the genetic and physiological programs of later maturation and ripening are set into motion early in fruit development and are not dependent on complete fruit expansion nor attachment to the plant.
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Affiliation(s)
- Yao Chen
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853
| | - Xuemei Tang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853
- US Department of Agriculture-Agricultural Research Service Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- US Department of Agriculture-Agricultural Research Service Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853
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21
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Rodrigues MV, de França DA, Rossini BC, da Silva RJ, Júnior JPA. Pathogenesis of Experimental Infection of Nile Tilapia (Oreochromis niloticus) with Nucleospora Braziliensis Pathology and Proteomic of Microsporidia. Acta Parasitol 2024; 69:1661-1673. [PMID: 39162926 DOI: 10.1007/s11686-024-00889-w] [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: 01/24/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024]
Abstract
The recent discovery of disease caused by Nucleospora braziliensis in Nile tilapia (Oreochromis niloticus) is important as it has highlighted the high prevalence of infection and associated mortality in cultured fish. Thus, this study conducted an experimental infection of this microsporidium to evaluate pathological alterations and conduct proteomic analysis. For pathological observation, samples of brain, eyes, gall bladder, gut, heart, kidney, liver, muscle, skin, spleen, and stomach tissue, were collected, and liquid chromatography-mass spectrometry (LC-MS/MS) was performed for proteomic analysis. The most prevalent lesions were brownish color of the liver, gill filament fusion, gut ischemia, hemorrhage of the lips and fins, hepatomegaly, spleen atrophy, splenomegaly, and stomach congestion. The most common microscopic lesions were degeneration, hemorrhage, and inflammation in the brain, gills, gut, kidney, liver, muscle, spleen, and stomach. The digested peptides were identified by LC-MS/MS and the intersection of each group showed that in the spleen there were 121 exclusive proteins in the infected sample and 252 in the control, while in the kidney, 129 proteins were identified in the infected specimen compared to 83 in the control. In conclusion, this study demonstrates the proteome profile of O. niloticus kidney and spleen tissue in response to infection with N. braziliensis.
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Affiliation(s)
| | - Danilo Alves de França
- Department of Veterinary Hygiene and Public Health, São Paulo State University (UNESP), São Paulo, Brazil
| | - Bruno Cesar Rossini
- Biotechnology Institute, São Paulo State University (UNESP), São Paulo, Brazil
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22
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Baytar AA, Yanar EG, Frary A, Doğanlar S. Association mapping and candidate gene identification for yield traits in European hazelnut ( Corylus avellana L.). PLANT DIRECT 2024; 8:e625. [PMID: 39170862 PMCID: PMC11336203 DOI: 10.1002/pld3.625] [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: 02/12/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/23/2024]
Abstract
European hazelnut (Corylus avellana L.) is an important nut crop due to its nutritional benefits, culinary uses, and economic value. Türkiye is the leading producer of hazelnut, followed by Italy and the United States. Quantitative trait locus studies offer promising opportunities for breeders and geneticists to identify genomic regions controlling desirable traits in hazelnut. A genome-wide association analysis was conducted with 5,567 single nucleotide polymorphisms on a Turkish core set of 86 hazelnut accessions, revealing 189 quantitative trait nucleotides (QTNs) associated with 22 of 31 traits (p < 2.9E-07). These QTNs were associated with plant and leaf, phenological, reproductive, nut, and kernel traits. Based on the close physical distance of QTNs associated with the same trait, we identified 23 quantitative trait loci. Furthermore, we identified 23 loci of multiple QTs comprising chromosome locations associated with more than one trait at the same position or in close proximity. A total of 159 candidate genes were identified for 189 QTNs, with 122 of them containing significant conserved protein domains. Some candidate matches to known proteins/domains were highly significant, suggesting that they have similar functions as their matches. This comprehensive study provides valuable insights for the development of breeding strategies and the improvement of hazelnut and enhances the understanding of the genetic architecture of complex traits by proposing candidate genes and potential functions.
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Affiliation(s)
- Asena Akköse Baytar
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
| | - Ertuğrul Gazi Yanar
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
| | - Anne Frary
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
| | - Sami Doğanlar
- Department of Molecular Biology and Genetics, Faculty of ScienceIzmir Institute of TechnologyIzmirTürkiye
- Plant Science and Technology Application and Research CenterIzmir Institute of TechnologyIzmirTürkiye
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23
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Zhao N, Li K, Ma H, Hu L, Yang Y, Liu L. Molecular Characterization of Odorant-Binding Protein Genes Associated with Host-Seeking Behavior in Oides leucomelaena. Int J Mol Sci 2024; 25:9436. [PMID: 39273382 PMCID: PMC11394801 DOI: 10.3390/ijms25179436] [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: 08/06/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
The identification of odorant-binding proteins (OBPs) involved in host location by Oides leucomelaena (O. leucomelaena Weise, 1922, Coleoptera, Galerucinae) is significant for its biological control. Tools in the NCBI database were used to compare and analyze the transcriptome sequences of O. leucomelaena with OBP and other chemosensory-related proteins of other Coleoptera insects. Subsequently, MEGA7 was utilized for OBP sequence alignment and the construction of a phylogenetic tree, combined with expression profiling to screen for candidate antennae-specific OBPs. In addition, fumigation experiments with star anise volatiles were conducted to assess the antennae specificity of the candidate OBPs. Finally, molecular docking was employed to speculate on the binding potential of antennae-specific OBPs with star anise volatiles. The study identified 42 candidate OBPs, 8 chemosensory proteins and 27 receptors. OleuOBP3, OleuOBP5, and OleuOBP6 were identified as classic OBP family members specific to the antennae, which was confirmed by volatile fumigation experiments. Molecular docking ultimately clarified that OleuOBP3, OleuOBP5, and OleuOBP6 all exhibit a high affinity for β-caryophyllene among the star anise volatiles. We successfully obtained three antennae-specific OBPs from O. leucomelaena and determined their high-affinity volatiles, providing a theoretical basis for the development of attractants in subsequent stages.
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Affiliation(s)
- Ning Zhao
- College of Biological Science and Food Engineering, Southwest Forestry University, Kunming 650224, China
| | - Kai Li
- College of Biological Science and Food Engineering, Southwest Forestry University, Kunming 650224, China
| | - Huifen Ma
- Yunnan Academy of Forestry and Grassland, Kunming 650224, China
| | - Lianrong Hu
- Yunnan Academy of Forestry and Grassland, Kunming 650224, China
| | - Yingxue Yang
- College of Biological Science and Food Engineering, Southwest Forestry University, Kunming 650224, China
| | - Ling Liu
- Yunnan Academy of Forestry and Grassland, Kunming 650224, China
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24
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Wang Y, Wang H, Song H. Transcriptome data for an ancient 'living-fossil' mollusc, Entemnotrochus rumphii. Sci Data 2024; 11:919. [PMID: 39181877 PMCID: PMC11344847 DOI: 10.1038/s41597-024-03700-7] [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: 04/19/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
The Pleurotomarioidea, commonly referred to as slit shells, constitute one of the most ancient and enduring lineages within the phylum Mollusca, with its fossil record tracing back to the Upper Cambrian epoch. Its rareness and evolutionary antiquity surpass even that of the nautilus. In this study, we conducted the first transcriptome sequencing and analyses of Entemnotrochus rumphii (Schepman, 1879), a representative species of Pleurotomarioidea. Full-length transcriptome sequencing of E. rumphii was performed using the PacBio Sequel II platform with SMRT technology. A total of 64.38 gigabytes of data and 964,550 polymerase reads were generated, resulting in 28,068,998 subreads after data filtering. After de-duplication, correction, and clustering, we identified 19,273 genes. Additionally, next-generation sequencing was performed on 11 tissues of E. rumphii. This investigation provides a detailed portrayal and analytical scrutiny of its transcriptomic landscape.
