1
|
Palekyte A, Morkowska A, Billington O, Morris-Jones S, Millard J, Marakalala MJ, Owolabi O, Sambou B, Zumla A, Sutherland JS, McHugh TD, Honeyborne I. Acetic Acid Enables Molecular Enumeration of Mycobacterium tuberculosis from Sputum and Eliminates the Need for a Biosafety Level 3 Laboratory. Clin Chem 2024; 70:642-652. [PMID: 38479728 DOI: 10.1093/clinchem/hvae013] [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: 09/26/2023] [Accepted: 12/08/2023] [Indexed: 04/04/2024]
Abstract
BACKGROUND Improved monitoring of Mycobacterium tuberculosis response to treatment is urgently required. We previously developed the molecular bacterial load assay (MBLA), but it is challenging to integrate into the clinical diagnostic laboratory due to a labor-intensive protocol required at biosafety level 3 (BSL-3). A modified assay was needed. METHODS The rapid enumeration and diagnostic for tuberculosis (READ-TB) assay was developed. Acetic acid was tested and compared to 4 M guanidine thiocyanate to be simultaneously bactericidal and preserve mycobacterial RNA. The extraction was based on silica column technology and incorporated low-cost reagents: 3 M sodium acetate and ethanol for the RNA extraction to replace phenol-chloroform. READ-TB was fully validated and compared directly to the MBLA using sputa collected from individuals with tuberculosis. RESULTS Acetic acid was bactericidal to M. tuberculosis with no significant loss in 16S rRNA or an unprotected mRNA fragment when sputum was stored in acetic acid at 25°C for 2 weeks or -20°C for 1 year. This novel use of acetic acid allows processing of sputum for READ-TB at biosafety level 2 (BSL-2) on sample receipt. READ-TB is semiautomated and rapid. READ-TB correlated with the MBLA when 85 human sputum samples were directly compared (R2 = 0.74). CONCLUSIONS READ-TB is an improved version of the MBLA and is available to be adopted by clinical microbiology laboratories as a tool for tuberculosis treatment monitoring. READ-TB will have a particular impact in low- and middle-income countries (LMICs) for laboratories with no BSL-3 laboratory and for clinical trials testing new combinations of anti-tuberculosis drugs.
Collapse
Affiliation(s)
- Ana Palekyte
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Anna Morkowska
- Imperial College London, Infection and Immunity, Department of Microbiology, Charing Cross Hospital, London, United Kingdom
| | | | - Stephen Morris-Jones
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - James Millard
- Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, United Kingdom
- Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
- Africa Health Research Institute, Durban, South Africa
| | | | - Olumuyiwa Owolabi
- Vaccines and Immunity, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Basil Sambou
- Vaccines and Immunity, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
- National Institute of Health and Research Biomedical Research Centre, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Jayne S Sutherland
- Vaccines and Immunity, MRC Unit The Gambia at The London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Isobella Honeyborne
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| |
Collapse
|
2
|
Barragan AC, Collenberg M, Schwab R, Kersten S, Kerstens MHL, Požárová D, Bezrukov I, Bemm F, Kolár F, Weigel D. Deleterious phenotypes in wild Arabidopsis arenosa populations are common and linked to runs of homozygosity. G3 (BETHESDA, MD.) 2024; 14:jkad290. [PMID: 38124484 PMCID: PMC10917499 DOI: 10.1093/g3journal/jkad290] [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: 07/07/2023] [Revised: 07/07/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.
Collapse
Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- The Sainsbury Laboratory, Norwich NR4 7UH, UK
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Catalent, 73614 Schorndorf, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Institute of Plant Breeding, University of Hohenheim, 70599 Stuttgart, Germany
| | - Merijn H L Kerstens
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Department of Plant Developmental Biology, Wageningen University and Research, 6708 PB, Wageningen, Netherlands
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
- The MAMA AI, 100 00 Prague, Czech Republic
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- KWS Saat, 37574 Einbeck, Germany
| | - Filip Kolár
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| |
Collapse
|
3
|
Kant K, Rigó G, Faragó D, Benyó D, Tengölics R, Szabados L, Zsigmond L. Mutation in Arabidopsis mitochondrial Pentatricopeptide repeat 40 gene affects tolerance to water deficit. PLANTA 2024; 259:78. [PMID: 38427069 PMCID: PMC10907415 DOI: 10.1007/s00425-024-04354-w] [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: 10/31/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Abstract
MAIN CONCLUSION The Arabidopsis Pentatricopeptide repeat 40 (PPR40) insertion mutants have increased tolerance to water deficit compared to wild-type plants. Tolerance is likely the consequence of ABA hypersensitivity of the mutants. Plant growth and development depend on multiple environmental factors whose alterations can disrupt plant homeostasis and trigger complex molecular and physiological responses. Water deficit is one of the factors which can seriously restrict plant growth and viability. Mitochondria play an important role in cellular metabolism, energy production, and redox homeostasis. During drought and salinity stress, mitochondrial dysfunction can lead to ROS overproduction and oxidative stress, affecting plant growth and survival. Alternative oxidases (AOXs) and stabilization of mitochondrial electron transport chain help mitigate ROS damage. The mitochondrial Pentatricopeptide repeat 40 (PPR40) protein was implicated in stress regulation as ppr40 mutants were found to be hypersensitive to ABA and high salinity during germination. This study investigated the tolerance of the knockout ppr40-1 and knockdown ppr40-2 mutants to water deprivation. Our results show that these mutants display an enhanced tolerance to water deficit. The mutants had higher relative water content, reduced level of oxidative damage, and better photosynthetic parameters in water-limited conditions compared to wild-type plants. ppr40 mutants had considerable differences in metabolic profiles and expression of a number of stress-related genes, suggesting important metabolic reprogramming. Tolerance to water deficit was also manifested in higher survival rates and alleviated growth reduction when watering was suspended. Enhanced sensitivity to ABA and fast stomata closure was suggested to lead to improved capacity for water conservation in such environment. Overall, this study highlights the importance of mitochondrial functions and in particular PPR40 in plant responses to abiotic stress, particularly drought.
Collapse
Affiliation(s)
- Kamal Kant
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Gábor Rigó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Dóra Faragó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Dániel Benyó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Roland Tengölics
- Institute of Biochemistry, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - László Szabados
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary.
| | - Laura Zsigmond
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| |
Collapse
|
4
|
Furuta K, Kawakubo S, Sasaki J, Masuta C. An Inexpensive System for Rapid and Accurate On-site Detection of Garlic-Infected Viruses by Agarose Gel Electrophoresis Followed by Array Assay. THE PLANT PATHOLOGY JOURNAL 2024; 40:40-47. [PMID: 38326957 PMCID: PMC10850529 DOI: 10.5423/ppj.ft.11.2023.0146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024]
Abstract
Garlic can be infected by a variety of viruses, but mixed infections with leek yellow stripe virus, onion yellow dwarf virus, and allexiviruses are the most damaging, so an easy, inexpensive on-site method to simultaneously detect at least these three viruses with a certain degree of accuracy is needed to produce virus-free plants. The most common laboratory method for diagnosis is multiplex reverse transcription polymerase chain reaction (RT-PCR). However, allexiviruses are highly diverse even within the same species, making it difficult to design universal PCR primers for all garlic-growing regions in the world. To solve this problem, we developed an inexpensive on-site detection system for the three garlic viruses that uses a commercial mobile PCR device and a compact electrophoresis system with a blue light. In this system, virus-specific bands generated by electrophoresis can be identified by eye in real time because the PCR products are labeled with a fluorescent dye, FITC. Because the electrophoresis step might eventually be replaced with a lateral flow assay (LFA), we also demonstrated that a uniplex LFA can be used for virus detection; however, multiplexing and a significant cost reduction are needed before it can be used for on-site detection.
Collapse
Affiliation(s)
| | - Shusuke Kawakubo
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Jun Sasaki
- Ornamental Plants and Vegetables Research Center, Takikawa 073-0026, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| |
Collapse
|
5
|
Benyó D, Bató E, Faragó D, Rigó G, Domonkos I, Labhane N, Zsigmond L, Prasad M, Nagy I, Szabados L. The zinc finger protein 3 of Arabidopsis thaliana regulates vegetative growth and root hair development. FRONTIERS IN PLANT SCIENCE 2024; 14:1221519. [PMID: 38250442 PMCID: PMC10796524 DOI: 10.3389/fpls.2023.1221519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
Introduction Zinc finger protein 3 (ZFP3) and closely related C2H2 zinc finger proteins have been identified as regulators of abscisic acid signals and photomorphogenic responses during germination. Whether ZFP3 and related ZFP factors regulate plant development is, however, not known. Results ZFP3 overexpression reduced plant growth, limited cell expansion in leaves, and compromised root hair development. The T-DNA insertion zfp3 mutant and transgenic lines with silenced ZFP1, ZFP3, ZFP4, and ZFP7 genes were similar to wild-type plants or had only minor differences in plant growth and morphology, probably due to functional redundancy. RNAseq transcript profiling identified ZFP3-controlled gene sets, including targets of ABA signaling with reduced transcript abundance. The largest gene set that was downregulated by ZFP3 encoded regulatory and structural proteins in cell wall biogenesis, cell differentiation, and root hair formation. Chromatin immunoprecipitation confirmed ZFP3 binding to several target promoters. Discussion Our results suggest that ZFP3 and related ZnF proteins can modulate cellular differentiation and plant vegetative development by regulating the expression of genes implicated in cell wall biogenesis.
Collapse
Affiliation(s)
- Dániel Benyó
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Emese Bató
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Dóra Faragó
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Gábor Rigó
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Ildikó Domonkos
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Nitin Labhane
- Department of Botany, Bhavan’s College, Mumbai, Maharashtra, India
| | - Laura Zsigmond
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Melvin Prasad
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - István Nagy
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- SeqOmics Biotechnology Ltd, Mórahalom, Hungary
| | - László Szabados
- Instiute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| |
Collapse
|
6
|
Duque-Jaramillo A, Ulmer N, Alseekh S, Bezrukov I, Fernie AR, Skirycz A, Karasov TL, Weigel D. The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava. THE NEW PHYTOLOGIST 2023; 240:1961-1975. [PMID: 37667565 DOI: 10.1111/nph.19241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
The opportunistic pathogen Pseudomonas viridiflava colonizes > 50 agricultural crop species and is the most common Pseudomonas in the phyllosphere of European Arabidopsis thaliana populations. Belonging to the P. syringae complex, it is genetically and phenotypically distinct from well-characterized P. syringae sensu stricto. Despite its prevalence, we lack knowledge of how A. thaliana responds to its native isolates at the molecular level. Here, we characterize the host response in an A. thaliana - P. viridiflava pathosystem. We measured host and pathogen growth in axenic infections and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility to P. viridiflava infection. Infection with P. viridiflava increased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared with a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA. The JA/ethylene pathway is important for suppression of P. viridiflava, yet suppression capacity varies between accessions. Our results shed light on how A. thaliana can suppress the ever-present P. viridiflava, but further studies are needed to understand how P. viridiflava evades this suppression to spread broadly across A. thaliana populations.
Collapse
Affiliation(s)
| | - Nina Ulmer
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ilja Bezrukov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, 14850, USA
| | - Talia L Karasov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, University of Utah, Salt Lake City, 84112, USA
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72074, Germany
| |
Collapse
|
7
|
Canales J, Verdejo JF, Calderini DF. Transcriptome and Physiological Analysis of Rapeseed Tolerance to Post-Flowering Temperature Increase. Int J Mol Sci 2023; 24:15593. [PMID: 37958577 PMCID: PMC10648292 DOI: 10.3390/ijms242115593] [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: 09/01/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Climate-change-induced temperature fluctuations pose a significant threat to crop production, particularly in the Southern Hemisphere. This study investigates the transcriptome and physiological responses of rapeseed to post-flowering temperature increases, providing valuable insights into the molecular mechanisms underlying rapeseed tolerance to heat stress. Two rapeseed genotypes, Lumen and Solar, were assessed under control and heat stress conditions in field experiments conducted in Valdivia, Chile. Results showed that seed yield and seed number were negatively affected by heat stress, with genotype-specific responses. Lumen exhibited an average of 9.3% seed yield reduction, whereas Solar showed a 28.7% reduction. RNA-seq analysis of siliques and seeds revealed tissue-specific responses to heat stress, with siliques being more sensitive to temperature stress. Hierarchical clustering analysis identified distinct gene clusters reflecting different aspects of heat stress adaptation in siliques, with a role for protein folding in maintaining silique development and seed quality under high-temperature conditions. In seeds, three distinct patterns of heat-responsive gene expression were observed, with genes involved in protein folding and response to heat showing genotype-specific expression. Gene coexpression network analysis revealed major modules for rapeseed yield and quality, as well as the trade-off between seed number and seed weight. Overall, this study contributes to understanding the molecular mechanisms underlying rapeseed tolerance to heat stress and can inform crop improvement strategies targeting yield optimization under changing environmental conditions.
Collapse
Affiliation(s)
- Javier Canales
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - José F. Verdejo
- Graduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile;
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile
| |
Collapse
|
8
|
Ko HJ, Jang HA, Park KB, Kim CE, Patnaik BB, Lee YS, Han YS, Jo YH. IKKβ regulates antimicrobial innate immune responses in the yellow mealworm, Tenebrio molitor. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104761. [PMID: 37331676 DOI: 10.1016/j.dci.2023.104761] [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: 03/29/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Toll and IMD pathways regulate antimicrobial innate immune responses in insect model systems. The transcriptional activation of antimicrobial peptides (AMPs) confers humoral immunity in the host against invaded pathogens. The IKK kinase complex (IKKα, IKKβ, and the regulatory subunit IKKγ/NEMO) centrally regulates the NF-κB response to various stimuli. It triggers an appropriate antimicrobial immune response in the host. In this study, a TmIKKβ (or TmIrd5) homolog was screened from the RNA-seq database of the coleopteran beetle, Tenebrio molitor. A single exon characterizes the TmIKKβ gene, and the open reading frame (ORF) comprises of 2112 bp that putatively encodes a polypeptide of 703 amino acid residues. TmIKKβ contains a serine/threonine kinase domain and is phylogenetically close to Tribolium castaneum IKKβ homolog (TcIKKβ). TmIKKβ transcripts were highly expressed in the early pupal (P1) and adult (A5) stages. Among the tissues, TmIKKβ showed higher expression in the integument of the last instar larvae and the fat body and hemocytes of 5-day-old adults. TmIKKβ mRNA was upregulated post-E. coli challenge to the host. Moreover, RNAi-based TmIKKβ mRNA silencing increased host larvae' susceptibility against E. coli, S. aureus and C. albicans. TmIKKβ RNAi in the fat body led to a downregulation in mRNA expression of ten out of fourteen AMP genes, including TmTenecin1, -2, and -4; TmDefensin, and -like; TmColeoptericinA, and -B; and TmAttacin1a, -1b, and -2, suggesting the requirement of the gene in antimicrobial innate immune responses. Further, a decrease in the mRNA expression of NF-κB factors such as TmRelish, TmDorsal1, and TmDorsal2 in the fat body of T. molitor larvae was observed post-microorganisms challenge. Thus, TmIKKβ regulates antimicrobial innate immune responses in T. molitor.