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Affiliation(s)
- Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Haiyan Wang
- Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 101400, China.
| | - Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China.
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 101400, China.
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25
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Marques J, Seabra SG, Almeida I, Gomes J, Alves AC, Silveira H. Long-term blood-free rearing of Anopheles mosquitoes with no effect on fitness, Plasmodium infectivity nor microbiota composition. Sci Rep 2024; 14:19473. [PMID: 39174598 PMCID: PMC11341565 DOI: 10.1038/s41598-024-70090-6] [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: 04/04/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
Mosquito-borne diseases kill millions of people each year. Therefore, many innovative research and population control strategies are being implemented but, most of them require large-scale production of mosquitoes. Mosquito rearing depends on fresh blood from human donors, experimentation animals or slaughterhouses, which constitutes a strong drawback since high blood quantities are needed, raising ethical and financial constraints. To eliminate blood dependency and the use of experimentation animals, we previously developed BLOODless, a patented diet that represents an important advance towards sustainable mosquito breeding in captivity. BLOODless diet was used to maintain a colony of Anopheles stephensi for 40 generations. Bloodmeal appetite, fitness, Plasmodium berghei infectivity, whole genome sequencing and microbiota were evaluated over time. Here we show that BLOODless can be implemented in Anopheles insectaries since it allows long-term rearing of mosquitoes in captivity, without a detectable effect on their fitness, infectivity, nor on their midgut and salivary microbiota composition.
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Affiliation(s)
- Joana Marques
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, IHMT-NOVA, Rua da Junqueira 100, 1349-008, Lisboa, Portugal.
| | - Sofia G Seabra
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, IHMT-NOVA, Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - Inês Almeida
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, IHMT-NOVA, Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - Joana Gomes
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, IHMT-NOVA, Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - Ana Catarina Alves
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, IHMT-NOVA, Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - Henrique Silveira
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, IHMT-NOVA, Rua da Junqueira 100, 1349-008, Lisboa, Portugal.
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26
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Yue L, Wang Y, Wang C, Niu S, Dong X, Guan Y, Chen S. Empagliflozin improves aortic injury in obese mice by regulating fatty acid metabolism. Open Med (Wars) 2024; 19:20241012. [PMID: 39176252 PMCID: PMC11340858 DOI: 10.1515/med-2024-1012] [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: 02/18/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024] Open
Abstract
Background Empagliflozin has been shown in clinical studies to lower the risk of adverse cardiovascular events. Using proteomics, the current study aims to determine whether empagliflozin reduces aortic alterations in obese mice and to investigate its molecular mechanism of action. Methods We constructed obese mice and then treated them with empagliflozin. Changes in the weight of the mice were recorded. Blood glucose and lipid levels were measured in each group of mice, and changes in pulse wave velocity and aortic structure were recorded. In addition, changes in aortic protein expression were detected by proteomics and analyzed bioinformatically. Results Proteomics results showed that 507 differentially expressed proteins (DEPs) were identified in the comparison of normal and obese mice, while 90 DEPs were identified in the comparison of obese and empagliflozin-treated mice. Examination of these three groups revealed that DEPs were largely associated with the digestion of unsaturated fats. Among them, empagliflozin significantly reduced the expression of fatty acid synthase (FASN), acyl-CoA desaturase 3 (SCD3), ACSL1. and ACSL5 in the aorta of obesity-induced mice, and there was a close relationship between the four. Conclusion Empagliflozin reduced the protein expression of FASN, SCD3, ACSL1, and ACSL5 in the aorta of obese mice and improved aortic fatty acid metabolism and reduced vascular stiffness for vasoprotective effects.
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Affiliation(s)
- Lin Yue
- Department of Endocrinology, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, P.R. China
| | - Yue Wang
- Department of Ultrasonography, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, P.R. China
| | - Cuiying Wang
- Department of Endocrinology, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, P.R. China
| | - Shu Niu
- Department of Endocrinology, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, 050000, P.R. China
| | - Xihong Dong
- Department of Endocrinology, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, P.R. China
| | - Yaqing Guan
- Department of Endocrinology, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, P.R. China
| | - Shuchun Chen
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, Hebei, 050000, P.R. China
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Vela S, Wolf ESA, Rollins JA, Cuevas HE, Vermerris W. Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1437344. [PMID: 39220294 PMCID: PMC11362643 DOI: 10.3389/ffunb.2024.1437344] [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: 05/23/2024] [Accepted: 07/19/2024] [Indexed: 09/04/2024]
Abstract
In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen Colletotrichum sublineola, the causal agent of anthracnose, a problematic disease of sorghum (Sorghum bicolor (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum-C. sublineola interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and C. sublineola can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with C. sublineola. Approximately 0.3% and 93% of the reads mapped to the genomes of C. sublineola and Sorghum bicolor, respectively. Expression profiling of in vitro versus in planta C. sublineola at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by C. sublineola were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of C. sublineola but also supports the long-term goal of developing resistant sorghum cultivars.
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Affiliation(s)
- Saddie Vela
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Emily S. A. Wolf
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Jeffrey A. Rollins
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Hugo E. Cuevas
- United States Department of Agriculture, Agricultural Research Service, Tropical Agriculture Research Station, Mayagüez, PR, United States
| | - Wilfred Vermerris
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL, United States
- University of Florida Genetics Institute, Gainesville, FL, United States
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Fischer ML, Schmidtberg H, Tidswell O, Weiss B, Dersch L, Lüddecke T, Wielsch N, Kaltenpoth M, Vilcinskas A, Vogel H. Divergent venom effectors correlate with ecological niche in neuropteran predators. Commun Biol 2024; 7:981. [PMID: 39134630 PMCID: PMC11319779 DOI: 10.1038/s42003-024-06666-9] [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: 04/11/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Neuropteran larvae are fierce predators that use venom to attack and feed on arthropod prey. Neuropterans have adapted to diverse and sometimes extreme habitats, suggesting their venom may have evolved accordingly, but the ecology and evolution of venom deployment in different families is poorly understood. We applied spatial transcriptomics, proteomics, morphological analysis, and bioassays to investigate the venom systems in the antlion Euroleon nostras and the lacewing Chrysoperla carnea, which occupy distinct niches. Although the venom system morphology was similar in both species, we observed remarkable differences at the molecular level. E. nostras produces particularly complex venom secreted from three different glands, indicating functional compartmentalization. Furthermore, E. nostras venom and digestive tissues were devoid of bacteria, strongly suggesting that all venom proteins are of insect origin rather than the products of bacterial symbionts. We identified several toxins exclusive to E. nostras venom, including phospholipase A2 and several undescribed proteins with no homologs in the C. carnea genome. The compositional differences have significant ecological implications because only antlion venom conferred insecticidal activity, indicating its use for the immobilization of large prey. Our results indicate that molecular venom evolution plays a role in the adaptation of antlions to their unique ecological niche.