Collapse
Affiliation(s)
- Hye Jin Ko
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ho Am Jang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan City, 31538, Republic of Korea
| | - Ki Beom Park
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chang Eun Kim
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea; P.G Department of Biosciences and Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, Odisha, 756089, India
| | - Yong Seok Lee
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan City, 31538, Republic of Korea; Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Yeon Soo Han
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Yong Hun Jo
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan City, 31538, Republic of Korea.
| |
Collapse
|
9
|
Mira JP, Arenas-M A, Calderini DF, Canales J. Integrated Transcriptome Analysis Identified Key Expansin Genes Associated with Wheat Cell Wall, Grain Weight and Yield. PLANTS (BASEL, SWITZERLAND) 2023; 12:2868. [PMID: 37571021 PMCID: PMC10421294 DOI: 10.3390/plants12152868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
This research elucidates the dynamic expression of expansin genes during the wheat grain (Triticum aestivum L.) development process using comprehensive meta-analysis and experimental validation. We leveraged RNA-seq data from multiple public databases, applying stringent criteria for selection, and identified 60,852 differentially expressed genes across developmental stages. From this pool, 28,558 DEGs were found to exhibit significant temporal regulation in at least two different datasets and were enriched for processes integral to grain development such as carbohydrate metabolism and cell wall organization. Notably, 30% of the 241 known expansin genes showed differential expression during grain growth. Hierarchical clustering and expression level analysis revealed temporal regulation and distinct contributions of expansin subfamilies during the early stages of grain development. Further analysis using co-expression networks underscored the significance of expansin genes, revealing their substantial co-expression with genes involved in cell wall modification. Finally, qPCR validation and grain morphological analysis under field conditions indicated a significant negative correlation between the expression of select expansin genes, and grain size and weight. This study illuminates the potential role of expansin genes in wheat grain development and provides new avenues for targeted genetic improvements in wheat.
Collapse
Affiliation(s)
- Juan P. Mira
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (J.P.M.); (A.A.-M.)
| | - Anita Arenas-M
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (J.P.M.); (A.A.-M.)
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile; (J.P.M.); (A.A.-M.)
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| |
Collapse
|
10
|
Baldelli A, Koivisto L, Oguzlu H, Guo Y, Häkkinen L, Pratap Singh A, Larjava H. Spray-dried microparticles of encapsulated gefitinib for slow-release localized treatment of periodontal disease. Int J Pharm 2023:123137. [PMID: 37364780 DOI: 10.1016/j.ijpharm.2023.123137] [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: 01/31/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
Periodontal disease (PD) can be prevented by local or systemic application of epidermal growth factor receptor inhibitors (EGFRIs) that stabilize αvβ6 integrin levels in the periodontal tissue, leading to an increase in the expression of anti-inflammatory cytokines, such as transforming growth factor-β1. Systemic EGFRIs have side effects and, therefore, local treatment of PD applied into the periodontal pockets would be preferrable. Thus, we have developed slow-release three-layered microparticles of gefitinib, a commercially available EGFRI. A combination of different polymers [cellulose acetate butyrate (CAB), Poly (D, L-lactide-co-glycolide) (PLGA) and ethyl cellulose (EC)] and sugars [D-mannose, D-mannitol and D-(+)-trehalose dihydrate] were used for the encapsulation. The optimal formulation was composed of CAB, EC, PLGA, mannose and gefitinib (0.59, 0.24, 0.09, 1, and 0.005 mg/ml, respectively; labeled CEP-gef), and created microparticles of 5.7 ± 2.3 µm in diameter, encapsulation efficiency of 99.98%, and a release rate of more than 300 hours. A suspension of this microparticle formulation blocked EGFR phosphorylation and restored αvβ6 integrin levels in oral epithelial cells, while the respective control microparticles showed no effect.
Collapse
Affiliation(s)
| | - Leeni Koivisto
- Faculty of Dentistry, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Hale Oguzlu
- Sustainable Functional Biomaterials Laboratory, Department of Wood Science, The University of British Columbia
| | - Yigong Guo
- Food and Land Systems, The University of British Columbia
| | - Lari Häkkinen
- Faculty of Dentistry, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Hannu Larjava
- Faculty of Dentistry, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
11
|
Uchiyama S, Imamura Y, Matsuura T. A thermal cycler-based, homogenization-free plant total nucleic acid extraction method for plant viruses and viroids assay. J Virol Methods 2023; 313:114666. [PMID: 36539042 DOI: 10.1016/j.jviromet.2022.114666] [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: 08/15/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
In this study, we report a plant total nucleic acid (TNA) extraction method for nucleic acid (NA)-based assays of plant viruses and viroids. This method combines NA release by incubating sliced plant tissue in solution and NA purification using silica spin column. The method is performed using a thermal cycler and microcentrifuge and does not involve tissue homogenization. For a wide range of plant species, TNA can be extracted from petioles, midribs, and stems, in 30 min. PCR/RT-PCR assays using extracts from this method detected all three DNA viruses, 14 RNA viruses, and 4 viroids tested and plant internal controls were also available. This method does not involve hazardous chemicals, is cost-effective. The method is readily implemented in various laboratories, a simple, rapid, and labor-saving option for NA-based assays of plant viruses and viroids.
Collapse
Affiliation(s)
- Shuichi Uchiyama
- Narita Sub-station, Yokohama Plant Protection Station, 2159, Aza Tennamino, Komaino, Narita 282-0021, Japan.
| | - Yuya Imamura
- Tsukuba Farm, Yokohama Plant Protection Station, 1-7, Nagamine, Tsukuba 305-0052, Japan
| | - Takayuki Matsuura
- Research Division, Yokohama Plant Protection Station, 1-16-10, Shin Yamashita, Naka-ku, Yokohama 231-0801, Japan
| |
Collapse
|
12
|
Srikant T, Yuan W, Berendzen KW, Contreras-Garrido A, Drost HG, Schwab R, Weigel D. Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation. Genome Biol 2022; 23:263. [PMID: 36539836 PMCID: PMC9768921 DOI: 10.1186/s13059-022-02833-5] [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: 07/15/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Despite its conserved role on gene expression and transposable element (TE) silencing, genome-wide CG methylation differs substantially between wild Arabidopsis thaliana accessions. RESULTS To test our hypothesis that global reduction of CG methylation would reduce epigenomic, transcriptomic, and phenotypic diversity in A. thaliana accessions, we knock out MET1, which is required for CG methylation, in 18 early-flowering accessions. Homozygous met1 mutants in all accessions suffer from common developmental defects such as dwarfism and delayed flowering, in addition to accession-specific abnormalities in rosette leaf architecture, silique morphology, and fertility. Integrated analysis of genome-wide methylation, chromatin accessibility, and transcriptomes confirms that MET1 inactivation greatly reduces CG methylation and alters chromatin accessibility at thousands of loci. While the effects on TE activation are similarly drastic in all accessions, the quantitative effects on non-TE genes vary greatly. The global expression profiles of accessions become considerably more divergent from each other after genome-wide removal of CG methylation, although a few genes with diverse expression profiles across wild-type accessions tend to become more similar in mutants. Most differentially expressed genes do not exhibit altered chromatin accessibility or CG methylation in cis, suggesting that absence of MET1 can have profound indirect effects on gene expression and that these effects vary substantially between accessions. CONCLUSIONS Systematic analysis of MET1 requirement in different A. thaliana accessions reveals a dual role for CG methylation: for many genes, CG methylation appears to canalize expression levels, with methylation masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.