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Affiliation(s)
- Maike Laura Fischer
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Henrike Schmidtberg
- Institute for Insect Biotechnology, Justus Liebig University, Giessen, Germany
| | - Olivia Tidswell
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Benjamin Weiss
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ludwig Dersch
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Tim Lüddecke
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Natalie Wielsch
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University, Giessen, Germany
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Heiko Vogel
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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Fernandes P, Pimentel D, Ramiro RS, Silva MDC, Fevereiro P, Costa RL. Dual transcriptomic analysis reveals early induced Castanea defense-related genes and Phytophthora cinnamomi effectors. FRONTIERS IN PLANT SCIENCE 2024; 15:1439380. [PMID: 39188543 PMCID: PMC11345161 DOI: 10.3389/fpls.2024.1439380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/05/2024] [Indexed: 08/28/2024]
Abstract
Phytophthora cinnamomi Rands devastates forest species worldwide, causing significant ecological and economic impacts. The European chestnut (Castanea sativa) is susceptible to this hemibiotrophic oomycete, whereas the Asian chestnuts (Castanea crenata and Castanea mollissima) are resistant and have been successfully used as resistance donors in breeding programs. The molecular mechanisms underlying the different disease outcomes among chestnut species are a key foundation for developing science-based control strategies. However, these are still poorly understood. Dual RNA sequencing was performed in C. sativa and C. crenata roots inoculated with P. cinnamomi. The studied time points represent the pathogen's hemibiotrophic lifestyle previously described at the cellular level. Phytophthora cinnamomi expressed several genes related to pathogenicity in both chestnut species, such as cell wall-degrading enzymes, host nutrient uptake transporters, and effectors. However, the expression of effectors related to the modulation of host programmed cell death (elicitins and NLPs) and sporulation-related genes was higher in the susceptible chestnut. After pathogen inoculation, 1,556 and 488 genes were differentially expressed by C. crenata and C. sativa, respectively. The most significant transcriptional changes occur at 2 h after inoculation (hai) in C. sativa and 48 hai in C. crenata. Nevertheless, C. crenata induced more defense-related genes, indicating that the resistant response to P. cinnamomi is controlled by multiple loci, including several pattern recognition receptors, genes involved in the phenylpropanoid, salicylic acid and ethylene/jasmonic acid pathways, and antifungal genes. Importantly, these results validate previously observed cellular responses for C. crenata. Collectively, this study provides a comprehensive time-resolved description of the chestnut-P. cinnamomi dynamic, revealing new insights into susceptible and resistant host responses and important pathogen strategies involved in disease development.
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Affiliation(s)
- Patrícia Fernandes
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Diana Pimentel
- InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
| | | | - Maria do Céu Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Fevereiro
- InnovPlantProtect Collaborative Laboratory, Elvas, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB, Green-It Unit), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Rita Lourenço Costa
- Instituto Nacional de Investigação Agrária e Veterinária I.P., Oeiras, Portugal
- Centro de Estudos Florestais, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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Huerlimann R, Roux N, Maeda K, Pilieva P, Miura S, Chen HC, Izumiyama M, Laudet V, Ravasi T. The transcriptional landscape underlying larval development and metamorphosis in the Malabar grouper ( Epinephelus malabaricus). eLife 2024; 13:RP94573. [PMID: 39120998 PMCID: PMC11315451 DOI: 10.7554/elife.94573] [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] [Indexed: 08/11/2024] Open
Abstract
Most teleost fishes exhibit a biphasic life history with a larval oceanic phase that is transformed into morphologically and physiologically different demersal, benthic, or pelagic juveniles. This process of transformation is characterized by a myriad of hormone-induced changes, during the often abrupt transition between larval and juvenile phases called metamorphosis. Thyroid hormones (TH) are known to be instrumental in triggering and coordinating this transformation but other hormonal systems such as corticoids, might be also involved as it is the case in amphibians. In order to investigate the potential involvement of these two hormonal pathways in marine fish post-embryonic development, we used the Malabar grouper (Epinephelus malabaricus) as a model system. We assembled a chromosome-scale genome sequence and conducted a transcriptomic analysis of nine larval developmental stages. We studied the expression patterns of genes involved in TH and corticoid pathways, as well as four biological processes known to be regulated by TH in other teleost species: ossification, pigmentation, visual perception, and metabolism. Surprisingly, we observed an activation of many of the same pathways involved in metamorphosis also at an early stage of the larval development, suggesting an additional implication of these pathways in the formation of early larval features. Overall, our data brings new evidence to the controversial interplay between corticoids and thyroid hormones during metamorphosis as well as, surprisingly, during the early larval development. Further experiments will be needed to investigate the precise role of both pathways during these two distinct periods and whether an early activation of both corticoid and TH pathways occurs in other teleost species.
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Affiliation(s)
- Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook UniversityTownsvilleAustralia
| | - Natacha Roux
- Computational Neuroethology Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
| | - Ken Maeda
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
| | - Polina Pilieva
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
| | - Saori Miura
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
| | - Hsiao-chian Chen
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaJiau ShiTaiwan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate UniversityOnna-sonJapan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleAustralia
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Aarthi N, Dubey VK, Shylesha AN, Kukreti A, Patil J, Chandrashekara KM, Aravindaram K, Seegenahalli R, Shivakumar N, Channappa M. Insights into the whole genome sequence of Bacillus thuringiensis NBAIR BtPl, a strain toxic to the melon fruit fly, Zeugodacus cucurbitae. Curr Genet 2024; 70:13. [PMID: 39101952 DOI: 10.1007/s00294-024-01298-2] [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: 05/10/2024] [Revised: 07/16/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024]
Abstract
Bacillus thuringiensis is the most widely used biopesticide, targets a diversity of insect pests belonging to several orders. However, information regarding the B. thuringiensis strains and toxins targeting Zeugodacus cucurbitae is very limited. Therefore, in the present study, we isolated and identified five indigenous B. thuringiensisstrains toxic to larvae of Z. cucurbitae. However, of five strains NBAIR BtPl displayed the highest mortality (LC50 = 37.3 μg/mL) than reference strain B. thuringiensis var. israelensis (4Q1) (LC50 = 45.41 μg/mL). Therefore, the NBAIR BtPl was considered for whole genome sequencing to identify the cry genes present in it. Whole genome sequencing of our strain revealed genome size of 6.87 Mb with 34.95% GC content. Homology search through the BLAST algorithm revealed that NBAIR BtPl is 99.8% similar to B. thuringiensis serovar tolworthi, and gene prediction through Prokka revealed 7406 genes, 7168 proteins, 5 rRNAs, and 66 tRNAs. BtToxin_Digger analysis of NBAIR BtPl genome revealed four cry gene families: cry1, cry2, cry8Aa1, and cry70Aa1. When tested for the presence of these four cry genes in other indigenous strains, results showed that cry70Aa1 was absent. Thus, the study provided a basis for predicting cry70Aa1 be the possible reason for toxicity. In this study apart from novel genes, we also identified other virulent genes encoding zwittermicin, chitinase, fengycin, and bacillibactin. Thus, the current study aids in predicting potential toxin-encoding genes responsible for toxicity to Z. cucurbitae and thus paves the way for the development of B. thuringiensis-based formulations and transgenic crops for management of dipteran pests.
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Affiliation(s)
- Nekkanti Aarthi
- Department of Entomology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, 492 012, India
| | - Vinod K Dubey
- Department of Entomology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, 492 012, India
| | - Arakalagud N Shylesha
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Aditya Kukreti
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Jagadeesh Patil
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Keerthi M Chandrashekara
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, 560 089, India
| | - Kandan Aravindaram
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Ruqiya Seegenahalli
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Nanditha Shivakumar
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India
| | - Manjunatha Channappa
- Insect Bacteriology Laboratory, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560 024, India.
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Yang J, Luo W, Geng Y, Wei H, Wang J, Gao M, Tang J, Li M, Wang Y, Yan X. SSR Marker Acquisition and Application from Transcriptome of Captive Chinese Forest Musk Deer (Moschus berezovskii). Biochem Genet 2024; 62:3215-3230. [PMID: 38095737 DOI: 10.1007/s10528-023-10595-3] [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: 12/01/2022] [Accepted: 11/08/2023] [Indexed: 07/31/2024]
Abstract
Forest musk deer (Moschus berezovskii) is one of the most endangered medicinally important wild animals in the world. Forest musk deer farming is the main way of production of musk. However, the single provenance and lack of genetic information lead to reduced genetic diversity of forest musk deer. Therefore, more SSR markers need to be developed to identify forest musk deer germplasm. In this study, bone marrow derived mesenchymal cells were used to construct cDNA library for transcriptome sequencing. The datasets were de novo assembled and annotated. 9 polymorphic simple sequence repeat (SSR) markers were finally identified and used to detect population genetic diversity. 6.07 Gb clean data were generated using Illumina sequencing technology, and de novo assembled into 138,591 transcripts and 81,553 unigenes. 5,777 simple sequence repeats (SSRs) were identified, in which there were 578 repeating motif types, with mono-nucleotide and tri-nucleotides comprising 55.88% and 25.60%, respectively. 100 primer pairs were designed to validate amplification and polymorphism using DNA from fecal samples. 9 polymorphic SSRs were developed and used to detect population genetic diversity of 122 forest musk deer in 2 farms. The average number of alleles per locus varied from 4 to 15 (average = 8.3). The observed heterozygosity (HO) per locus ranged from 0.102 to 0.941, while the expected heterozygosity (HE) per locus was from 0.111 to 0.651. All loci deviated significantly from the Hardy-Weinberg equilibrium (p < 0.001). The polymorphism information content (PIC) of these loci varied from 0.108 to 0.619. 9 polymorphic SSR markers were developed in this research. These sites can be used for breeding planning and conservation of germplasm resources.
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Affiliation(s)
- Jing Yang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Weiqiang Luo
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Yangyang Geng
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Hao Wei
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Junjian Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Mengxi Gao
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Jie Tang
- Northwest Institute of Endangered Zoological Species, Shaanxi Institute of Zoology, 710032, Xi'an, China
| | - Mengyu Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China
| | - Yan Wang
- Northwest Institute of Endangered Zoological Species, Shaanxi Institute of Zoology, 710032, Xi'an, China.
| | - Xingrong Yan
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, 710069, Xi'an, China.
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Nguyen HTT, Zhao M, Wang T, Dang BT, Geffen AJ, Cummins SF. Sea anemone-anemonefish symbiosis: Behavior and mucous protein profiling. JOURNAL OF FISH BIOLOGY 2024; 105:603-618. [PMID: 38747400 DOI: 10.1111/jfb.15772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 08/20/2024]
Abstract
Fish species of the genus Amphiprion (Perciformes: Pomacentridae) seek protection from predators among the tentacles of sea anemones as their natural habitat, where they live essentially unharmed from stinging by the host's nematocysts. The skin mucus of these anemonefish has been suggested as a protective mechanism that prevents the discharge of the nematocysts upon contact. Whereas some anemonefish species seem to produce their own protective mucous coating, others may acquire mucus (or biomolecules within) from the sea anemone during an acclimation period. In controlled experiments, we show that Amphiprion ocellaris acclimated successfully to their natural host anemone species Stichodactyla gigantea, and also to Stichodactyla haddoni, and in some cases Heteractis crispa, neither of which are natural host species. No symbiosis was observed for three other anemone species tested, Entacmaea quadricolor, Macrodactyla doreensis, and Heteractis malu. We explored the skin mucous protein profile from naive and experienced A. ocellaris during their acclimation to natural and unnatural host anemones. We confidently report the presence of metabolic and structural proteins in the skin mucus of all samples, likely involved in immunological defense, molecular transport, stress response, and signal transduction. For those anemonefish that established symbiosis, there was a clear increase in ribosomal-type proteins. We additionally provide evidence for the presence of anemone proteins only in the skin mucus of individuals that established symbiosis. Our results support previous speculation of the role of skin mucous-associated proteins in anemonefish-anemone symbiosis. Further exploration of these mucosal proteins could reveal the mechanism of anemonefish acclimation to host anemones.
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Affiliation(s)
- Hai-Thanh T Nguyen
- Biotechnology Department, Institute for Biotechnology and Environment, Nha Trang University, Nha Trang City, Vietnam
| | - Min Zhao
- Biotechnology Deparment, Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Tianfang Wang
- Biotechnology Deparment, Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Binh T Dang
- Biotechnology Department, Institute for Biotechnology and Environment, Nha Trang University, Nha Trang City, Vietnam
| | - Audrey J Geffen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Life Sciences, Imperial College London, London, UK
| | - Scott F Cummins
- Biotechnology Deparment, Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
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Rashid MHU, Yi EKJ, Amin NDM, Ismail MN. An Empirical Analysis of Sacha Inchi (Plantae: Plukenetia volubilis L.) Seed Proteins and Their Applications in the Food and Biopharmaceutical Industries. Appl Biochem Biotechnol 2024; 196:4823-4836. [PMID: 37979081 DOI: 10.1007/s12010-023-04783-5] [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] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Sacha Inchi (Plukenetia volubilis L.) is a plant native in the Amazon rainforest in South America known for its edible seeds, which are rich in lipids, proteins, vitamin E, polyphenols, minerals, and amino acids. Rural communities in developing nations have been using this plant for its health benefits, including as a topical cream for rejuvenating and revitalising skin and as a treatment for muscle pain and rheumatism. Although Sacha Inchi oil has been applied topically to soften skin, treat skin diseases, and heal wounds, its protein-rich seeds have not yet received proper attention for extensive investigation. Proteins in Sacha Inchi seeds are generally known to have antioxidant and antifungal activities and are extensively used nowadays in making protein-rich food alternatives worldwide. Notably, large-scale use of seed proteins has begun in nanoparticle and biofusion technologies related to the human health-benefitting sector. To extract and identify their proteins, the current study examined Sacha Inchi seeds collected from the Malaysian state of Kedah. Our analysis revealed a protein concentration of 73.8 ± 0.002 mg/g of freeze-dried seed flour. Employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) and PEAKS studio analysis, we identified 217 proteins in the seed extract, including 152 with known proteins and 65 unknown proteins. This study marks a significant step towards comprehensively investigating the protein composition of Sacha Inchi seeds and elucidating their potential applications in the food and biopharmaceutical sectors. Our discoveries not only enhance our knowledge of Sacha Inchi's nutritional characteristics but also pave the way for prospective research and innovative advancements in the realms of functional food and health-related domains.