Collapse
Affiliation(s)
- Thanvi Srikant
- grid.419580.10000 0001 0942 1125Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany ,grid.5801.c0000 0001 2156 2780Present address: Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Wei Yuan
- grid.419580.10000 0001 0942 1125Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Kenneth Wayne Berendzen
- grid.10392.390000 0001 2190 1447Plant Transformation and Flow Cytometry Facility, ZMBP, University of Tübingen, Tübingen, Germany
| | - Adrián Contreras-Garrido
- grid.419580.10000 0001 0942 1125Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Hajk-Georg Drost
- grid.419580.10000 0001 0942 1125Computational Biology Group, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Rebecca Schwab
- grid.419580.10000 0001 0942 1125Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Detlef Weigel
- grid.419580.10000 0001 0942 1125Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| |
Collapse
|
13
|
Acevedo-Siaca LG, Głowacka K, Driever SM, Salesse-Smith CE, Lugassi N, Granot D, Long SP, Kromdijk J. Guard-cell-targeted overexpression of Arabidopsis Hexokinase 1 can improve water use efficiency in field-grown tobacco plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5745-5757. [PMID: 35595294 PMCID: PMC9467653 DOI: 10.1093/jxb/erac218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Water deficit currently acts as one of the largest limiting factors for agricultural productivity worldwide. Additionally, limitation by water scarcity is projected to continue in the future with the further onset of effects of global climate change. As a result, it is critical to develop or breed for crops that have increased water use efficiency and that are more capable of coping with water scarce conditions. However, increased intrinsic water use efficiency (iWUE) typically brings a trade-off with CO2 assimilation as all gas exchange is mediated by stomata, through which CO2 enters the leaf while water vapor exits. Previously, promising results were shown using guard-cell-targeted overexpression of hexokinase to increase iWUE without incurring a penalty in photosynthetic rates or biomass production. Here, two homozygous transgenic tobacco (Nicotiana tabacum) lines expressing Arabidopsis Hexokinase 1 (AtHXK1) constitutively (35SHXK2 and 35SHXK5) and a line that had guard-cell-targeted overexpression of AtHXK1 (GCHXK2) were evaluated relative to wild type for traits related to photosynthesis and yield. In this study, iWUE was significantly higher in GCHXK2 compared with wild type without negatively impacting CO2 assimilation, although results were dependent upon leaf age and proximity of precipitation event to gas exchange measurement.
Collapse
Affiliation(s)
- Liana G Acevedo-Siaca
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Katarzyna Głowacka
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Steven M Driever
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Coralie E Salesse-Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nitsan Lugassi
- Institute of Plant Sciences, Agricultural Research Organisation, The Volcani Center, Bet Dagan, Israel
| | - David Granot
- Institute of Plant Sciences, Agricultural Research Organisation, The Volcani Center, Bet Dagan, Israel
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Lancaster Environment Centre, University of Lancaster, Lancaster, UK
| | - Johannes Kromdijk
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| |
Collapse
|
14
|
Simple and Economical Extraction of Viral RNA and Storage at Ambient Temperature. Microbiol Spectr 2022; 10:e0085922. [PMID: 35647876 PMCID: PMC9241768 DOI: 10.1128/spectrum.00859-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA extraction is essential for the molecular detection of common viral pathogens. However, available extraction methods and the need for ultra-cold storage limit molecular testing in resource-constrained settings. Herein, we describe the development of an economical RNAExtraction and Storage (RNAES) protocol that eliminates requirements for instrumentation, expensive materials, and preserved cold chain. Through an iterative process, we optimized viral lysis and RNA binding to and elution from glass fiber membranes included in simple RNAES packets. Efficient viral lysis was achieved with a nontoxic buffer containing sucrose, KCl, proteinase K, and carrier RNA. Viral RNA binding to glass fiber membranes was concentration dependent across seven orders of magnitude (4.0–10.0 log10 copies/μL) and significantly increased with an acidic arginine binding buffer. For the clinical evaluation, 36 dengue virus (DENV)-positive serum samples were extracted in duplicate with the optimized RNAES protocol and once in an EMAG instrument (bioMérieux). DENV RNA was successfully extracted from 71/72 replicates (98.6%) in the RNAES protocol, and real-time RT-PCR cycle threshold (CT) values correlated between extraction methods. DENV RNA, extracted from clinical samples, was stable when stored on dried RNAES membranes at ambient temperature for up to 35 days, with median eluate RNA concentration decreasing by 0.18 and 0.29 log10 copies/μL between day 0 and days 7 and 35, respectively. At a cost of $0.08/sample, RNAES packets address key limitations to available protocols and may increase capacity for molecular detection of RNA viruses. IMPORTANCE RNA extraction methods and ultra-cold storage requirements limit molecular testing for common viruses. We developed a simple, flexible, and economical method that simultaneously addresses these limitations. At $0.08/sample, the new RNAExtraction and Storage (RNAES) protocol successfully extracted viral RNA from acute-phase sera and provided stable, ambient-temperature RNA storage for 35 days. Using this approach, we expect to improve RNA virus detection and outbreak response in resource-constrained settings.
Collapse
|
15
|
Alster S, Dafa-Berger A, Gafni A, Levy M. Pseudozyma aphidis Suppresses Microbe-Associated Molecular Pattern (MAMP)-Triggered Callose Deposition and Can Penetrate Leaf Tissue. Microbiol Spectr 2022; 10:e0263821. [PMID: 35234494 PMCID: PMC8941903 DOI: 10.1128/spectrum.02638-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
Beneficial microorganisms need to overcome the plant defense system to establish on or within plant tissues. Like pathogens, beneficial microbes can manipulate a plant's immunity pathways, first by suppressing and hiding to establish on the host and then by inducing resistance to protect the plant. In the current study, we demonstrated that although Pseudozyma aphidis can activate microbe-associated molecular pattern (MAMP)-associated genes, it does not activate MAMP-triggered callose deposition and can, moreover, suppress such deposition triggered by Flg22 or chitin. While MAMP-associated gene activation by P. aphidis was not dependent on salicylic acid, jasmonic acid, or ethylene signaling, suppression of MAMP-triggered callose deposition required the salicylic acid and jasmonic acid signaling factors JAR1-1 and E3 ubiquitin ligase COI1 yet did not rely on EIN2, NPR1, or the transcription factor JIN1/MYC2. We also demonstrated the ability of P. aphidis, known to be an epiphytic yeast-like organism, to penetrate the stomata and establish within plant tissues, as do endophytes. These results thus demonstrate the potential of P. aphidis to suppress MAMP-elicited defenses in order to establish on and within host plant tissues. IMPORTANCE Our study demonstrates the ability of P. aphidis to penetrate into plant tissues, where it avoids and overcomes plant defense systems in order to establish and subsequently protect the plant.