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Affiliation(s)
- Mohammad Harun Ur Rashid
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11900, Penang, Malaysia
| | - Erica Kok Jia Yi
- International Medical University Malaysia, Kuala Lumpur, Malaysia
| | - Nor Datiakma Mat Amin
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11900, Penang, Malaysia
- Natural Products Division, Forest Research Institute of Malaysia (FRIM), 52109, Kepong, Selangor, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia (USM), 11900, Penang, Malaysia.
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia (USM), 11800, Penang, Malaysia.
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35
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Heckmann A, Perochon A, Doohan FM. Genome-wide analysis of salicylic acid and jasmonic acid signalling marker gene families in wheat. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:691-704. [PMID: 38864777 DOI: 10.1111/plb.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Jasmonic acid (JA) and salicylic acid (SA) phytohormone pathways are important regulators of stress tolerance. Knowledge regarding the diversity, phylogeny and functionality of wheat genes involved in JA and SA response is limited. Using Arabidopsis, rice and wheat genomic and wheat disease transcriptomic data, we deduced the size, phylogenetic diversity and pathogen-responsiveness of seven hormone-responsive gene families, and thus selected 14 candidates as potential hormone responsive gene markers. Gene-specific expression studies assessed the impact of exogenous JA and SA on their transcriptional activation in leaves of two distinct wheat cultivars. RNAseq data were interrogated to assess their disease responsiveness and tissue-specific expression. This study elucidated the number, phylogeny and pathogen-responsiveness of wheat genes from seven families, including 12 TaAOS, 6 TaJAMyb, 256 TaWRKY group III, 85 TaPR1, 205 TaPR2, 76 TaPR3 and 124 TaPR5. This included the first description of the wheat AOS, JAMyb, PR2, PR3 and PR5 gene families. Gene expression studies delineated TaAOS1-5B and TaJAMyb-4A as JA-responsive in leaves, but not significantly responsive to SA treatment, while TaWRKY45-B was a SA- but not a JA-responsive marker. Other candidate genes were either unresponsive or non-specific to SA or JA. Our findings highlight that all seven gene families are greatly expanded in wheat as compared to other plants (up to 7.6-fold expansion), and demonstrate disparity in the response to biotic stress between some homoeologous and paralogous sequences within these families. The SA- and JA-responsive marker genes identified herein will prove useful tools to monitor these signalling pathways in wheat.
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Affiliation(s)
- A Heckmann
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - A Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - F M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
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Lou H, Zheng S, Chen W, Yu W, Jiang H, Farag MA, Xiao J, Wu J, Song L. Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel. J Adv Res 2024; 62:1-14. [PMID: 36639025 PMCID: PMC11331172 DOI: 10.1016/j.jare.2023.01.007] [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: 10/18/2021] [Revised: 12/21/2022] [Accepted: 01/08/2023] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Torreya grandis is a gymnosperm belonging to Taxodiaceae. As an economically important tree, its kernels are edible and rich in oil with high unsaturated fatty acids, such as sciadonic acid. However, the kernels from different T. grandis landraces exhibit fatty acid and oil content variations. OBJECTIVES As a gymnosperm, does T. grandis have special regulation mechanisms for oil biosynthesis? The aim of this study was to dissect the genetic architecture of fatty acid and oil content and the underlying mechanism in T. grandis. METHODS We constructed a high integrity reference sequence of expressed regions of the genome in T. grandis and performed transcriptome-referenced association study (TRAS) for 10 fatty acid and oil traits of kernels in the 170 diverse T. grandis landraces. To confirm the TRAS result, we performed functional validation and molecular biology experiments for oil significantly associated genes. RESULTS We identified 41 SNPs from 34 transcripts significantly associated with 7 traits by TRAS (-log10 (P) greater than 6.0). Results showed that LOB domain-containing protein 40 (LBD40) and surfeit locus protein 1 (SURF1) may be indirectly involved in the regulation of oil and sciadonic acid biosynthesis, respectively. Moreover, overexpression of TgLBD40 significantly increased seed oil content. The nonsynonymous variant in the TgLBD40 coding region discovered by TRAS could alter the oil content in plants. Pearson's correlation analysis and dual-luciferase assay indicated that TgLBD40 positively enhanced oil accumulation by affecting oil biosynthesis pathway genes, such as TgDGAT1. CONCLUSION Our study provides new insights into the genetic basis of oil biosynthesis in T. grandis and demonstrates that integrating RNA sequencing and TRAS is a powerful strategy to perform association study independent of a reference genome for dissecting important traits in T. grandis.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; NFGA Engineering Research Center for Torreya grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Weiwu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini st., Cairo P.B. 11562, Egypt
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo - Ourense Campus, E-32004 Ourense, Spain.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; NFGA Engineering Research Center for Torreya grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; NFGA Engineering Research Center for Torreya grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
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Lapalu N, Simon A, Lu A, Plaumann PL, Amselem J, Pigné S, Auger A, Koch C, Dallery JF, O'Connell RJ. Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome. Microb Genom 2024; 10:001283. [PMID: 39166978 PMCID: PMC11338638 DOI: 10.1099/mgen.0.001283] [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: 12/19/2023] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
Colletotrichum destructivum (Cd) is a phytopathogenic fungus causing significant economic losses on forage legume crops (Medicago and Trifolium species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from Medicago sativa using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises ten core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15, 631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate-secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of Cd relative to the closely related Brassicaceae pathogen, Colletotrichum higginsianum. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of Cd that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen.
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Affiliation(s)
- Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Adeline Simon
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Antoine Lu
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Peter-Louis Plaumann
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, URGI, 78000 Versailles, France
| | - Sandrine Pigné
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Annie Auger
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Christian Koch
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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Hernández-Herreros N, Rodríguez A, Galán B, Auxiliadora Prieto M. Boosting hydrogen production in Rhodospirillum rubrum by syngas-driven photoheterotrophic adaptive evolution. BIORESOURCE TECHNOLOGY 2024; 406:130972. [PMID: 38876276 DOI: 10.1016/j.biortech.2024.130972] [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: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Rhodospirillum rubrum is a photosynthetic purple non-sulphur bacterium with great potential to be used for complex waste valorisation in biotechnological applications due to its metabolic versatility. This study investigates the production of hydrogen (H2) and polyhydroxyalkanoates (PHA) by R. rubrum from syngas under photoheterotrophic conditions. An adaptive laboratory evolution strategy (ALE) has been carried out to improve the yield of the process. After 200 generations, two evolved strains were selected that showed reduced lag phase and enhanced poly-3-hydroxybutyrate (PHB) and H2 synthesis compared to the parental strain. Genomic analysis of the photo-adapted (PA) variants showed four genes with single point mutations, including the photosynthesis gene expression regulator PpsR. The proteome of the variants suggested that the adapted variants overproduced H2 due to a more efficient CO oxidation through the CO-dehydrogenase enzyme complex and confirmed that energy acquisition was enhanced through overexpression of the photosynthetic system and metal cofactors essential for pigment biosynthesis.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Alberto Rodríguez
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Galán
- Microbial & Plant Biotechnology Department, Environmental Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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Kumaravel N, Ebinezer LB, Ashwin NMR, Franchin C, Battisti I, Carletti P, Ramesh Sundar A, Masi A, Malathi P, Viswanathan R, Arrigoni G. Comparative proteomics of sugarcane smut fungus - Sporisorium scitamineum unravels dynamic proteomic alterations during the dimorphic transition. J Proteomics 2024; 304:105230. [PMID: 38901800 DOI: 10.1016/j.jprot.2024.105230] [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: 12/11/2023] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Life cycle of the dimorphic sugarcane smut fungi, Sporisorium scitamineum, involves recognition and mating of compatible saprophytic yeast-like haploid sporidia (MAT-1 and MAT-2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of S. scitamineum, it has never been studied using a proteomic approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages was carried out. The stages were: the dimorphic transition period - haploid sporidial stage (MAT-1 and MAT-2); the transition phase (24 h post co-culturing (hpc)) and the dikaryotic mycelial stage (48 hpc). Functional categorization of differentially abundant proteins showed that the most altered biological processes were energy production, primary metabolism, especially, carbohydrate, amino acid, fatty acid, followed by translation, post-translation and protein turnover. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in S. scitamineum at the proteome level were highlighted. The catalogue of stage-specific and dimorphic transition-associated-proteins and potential effectors identified herein represents a list of potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in S. scitamineum. BIOLOGICAL SIGNIFICANCE: Being the first comparative proteomics analysis of S. scitamineum, this study comprehensively examined three pivotal life cycle stages of the pathogen: the non-pathogenic haploid phase, the transition phase, and the pathogenic dikaryotic mycelial stage. While previous studies have reported the sugarcane and S. scitamineum interactions, this study endeavored to specifically identify the proteins responsible for pathogenicity. By analyzing the proteomic alterations between the haploid and dikaryotic mycelial phases, the study revealed significant changes in metabolic pathway-associated proteins linked to energy production, notably oxidative phosphorylation, and the citrate cycle. Furthermore, this study successfully identified key metabolic pathways that undergo reprogramming during the transition from the non-pathogenic to the pathogenic stage. The study also deciphered the underlying mechanisms driving the morphological and physiological alterations crucial for the S. scitamineum virulence. By studying its life cycle stages, identifying the key metabolic pathways and stage-specific proteins, it provides unprecedented insights into the pathogenicity and potential avenues for intervention. As proteomics continues to advance, such studies pave the way for a deeper understanding of plant-pathogen interactions and the development of innovative strategies to mitigate the impact of devastating pathogens like S. scitamineum.
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Affiliation(s)
- Nalayeni Kumaravel
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - N M R Ashwin
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Biochemical Sciences Division, Council of Scientific and Industrial Research - National Chemical Laboratory, Pune 411008, Maharashtra, India.
| | - Cinzia Franchin
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
| | - Ilaria Battisti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Amalraj Ramesh Sundar
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Palaniyandi Malathi
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Rasappa Viswanathan
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Indian Council of Agricultural Research - Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh 226002, India.
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
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Sveholm E, Mattila H, Aro N, Valkonen M, Paasela T, Pakula TM. Transcriptomic and metabolic changes in Trichoderma reesei caused by mutation in xylanase regulator 1 (xyr1). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:106. [PMID: 39030601 PMCID: PMC11265206 DOI: 10.1186/s13068-024-02556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Trichoderma reesei is known for its ability to produce large amounts of extracellular proteins and is one of the most important industrially used filamentous fungus. Xylanase regulator 1 (XYR1) is the master regulator responsible for the activation of cellulase and hemicellulase gene expression under inducing conditions. It has been reported that strains with point mutations in certain areas of xyr1 bypass the need for inducing carbon source, allowing high (hemi)cellulase production even in the presence of glucose. These mutations also change the profile of produced proteins, shifting it more towards xylanase production, and increase the overall protein production in inducing conditions. However, how these mutations alter the metabolism and other cellular processes to cause these changes remains unclear. RESULTS In this study, we aimed to explore changes caused by a point mutation in xyr1 on transcriptomic and metabolic level to better understand the reasons behind the increased protein production in both repressing glucose and inducing lactose conditions. As expected, the expression of many carbohydrate-active enzyme (CAZy) genes was increased in the xyr1 mutant in both conditions. However, their induction was higher under inducing conditions. The xyr1 mutant strain built more biomass and produced more extracellular proteins during growth on lactose compared to the wild type xyr1 strain. Genes involved in oxidoreductive D-galactose catabolism pathway were upregulated in the xyr1 mutant strain, potentially contributing to the more efficient utilization of lactose. In addition to CAZy genes, clustering and enrichment analysis showed over-representation of mitochondria-related Gene Ontology terms in clusters where gene expression was higher in the xyr1 mutant, indicating that mitochondria play a role in the altered metabolic state associated with the xyr1 mutation. Metabolomics revealed that free tyrosine was more abundant in the xyr1 mutant strain in all measured timepoints, whereas multiple fatty acids were less abundant in the mutant strain on glucose. CONCLUSIONS The results contribute to more in-depth knowledge on T. reesei physiology growing under inducing and repressing carbon sources and gives new insights on the function of the master regulator XYR1. The vast data generated serve as a source for new targets for improved protein production.