Collapse
Affiliation(s)
- Shanee Alster
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avis Dafa-Berger
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aviva Gafni
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maggie Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
16
|
Lugassi N, Stein O, Egbaria A, Belausov E, Zemach H, Arad T, Granot D, Carmi N. Sucrose Synthase and Fructokinase Are Required for Proper Meristematic and Vascular Development. PLANTS 2022; 11:plants11081035. [PMID: 35448763 PMCID: PMC9025968 DOI: 10.3390/plants11081035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 11/25/2022]
Abstract
Sucrose synthase (SuSy) and fructokinase (FRK) work together to control carbohydrate flux in sink tissues. SuSy cleaves sucrose into fructose and UDP-glucose; whereas FRK phosphorylates fructose. Previous results have shown that suppression of the SUS1,3&4 genes by SUS-RNAi alters auxin transport in the shoot apical meristems of tomato plants and affects cotyledons and leaf structure; whereas antisense suppression of FRK2 affects vascular development. To explore the joint developmental roles of SuSy and FRK, we crossed SUS-RNAi plants with FRK2-antisense plants to create double-mutant plants. The double-mutant plants exhibited novel phenotypes that were absent from the parent lines. About a third of the plants showed arrested shoot apical meristem around the transition to flowering and developed ectopic meristems. Use of the auxin reporter DR5::VENUS revealed a significantly reduced auxin response in the shoot apical meristems of the double-mutant, indicating that auxin levels were low. Altered inflorescence phyllotaxis and significant disorientation of vascular tissues were also observed. In addition, the fruits and the seeds of the double-mutant plants were very small and the seeds had very low germination rates. These results show that SUS1,3&4 and FRK2 enzymes are jointly essential for proper meristematic and vascular development, and for fruit and seed development.
Collapse
Affiliation(s)
- Nitsan Lugassi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
| | - Ofer Stein
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Aiman Egbaria
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
| | - Eduard Belausov
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
| | - Hanita Zemach
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
| | - Tal Arad
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
| | - David Granot
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
| | - Nir Carmi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel; (N.L.); (O.S.); (A.E.); (E.B.); (H.Z.); (T.A.); (D.G.)
- Correspondence:
| |
Collapse
|
17
|
Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant. Nat Ecol Evol 2022; 6:383-396. [PMID: 35210578 PMCID: PMC8986537 DOI: 10.1038/s41559-022-01673-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/07/2021] [Indexed: 12/31/2022]
Abstract
The community structure in the plant-associated microbiome depends collectively on host–microbe, microbe–microbe and host–microbe–microbe interactions. The ensemble of interactions between the host and microbial consortia may lead to outcomes that are not easily predicted from pairwise interactions. Plant–microbe–microbe interactions are important to plant health but could depend on both host and microbe strain variation. Here we study interactions between groups of naturally co-existing commensal and pathogenic Pseudomonas strains in the Arabidopsis thaliana phyllosphere. We find that commensal Pseudomonas prompt a host response that leads to selective inhibition of a specific pathogenic lineage, resulting in plant protection. The extent of protection depends on plant genotype, supporting that these effects are host-mediated. Strain-specific effects are also demonstrated by one individual Pseudomonas isolate eluding the plant protection provided by commensals. Our work highlights how within-species genetic differences in both hosts and microbes can affect host–microbe–microbe dynamics. The authors conduct competition experiments with multiple strains of Pseudomonas (some pathogenic and some commensal) in the phylosphere microbiome of Arabidopsis plants, showing that both the host and the commensal strains interact to inhibit the pathogenic strains.
Collapse
|
18
|
Baliarsingh S, Sahoo S, Jo YH, Han YS, Sarkar A, Lee YS, Mohanty J, Patnaik BB. Molecular cloning, sequence characterization, and expression analysis of C-type lectin (CTL) and ER-Golgi intermediate compartment 53-kDa protein (ERGIC-53) homologs from the freshwater prawn, Macrobrachium rosenbergii. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2022; 30:1011-1035. [PMID: 35153391 PMCID: PMC8816683 DOI: 10.1007/s10499-022-00845-3] [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: 05/31/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Lectin protein families are diverse and multi-functional in crustaceans. The carbohydrate-binding domains (CRDs) of lectins recognize the molecular patterns associated with pathogens and orchestrate important roles in crustacean defense. In this study, two lectin homologs, a single CRD containing C-type lectin (CTL) and an L-type lectin (LTL) domain containing endoplasmic reticulum Golgi intermediate compartment 53 kDa protein (ERGIC-53) were identified from the freshwater prawn, Macrobrachium rosenbergii. The open reading frames of MrCTL and MrERGIC-53 were 654 and 1,515 bp, encoding polypeptides of 217 and 504 amino acids, respectively. Further, MrCTL showed a 20-amino acid transmembrane helix region and 10 carbohydrate-binding residues within the CRD. MrERGIC-53 showed a signal peptide region, a type-I transmembrane region, and a coiled-coil region at the C-terminus. Phylogenetic analysis revealed a close relationship between MrCTL and MrLectin and M. nipponense CTL (MnCTL), whereas MrERGIC-53 shared high sequence identity with Eriocheir sinensis ERGIC-53 and Penaeus vannamei MBL-1. A homology-based model predicted small carbohydrate-combining sites with a metal-binding site for ligand binding (Ca2+ binding site) in MrCTL and beta-sheets connected by short loops and beta-bends forming a dome-shaped beta-barrel structure representing the LTL domain of MrERGIC-53. Quantitative real-time polymerase chain reaction detected MrCTL and MrERGIC-53 transcripts in all examined tissues, with particularly high levels observed in hemocytes, hepatopancreas, and mucosal-associated tissues, such as the stomach and intestine. Further, the expression levels of MrCTL and MrERGIC-53 transcripts were remarkably altered after V. harveyi challenge, suggesting putative function in host innate immunity. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10499-022-00845-3.
Collapse
Affiliation(s)
- Snigdha Baliarsingh
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Vyasa Vihar, Nuapadhi, Balasore, 756089 Odisha India
| | - Sonalina Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 Odisha India
| | - Yong Hun Jo
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture, School of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yeon Soo Han
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture, School of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Arup Sarkar
- School of Biotech Sciences, Trident Academy of Creative Technology, Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, 751024 Odisha India
| | - Yong Seok Lee
- School of Life Sciences and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan City, Asan, South Korea
| | - Jyotirmaya Mohanty
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002 Odisha India
| | - Bharat Bhusan Patnaik
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Vyasa Vihar, Nuapadhi, Balasore, 756089 Odisha India
| |
Collapse
|
19
|
Arenas-M A, Castillo FM, Godoy D, Canales J, Calderini DF. Transcriptomic and Physiological Response of Durum Wheat Grain to Short-Term Heat Stress during Early Grain Filling. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010059. [PMID: 35009063 PMCID: PMC8747107 DOI: 10.3390/plants11010059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 05/14/2023]
Abstract
In a changing climate, extreme weather events such as heatwaves will be more frequent and could affect grain weight and the quality of crops such as wheat, one of the most significant crops in terms of global food security. In this work, we characterized the response of Triticum turgidum L. spp. durum wheat to short-term heat stress (HS) treatment at transcriptomic and physiological levels during early grain filling in glasshouse experiments. We found a significant reduction in grain weight (23.9%) and grain dimensions from HS treatment. Grain quality was also affected, showing a decrease in starch content (20.8%), in addition to increments in grain protein levels (14.6%), with respect to the control condition. Moreover, RNA-seq analysis of durum wheat grains allowed us to identify 1590 differentially expressed genes related to photosynthesis, response to heat, and carbohydrate metabolic process. A gene regulatory network analysis of HS-responsive genes uncovered novel transcription factors (TFs) controlling the expression of genes involved in abiotic stress response and grain quality, such as a member of the DOF family predicted to regulate glycogen and starch biosynthetic processes in response to HS in grains. In summary, our results provide new insights into the extensive transcriptome reprogramming that occurs during short-term HS in durum wheat grains.
Collapse
Affiliation(s)
- Anita Arenas-M
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile; (A.A.-M.); (F.M.C.)
- ANID—Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Francisca M. Castillo
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile; (A.A.-M.); (F.M.C.)
- ANID—Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Diego Godoy
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile;
| | - Javier Canales
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile; (A.A.-M.); (F.M.C.)
- ANID—Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Correspondence: (J.C.); (D.F.C.)
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia 5110566, Chile;
- Correspondence: (J.C.); (D.F.C.)
| |
Collapse
|
20
|
Amaral C, Antunes W, Moe E, Duarte AG, Lima LMP, Santos C, Gomes IL, Afonso GS, Vieira R, Teles HSS, Reis MS, da Silva MAR, Henriques AM, Fevereiro M, Ventura MR, Serrano M, Pimentel C. A molecular test based on RT-LAMP for rapid, sensitive and inexpensive colorimetric detection of SARS-CoV-2 in clinical samples. Sci Rep 2021; 11:16430. [PMID: 34385527 PMCID: PMC8361189 DOI: 10.1038/s41598-021-95799-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022] Open
Abstract
Until there is an effective implementation of COVID-19 vaccination program, a robust testing strategy, along with prevention measures, will continue to be the most viable way to control disease spread. Such a strategy should rely on disparate diagnostic tests to prevent a slowdown in testing due to lack of materials and reagents imposed by supply chain problems, which happened at the beginning of the pandemic. In this study, we have established a single-tube test based on RT-LAMP that enables the visual detection of less than 100 viral genome copies of SARS-CoV-2 within 30 min. We benchmarked the assay against the gold standard test for COVID-19 diagnosis, RT-PCR, using 177 nasopharyngeal RNA samples. For viral loads above 100 copies, the RT-LAMP assay had a sensitivity of 100% and a specificity of 96.1%. Additionally, we set up a RNA extraction-free RT-LAMP test capable of detecting SARS-CoV-2 directly from saliva samples, albeit with lower sensitivity. The saliva was self-collected and the collection tube remained closed until inactivation, thereby ensuring the protection of the testing personnel. As expected, RNA extraction from saliva samples increased the sensitivity of the test. To lower the costs associated with RNA extraction, we performed this step using an alternative protocol that uses plasmid DNA extraction columns. We also produced the enzymes needed for the assay and established an in-house-made RT-LAMP test independent of specific distribution channels. Finally, we developed a new colorimetric method that allowed the detection of LAMP products by the visualization of an evident color shift, regardless of the reaction pH.
Collapse
Affiliation(s)
- Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Wilson Antunes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr. Alfredo Bensaúde, 1849-012, Lisbon, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Luís M P Lima
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Cristiana Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Inês L Gomes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr. Alfredo Bensaúde, 1849-012, Lisbon, Portugal
| | - Gonçalo S Afonso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Ricardo Vieira
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr. Alfredo Bensaúde, 1849-012, Lisbon, Portugal
| | - Helena Sofia S Teles
- Centro de Medicina Naval-Marinha Portuguesa, Alfeite, 2810-001, Almada, Portugal
| | - Marisa S Reis
- Centro de Medicina Naval-Marinha Portuguesa, Alfeite, 2810-001, Almada, Portugal
| | | | - Ana Margarida Henriques
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Laboratório de Virologia, Av. República, Quinta do Marquês, 2780-157, Oeiras, Portugal
| | - Miguel Fevereiro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Laboratório de Virologia, Av. República, Quinta do Marquês, 2780-157, Oeiras, Portugal
| | - M Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal.
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal.
| |
Collapse
|
21
|
Juang DS, Juang TD, Dudley DM, Newman CM, Accola MA, Rehrauer WM, Friedrich TC, O'Connor DH, Beebe DJ. Oil immersed lossless total analysis system for integrated RNA extraction and detection of SARS-CoV-2. Nat Commun 2021; 12:4317. [PMID: 34262053 PMCID: PMC8280165 DOI: 10.1038/s41467-021-24463-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic exposed difficulties in scaling current quantitative PCR (qPCR)-based diagnostic methodologies for large-scale infectious disease testing. Bottlenecks include lengthy multi-step processes for nucleic acid extraction followed by qPCR readouts, which require costly instrumentation and infrastructure, as well as reagent and plastic consumable shortages stemming from supply chain constraints. Here we report an Oil Immersed Lossless Total Analysis System (OIL-TAS), which integrates RNA extraction and detection onto a single device that is simple, rapid, cost effective, and requires minimal supplies and infrastructure to perform. We validated the performance of OIL-TAS using contrived SARS-CoV-2 viral particle samples and clinical nasopharyngeal swab samples. OIL-TAS showed a 93% positive predictive agreement (n = 57) and 100% negative predictive agreement (n = 10) with clinical SARS-CoV-2 qPCR assays in testing clinical samples, highlighting its potential to be a faster, cheaper, and easier-to-deploy alternative for infectious disease testing. Bottlenecks in qPCR-based COVID-19 diagnostics include the lengthy multistep process and reagent shortages. Here the authors report OIL-TAS which integrates RNA extraction and detection into a single device.
Collapse
Affiliation(s)
- Duane S Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Terry D Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Christina M Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
22
|
Kelly G, Brandsma D, Egbaria A, Stein O, Doron-Faigenboim A, Lugassi N, Belausov E, Zemach H, Shaya F, Carmi N, Sade N, Granot D. Guard cells control hypocotyl elongation through HXK1, HY5, and PIF4. Commun Biol 2021; 4:765. [PMID: 34155329 PMCID: PMC8217561 DOI: 10.1038/s42003-021-02283-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
The hypocotyls of germinating seedlings elongate in a search for light to enable autotrophic sugar production. Upon exposure to light, photoreceptors that are activated by blue and red light halt elongation by preventing the degradation of the hypocotyl-elongation inhibitor HY5 and by inhibiting the activity of the elongation-promoting transcription factors PIFs. The question of how sugar affects hypocotyl elongation and which cell types stimulate and stop that elongation remains unresolved. We found that overexpression of a sugar sensor, Arabidopsis hexokinase 1 (HXK1), in guard cells promotes hypocotyl elongation under white and blue light through PIF4. Furthermore, expression of PIF4 in guard cells is sufficient to promote hypocotyl elongation in the light, while expression of HY5 in guard cells is sufficient to inhibit the elongation of the hy5 mutant and the elongation stimulated by HXK1. HY5 exits the guard cells and inhibits hypocotyl elongation, but is degraded in the dark. We also show that the inhibition of hypocotyl elongation by guard cells' HY5 involves auto-activation of HY5 expression in other tissues. It appears that guard cells are capable of coordinating hypocotyl elongation and that sugar and HXK1 have the opposite effect of light on hypocotyl elongation, converging at PIF4.