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Affiliation(s)
- Emmi Sveholm
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Hans Mattila
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Nina Aro
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Mari Valkonen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
| | - Tanja Paasela
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland.
| | - Tiina M Pakula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044, Espoo, Finland
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Garg P, Vanamamalai VK, Sharma S. In-silico analysis of cattle blood transcriptome to identify lncRNAs and their role during bovine tuberculosis. Sci Rep 2024; 14:16537. [PMID: 39019929 PMCID: PMC11255290 DOI: 10.1038/s41598-024-67001-0] [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: 03/01/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules with a length greater than 200 nucleotides that do not code for functional proteins. Although, genes play a vital role in immune response against a disease, it is less known that lncRNAs also contribute through gene regulation. Bovine tuberculosis is a significant zoonotic disease caused by Mycobacterium bovis (M. bovis) in cattle. Here, we report the in-silico analysis of the publicly available transcriptomic data of calves infected with M. bovis. A total of 51,812 lncRNAs were extracted across all the samples. A total of 216 genes and 260 lncRNAs were found to be differentially expressed across all the 4 conditions-infected vs uninfected at 8- and 20-week post-infection (WPI), 8 vs 20-WPI of both infected and uninfected. Gene Ontology and Functional annotation showed that 8 DEGs were annotated with immune system GOs and 2 DEGs with REACTOME immune system pathways. Co-expression analysis of DElncRNAs with DEGs revealed the involvement of lncRNAs with the genes annotated with Immune related GOs and pathways. Overall, our study sheds light on the dynamic transcriptomic changes in response to M. bovis infection, particularly highlighting the involvement of lncRNAs with immune-related genes. The identified immune pathways and gene-lncRNA interactions offer valuable insights for further research in understanding host-pathogen interactions and potential avenues for genetic improvement strategies in cattle.
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Affiliation(s)
- Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
- Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, Faridabad Rd, Faridabad, Haryana, 121001, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India.
- Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, Faridabad Rd, Faridabad, Haryana, 121001, India.
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Zhu ZS, Bu SH, Liu JX, Niu C, Wang L, Yuan H, Zhang L, Song Y. Label-free-based proteomics analysis reveals differential proteins of sheep, goat and cow milk. J Dairy Sci 2024:S0022-0302(24)01002-6. [PMID: 39004124 DOI: 10.3168/jds.2024-24998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
Regarding the limited information on species protein differences between sheep, goat, and cow milk, the differentially expressed proteins in sheep, goat, and cow milk and their functional differences are analyzed using label-free proteomics technology to identify potential biomarkers. 770 proteins and 2914 peptide segments were identified. The statistical analysis showed significant differences in the relative abundances of the 74 proteins among the sheep, goat, and cow milk. CSN3 and LALBA can be used as potential biomarkers for goat milk, XDH can be used as potential biomarkers for cow milk, and CTSB and BPIFB1 can be used as potential biomarkers for sheep milk. The functional analysis using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes showed that these significantly different proteins were enriched by different pathways including thyroid hormone synthesis and glycerol phospholipid metabolism. The data revealed differences in the amounts and physiological functions of the milk proteins of different species, which may provide an important basis for research on the nutritional composition of dairy products and adulteration identification technology.
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Affiliation(s)
- Z S Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - S H Bu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - J X Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - C Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - L Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - H Yuan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Zhou Y, Bai F, Xiao R, Chen M, Sun Y, Ye J. Proteomics and Its Combined Analysis with Transcriptomics: Liver Fat-Lowering Effect of Taurine in High-Fat Fed Grouper ( Epinephelus coioides). Animals (Basel) 2024; 14:2039. [PMID: 39061501 PMCID: PMC11274106 DOI: 10.3390/ani14142039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
In order to understand the intervention effect of taurine on liver fat deposition induced by high fat intake in the orange-spotted grouper (Epinephelus coioides), we performed proteomic analysis and association analysis with previously obtained transcriptomic data. Three isoproteic (47% crude protein) diets were designed to contain two levels of fat and were named as the 10% fat diet (10F), 15% fat diet (15F), and 15% fat with 1% taurine (15FT). The 10F diet was used as the control diet. After 8 weeks of feeding, the 15F diet exhibited comparable weight gain, feed conversion ratio, and hepatosomatic index as the 10F diet, but the former increased liver fat content vs. the latter. Feeding with the 15FT diet resulted in an improvement in weight gain and a reduction in feed conversion ratio, hepatosomatic index, and liver fat content compared with feeding the 15F diet. When comparing liver proteomic data between the 15F and 15FT groups, a total of 133 differentially expressed proteins (DEPs) were identified, of which 51 were upregulated DEPs and 82 were downregulated DEPs. Among these DEPs, cholesterol 27-hydroxylase, phosphatidate phosphatase LPIN, phosphatidylinositol phospholipase C, and 6-phosphofructo-2-kinase were further screened out and were involved in primary bile acid biosynthesis, glycerolipid metabolism, the phosphatidylinositol signaling system, and the AMPK signaling pathway as key DEPs in terms of alleviating liver fat deposition of taurine in high-fat fed fish. With the association analysis of transcriptomic and proteomic data through KEGG, three differentially expressed genes (atp1a, arf1_2, and plcd) and four DEPs (CYP27α1, LPIN, PLCD, and PTK2B) were co-enriched into five pathways related to fat metabolism including primary bile acid synthesis, bile secretion, glycerolipid metabolism, phospholipid D signaling, or/and phosphatidylinositol signaling. The results showed that dietary taurine intervention could trigger activation of bile acid biosynthesis and inhibition of triglyceride biosynthesis, thereby mediating the liver fat-lowering effects in high-fat fed orange-spotted grouper. The present study contributes some novel insight into the liver fat-lowering effects of dietary taurine in high-fat fed groupers.
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Affiliation(s)
| | | | | | | | | | - Jidan Ye
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College of Jimei University, Xiamen 361021, China; (Y.Z.); (F.B.); (R.X.); (M.C.); (Y.S.)
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Purayil GP, Saeed EE, Mathai AM, El-Tarabily KA, AbuQamar SF. A high-quality genome assembly and annotation of Thielaviopsis punctulata DSM102798. Sci Data 2024; 11:745. [PMID: 38982096 PMCID: PMC11233662 DOI: 10.1038/s41597-024-03458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/31/2024] [Indexed: 07/11/2024] Open
Abstract
Black scorch disease (BSD), caused by the fungal pathogen Thielaviopsis punctulata (Tp) DSM102798, poses a significant threat to date palm cultivation in the United Arab Emirates (UAE). In this study, Chicago and Hi-C libraries were prepared as input for the Dovetail HiRise pipeline to scaffold the genome of Tp DSM102798. We generated an assembly with a total length of 28.23 Mb comprising 1,256 scaffolds, and the assembly had a contig N50 of 18.56 kb, L50 of three, and a BUSCO completeness score of 98.6% for 758 orthologous genes. Annotation of this assembly produced 7,169 genes and 3,501 Gene Ontology (GO) terms. Compared to five other Thielaviopsis genomes, Tp DSM102798 exhibited the highest continuity with a cumulative size of 27.598 Mb for the first seven scaffolds, surpassing the assemblies of all examined strains. These findings offer a foundation for targeted strategies that enhance date palm resistance against BSD, and foster more sustainable and resilient agricultural systems.
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Affiliation(s)
- Gouthaman P Purayil
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Archana M Mathai
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
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45
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Poddar BJ, Khardenavis AA. Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04980-w. [PMID: 38980659 DOI: 10.1007/s12010-024-04980-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2024] [Indexed: 07/10/2024]
Abstract
In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.