Collapse
Affiliation(s)
- Gilor Kelly
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Danja Brandsma
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Aiman Egbaria
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Stein
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Adi Doron-Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Nitsan Lugassi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Eduard Belausov
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Hanita Zemach
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Felix Shaya
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Nir Carmi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Nir Sade
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - David Granot
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel.
| |
Collapse
|
23
|
Park J, Woo S, Kim J, Lee H, Yoo YE, Hong S. Rapid and simple single-chamber nucleic acid detection system prepared through nature-inspired surface engineering. Am J Cancer Res 2021; 11:6735-6745. [PMID: 34093850 PMCID: PMC8171086 DOI: 10.7150/thno.57153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Nucleic acid (NA)-based diagnostics enable a rapid response to various diseases, but current techniques often require multiple labor-intensive steps, which is a major obstacle to successful translation to a clinical setting. Methods: We report on a surface-engineered single-chamber device for NA extraction and in situ amplification without sample transfer. Our system has two reaction sites: a NA extraction chamber whose surface is patterned with micropillars and a reaction chamber filled with reagents for in situ polymerase-based NA amplification. These two sites are integrated in a single microfluidic device; we applied plastic injection molding for cost-effective, mass-production of the designed device. The micropillars were chemically activated via a nature-inspired silica coating to possess a specific affinity to NA. Results: As a proof-of-concept, a colorimetric pH indicator was coupled to the on-chip analysis of NA for the rapid and convenient detection of pathogens. The NA enrichment efficiency was dependent on the lysate incubation time, as diffusion controls the NA contact with the engineered surface. We could detect down to 1×103 CFU by the naked eye within one hour of the total assay time. Conclusion: We anticipate that the surface engineering technique for NA enrichment could be easily integrated as a part of various types of microfluidic chips for rapid and convenient nucleic acid-based diagnostics.
Collapse
|
24
|
Canales J, Verdejo J, Carrasco-Puga G, Castillo FM, Arenas-M A, Calderini DF. Transcriptome Analysis of Seed Weight Plasticity in Brassica napus. Int J Mol Sci 2021; 22:4449. [PMID: 33923211 PMCID: PMC8123204 DOI: 10.3390/ijms22094449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source-sink (S-S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S-S ratio. We found that a reduction in the S-S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW-SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield.
Collapse
Affiliation(s)
- Javier Canales
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile; (F.M.C.); (A.A.-M.)
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), 8331150 Santiago, Chile
| | - José Verdejo
- Graduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
| | - Gabriela Carrasco-Puga
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
| | - Francisca M. Castillo
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile; (F.M.C.); (A.A.-M.)
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), 8331150 Santiago, Chile
| | - Anita Arenas-M
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile; (F.M.C.); (A.A.-M.)
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), 8331150 Santiago, Chile
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
| |
Collapse
|
25
|
Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
Collapse
Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
26
|
Lebreton M, Sire S, Carayon JL, Malgouyres JM, Vignet C, Géret F, Bonnafé E. Low concentrations of oxazepam induce feeding and molecular changes in Radix balthica juveniles. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 230:105694. [PMID: 33316747 DOI: 10.1016/j.aquatox.2020.105694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
Psychotropics, especially benzodiazepines, are commonly prescribed worldwide. Poorly eliminated at wastewater treatment plants, they belong to a group of emerging contaminants. Due to their interaction with the GABAA receptor, they may affect the function of the nervous system of non-target organisms, such as aquatic organisms. The toxicity of oxazepam, a very frequently detected benzodiazepine in continental freshwater, has been largely studied in aquatic vertebrates over the last decade. However, its effects on freshwater non-vertebrates have received much less attention. We aimed to evaluate the long-term effects of oxazepam on the juvenile stage of a freshwater gastropod widespread in Europe, Radix balthica. Juveniles were exposed for a month to environmentally-relevant concentrations of oxazepam found in rivers (0.8 μg/L) and effluents (10 μg/L). Three main physiological functions were studied: feeding, growth, and locomotion. Additionally, gene expression analysis was performed to provide insights into toxicity mechanisms. There was a strong short-term activation of the feeding rate at low concentration, whereas the high dose resulted in long-term inhibition of food intake. A significant decrease in mortality rate was observed in juveniles exposed to the lowest dose. Shell growth and locomotor activity did not appear to be affected by oxazepam. Transcriptomic analysis revealed global over-expression of genes involved in the nervous regulation of the feeding, digestive, and locomotion systems after oxazepam exposure. The molecular analysis also revealed a possible interference of animal manipulation with the molecular effects induced by oxazepam exposure. Overall, these results improve our understanding of the effects of the psychoactive drug oxazepam on an aquatic mollusc gastropod.
Collapse
Affiliation(s)
- Morgane Lebreton
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| | - Sacha Sire
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| | - Jean-Luc Carayon
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| | - Jean-Michel Malgouyres
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| | - Caroline Vignet
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| | - Florence Géret
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| | - Elsa Bonnafé
- Biochimie et Toxicologie des Substances Bioactives, EA 7417, INU Champollion, Albi, France.
| |
Collapse
|
27
|
Frequent asymptomatic infection with tobacco ringspot virus on melon fruit. Virus Res 2020; 293:198266. [PMID: 33347906 DOI: 10.1016/j.virusres.2020.198266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 11/22/2022]
Abstract
Melon is one of the most popular fruits worldwide and has been bred into various cultivars. RNA-sequencing using healthy melon fruit was performed to determine differences in gene expression among cultivars. Unexpected RNA-seq results revealed that viruses asymptomatically infected fruits at a high frequency (16 of 21 fruits examined were infected) and that viral transcripts highly accumulated in comparison with host transcripts (15 %-75 % of total reads). Their nucleotide sequences and phylogenetic analyses indicated that more than 10 novel isolates of tobacco ringspot virus (TRSV) were found in melon fruits. Asymptomatic infection with TRSV on melon fruits was confirmed by both immunoblot and RT-PCR analyses. Numerous isolates of TRSV generated and maintained in melon fields, and this is likely due to their asymptomatic infections. This TRSV melon isolate infected Nicotiana benthamiana plants with stunting and yellowing symptoms. This is the first report of frequent and asymptomatic infection of TRSV in consumable melon fruits.
Collapse
|
28
|
Bukhari SI, Alfawaz H, Al-Dbass A, Bhat RS, Moubayed NMS, Bukhari W, Hassan SA, Merghani N, Elsamaligy S, El-Ansary A. Efficacy of Novavit in ameliorating the neurotoxicity of propionic acid. Transl Neurosci 2020; 11:134-146. [PMID: 33312719 PMCID: PMC7705989 DOI: 10.1515/tnsci-2020-0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/08/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023] Open
Abstract
Oxidative stress, abnormal fatty acid metabolism, and impaired gut microbiota play a serious role in the pathology of autism. The use of dietary supplements to improve the core symptoms of autism is a common therapeutic strategy. The present study analyzed the effects of oral supplementation with Novavit, a multi-ingredient supplement, on ameliorating oxidative stress and impaired lipid metabolism in a propionic acid (PPA)-induced rodent model of autism. Male western albino rats were divided into three groups. The first group is the control, the second group was given an oral neurotoxic dose of PPA (250 mg/kg body weight/day) for 3 days and then received buffered saline until the end of the experiment. The third group received Novavit (70 mg/kg body weight/day for 30 days after the 3-day PPA treatment). Markers of oxidative stress and impaired fatty acid metabolism were measured in brain homogenates obtained from each group. Novavit modulation of the gut microbiota was also evaluated. While PPA induced significant increases in lipid peroxides and 5-lipoxygenase, together with significantly decreased glutathione, and cyclooxygenase 2, oral supplementation with Novavit ameliorated PPA-induced oxidative stress and impaired fatty acid metabolism. Our results showed that the presence of multivitamins, coenzyme Q10, minerals, and colostrum, the major components of Novavit, protects against PPA-induced neurotoxicity.