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Affiliation(s)
- Bhagyashri J Poddar
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Hopper KR, Wang X, Kenis M, Seehausen ML, Abram PK, Daane KM, Buffington ML, Hoelmer KA, Kingham BF, Shevchenko O, Bernberg E. Genome divergence and reproductive incompatibility among populations of Ganaspis near brasiliensis. G3 (BETHESDA, MD.) 2024; 14:jkae090. [PMID: 38718200 PMCID: PMC11228843 DOI: 10.1093/g3journal/jkae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/12/2024] [Indexed: 07/09/2024]
Abstract
During the last decade, the spotted wing drosophila, Drosophila suzukii, has spread from eastern Asia to the Americas, Europe, and Africa. This fly attacks many species of cultivated and wild fruits with soft, thin skins, where its serrated ovipositor allows it to lay eggs in undamaged fruit. Parasitoids from the native range of D. suzukii may provide sustainable management of this polyphagous pest. Among these parasitoids, host-specificity testing has revealed a lineage of Ganaspis near brasiliensis, referred to in this paper as G1, that appears to be a cryptic species more host-specific to D. suzukii than other parasitoids. Differentiation among cryptic species is critical for introduction and subsequent evaluation of their impact on D. suzukii. Here, we present results on divergence in genomic sequences and architecture and reproductive isolation between lineages of Ganaspis near brasiliensis that appear to be cryptic species. We studied five populations, two from China, two from Japan, and one from Canada, identified as the G1 vs G3 lineages based on differences in cytochrome oxidase l sequences. We assembled and annotated the genomes of these populations and analyzed divergences in sequence and genome architecture between them. We also report results from crosses to test reproductive compatibility between the G3 lineage from China and the G1 lineage from Japan. The combined results on sequence divergence, differences in genome architectures, ortholog divergence, reproductive incompatibility, differences in host ranges and microhabitat preferences, and differences in morphology show that these lineages are different species. Thus, the decision to evaluate the lineages separately and only import and introduce the more host-specific lineage to North America and Europe was appropriate.
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Affiliation(s)
- Keith R Hopper
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Marc Kenis
- CABI, Rue des Grillons 1, CH-2800 Delémont, Switzerland
| | | | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, 6947 Highway 7, PO Box 1000, Agassiz, BC V0 M 1A2, Canada
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720-3114, USA
| | - Matthew L Buffington
- United States Department of Agriculture, Agricultural Research Service, Washington, c/o Smithsonian Institution, National Museum of Natural History, 10th and Constitution NW, MRC-168, Washington, DC 20013-7012, USA
| | - Kim A Hoelmer
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
| | - Olga Shevchenko
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
| | - Erin Bernberg
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
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47
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Hull KL, Greenwood MP, Lloyd M, Brink-Hull M, Bester-van der Merwe AE, Rhode C. Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38963286 DOI: 10.1111/imb.12940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.
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Affiliation(s)
- Kelvin L Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Melissa Lloyd
- Research and Development Department, Insect Technology Group Holdings UK Ltd., Guildford, UK
| | - Marissa Brink-Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Scott CJR, McGregor NGS, Leadbeater DR, Oates NC, Hoßbach J, Abood A, Setchfield A, Dowle A, Overkleeft HS, Davies GJ, Bruce NC. Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates. Microbiol Spectr 2024; 12:e0394323. [PMID: 38757984 PMCID: PMC11218486 DOI: 10.1128/spectrum.03943-23] [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: 11/14/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.
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Affiliation(s)
- Conor J R Scott
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Janina Hoßbach
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Alexander Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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49
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Simphor E, Rognon A, Vignal E, Henry S, Allienne JF, Turtoi A, Chaparro C, Galinier R, Duval D, Gourbal B. Combining a transcriptomic approach and a targeted metabolomics approach for deciphering the molecular bases of compatibility phenotype in the snail Biomphalaria glabrata toward Schistosoma mansoni. Acta Trop 2024; 255:107212. [PMID: 38641222 DOI: 10.1016/j.actatropica.2024.107212] [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: 01/02/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024]
Abstract
Biomphalaria glabrata is a freshwater snail and the obligatory intermediate host of Schistosoma mansoni parasite, the etiologic agent of intestinal Schistosomiasis, in South America and Caribbean. Interestingly in such host-parasite interactions, compatibility varies between populations, strains or individuals. This observed compatibility polymorphism is based on a complex molecular-matching-phenotype, the molecular bases of which have been investigated in numerous studies, notably by comparing between different strains or geographical isolates or clonal selected snail lines. Herein we propose to decipher the constitutive molecular support of this interaction in selected non-clonal resistant and susceptible snail strain originating from the same natural population from Brazil and thus having the same genetic background. Thanks to a global RNAseq transcriptomic approach on whole snail, we identified a total of 328 differentially expressed genes between resistant and susceptible phenotypes among which 129 were up-regulated and 199 down-regulated. Metabolomic studies were used to corroborate the RNAseq results. The activation of immune genes and specific metabolic pathways in resistant snails might provide them with the capacity to better respond to parasite infection.
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Affiliation(s)
- Elodie Simphor
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Anne Rognon
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Emmanuel Vignal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Sylvain Henry
- Platform for Translational Oncometabolomics, Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | | | - Andrei Turtoi
- Platform for Translational Oncometabolomics, Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France; Tumor Microenvironment and Resistance to Therapy Laboratory, Institut de Recherche en Cancérologie de Montpellier, Université de Montpellier, INSERM, U1194, Montpellier, France
| | - Cristian Chaparro
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Richard Galinier
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - David Duval
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France.
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50
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Mori BA, Coutu C, Erlandson MA, Hegedus DD. Exploring the contribution of the salivary gland and midgut to digestion in the swede midge (Contarinia nasturtii) through a genomics-guided approach. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 116:e22135. [PMID: 39038196 DOI: 10.1002/arch.22135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/24/2024]
Abstract
The larvae of Contarinia nasturtii (Kieffer) (Diptera: Cecidomyiidae), the swede midge, targets the meristem of brassica crops where they induce the formation of galls and disrupt seed and vegetable production. Previously, we examined the salivary gland transcriptome of newly-hatched first instar larvae as they penetrated the host and initiated gall formation. Here we examine the salivary gland and midgut transcriptome of third instar larvae and provide evidence for cooperative nutrient acquisition beginning with secretion of enzymes and feeding facilitators followed by gastrointestinal digestion. Sucrose, presumably obtained from the phloem, appeared to be a major nutrient source as several α-glucosidases (sucrases, maltases) and β-fructofuranosidases (invertases) were identified. Genes encoding β-fructofuranosidases/invertases were among the most highly expressed in both tissues and represented two distinct gene families that may have originated via horizontal gene transfer from bacteria. The importance of the phloem as a nutrient source is underscored by the expression of genes encoding regucalcin and ARMET (arginine-rich mutated in early stages of tumor) which interfere with calcium signalling and prevent sieve tube occlusion. Lipids, proteins, and starch appear to serve as a secondary nutrient sources. Genes encoding enzymes involved in the detoxification of glucosinolates (myrosinases, arylsulfatases, and glutathione-S-transferases) were expressed indicative of Brassicaceae host specialization. The midgut expressed simple peritrophins and mucins typical of those found in Type II peritrophic matrices, the first such description for a gall midge.
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Affiliation(s)
- Boyd A Mori
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Martin A Erlandson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
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