Collapse
Affiliation(s)
- Sarah I. Bukhari
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hanan Alfawaz
- Department of Food Science and Nutrition, College of Food Science and Agriculture, King Saud University, Riyadh, Saudi Arabia
| | - Abeer Al-Dbass
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ramesa Shafi Bhat
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nadine MS Moubayed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wadha Bukhari
- Central Laboratory, Female Center for Medical Studies and Scientific Section, King Saud University, P O Box 22452, Riyadh, Saudi Arabia
| | | | - Nada Merghani
- Central Laboratory, Female Center for Medical Studies and Scientific Section, King Saud University, P O Box 22452, Riyadh, Saudi Arabia
| | - Samar Elsamaligy
- Department of Pharamaceutics and Industrial Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Afaf El-Ansary
- Central Laboratory, Female Center for Medical Studies and Scientific Section, King Saud University, P O Box 22452, Riyadh, Saudi Arabia
- Therapeutic Department, National Research Centre, Dokki, Egypt
| |
Collapse
|
29
|
Keshavarz M, Jo YH, Edosa TT, Han YS. Tenebrio molitor PGRP-LE Plays a Critical Role in Gut Antimicrobial Peptide Production in Response to Escherichia coli. Front Physiol 2020; 11:320. [PMID: 32372972 PMCID: PMC7179671 DOI: 10.3389/fphys.2020.00320] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/20/2020] [Indexed: 12/15/2022] Open
Abstract
Invading pathogens are recognized by peptidoglycan recognition proteins (PGRPs) that induce translocation of NF-κB transcription proteins and expression of robust antimicrobial peptides (AMPs). Tenebrio molitor PGRP-LE (TmPGRP-LE) has been previously identified as a key sensor of Listeria monocytogenes infection. Here, we present that TmPGRP-LE is highly expressed in the gut of T. molitor larvae and 5-day-old adults in the absence of microbial infection. In response to Escherichia coli and Candida albicans infections, TmPGRP-LE mRNA levels are significantly upregulated in both the fat body and gut. Silencing of TmPGRP-LE by RNAi rendered T. molitor significantly more susceptible to challenge by E. coli infection and, to a lesser extent, Staphylococcus aureus and C. albicans infections. Reduction of TmPGRP-LE levels in the larval gut resulted in downregulation of eight AMP genes following exposure to E. coli, S. aureus, and C. albicans. However, the transcriptional levels of AMPs more rapidly reached a higher level in the dsEGFP-treated larval gut after challenge with E. coli, which may suggest that AMPs induction were more sensitive to E. coli than S. aureus and C. albicans. In addition, TmPGRP-LE RNAi following E. coli and C. albicans challenges had notable effects on TmRelish, TmDorsal X1 isoform (TmDorX1), and TmDorX2 expression level in the fat body and gut. Taken together, TmPGRP-LE acts as an important gut microbial sensor that induces AMPs via Imd activation in response to E. coli, whereas involvement of TmPGRP-LE in AMPs synthesize is barely perceptible in the hemocytes and fat body.
Collapse
Affiliation(s)
- Maryam Keshavarz
- Department of Applied Biology, College of Agriculture and Life Sciences, Institute of Environmentally-Friendly Agriculture (IEFA), Chonnam National University, Gwangju, South Korea
| | - Yong Hun Jo
- Department of Applied Biology, College of Agriculture and Life Sciences, Institute of Environmentally-Friendly Agriculture (IEFA), Chonnam National University, Gwangju, South Korea
| | - Tariku Tesfaye Edosa
- Department of Applied Biology, College of Agriculture and Life Sciences, Institute of Environmentally-Friendly Agriculture (IEFA), Chonnam National University, Gwangju, South Korea
| | - Yeon Soo Han
- Department of Applied Biology, College of Agriculture and Life Sciences, Institute of Environmentally-Friendly Agriculture (IEFA), Chonnam National University, Gwangju, South Korea
| |
Collapse
|
30
|
TmPGRP-SA regulates Antimicrobial Response to Bacteria and Fungi in the Fat Body and Gut of Tenebrio molitor. Int J Mol Sci 2020; 21:ijms21062113. [PMID: 32204438 PMCID: PMC7139795 DOI: 10.3390/ijms21062113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/09/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial immune response is mediated by a signal-transducing sensor, peptidoglycan recognition protein-SA (PGRP-SA), that can recognize non-self molecules. Although several studies have focused on the involvement of Drosophila PGRP-SA in antimicrobial peptide (AMP) expression in response to infections, studies on its role in Tenebrio molitor are lacking. Here, we present a functional analysis of T. molitor PGRP-SA (TmPGRP-SA). In the absence of microbes, TmPGRP-SA was highly expressed in the late-larval fat body, followed by hemocytes, and gut. Interestingly, following Escherichia coli, Staphylococcus aureus, and Candida albicans infections, the mRNA level of TmPGRP-SA was significantly upregulated in both the fat body and gut. TmPGRP-SA silencing had a significant effect on the mortality rates for all the microbes tested. Moreover, TmPGRP-SA is required for regulating the expression of eight AMP genes namely TmTenecin-1, -2, and -4; TmDefensin-1 and -2; TmColeoptericin-1; and TmAttacin-1b and -2 in the fat body in response to E. coli and S. aureus infections. TmPGRP-SA is essential for the transcription of TmTenecin-2, -4; TmDefensin-2; TmColeoptericin-1, -2; and TmAttacin-1a, -1b, and -2 in the gut upon E. coli and C. albicans infections. However, TmPGRP-SA does not regulate AMP expression in the hemocytes. Additionally, TmDorsal isoform X2, a downstream Toll transcription factor, was downregulated in TmPGRP-SA-silenced larval fat body following E. coli and S. aureus challenges, and in the gut following E. coli and C. albicans challenges.
Collapse
|
31
|
Two Roles for the Tenebrio molitor Relish in the Regulation of Antimicrobial Peptides and Autophagy-Related Genes in Response to Listeria monocytogenes. INSECTS 2020; 11:insects11030188. [PMID: 32188156 PMCID: PMC7142762 DOI: 10.3390/insects11030188] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/04/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022]
Abstract
Relish is a key NF-κB transcription factor of the immune-deficiency (Imd) pathway that combats infection by regulating antimicrobial peptides (AMPs). Understanding of the fundamental role of Tenebrio molitor Relish (TmRelish) in controlling of Listeria monocytogenes virulence through the regulation of both AMPs and autophagy-related (ATG) genes is unclear. Here, we show that TmRelish transcripts were highly abundant in the larval fat body and hemocytes compared to the gut upon L. monocytogenes infection. Furthermore, significant mortality was observed in TmRelish-silenced larvae after intracellular insult. To investigate the cause of this lethality, we measured the induction of AMPs and ATG genes in the TmRelish dsRNA-treated T. molitor larvae. The expression of TmTenecin-1, TmTenecin-4, TmColeptericin-1, TmAttacin-2, and TmCecropin-2 were suppressed in the fat body and hemocytes of dsTmRelish-injected larvae during L. monocytogenes infection. In addition, TmRelish knockdown led to a noticeable downregulation of TmATG1 (a serine-threonine protein kinase) in the fat body and hemocytes of young larvae 6 h post-infection (pi). The notable increase of autophagy genes in the early stage of infection (6 h pi), suggesting autophagy response is crucial for Listeria clearance. Taken together, these results suggest that TmRelish plays pivotal roles in not only regulation of AMP genes but also induction of autophagy genes in response to L. monocytogenes challenge in fat body and hemocytes of T. molitor larvae. Furthermore, negative regulation of several AMPs by TmRelish in the fat body, hemocytes, and gut leaves open the possibility of a crosstalk between Toll and Imd pathway.
Collapse
|
32
|
TmSpz4 Plays an Important Role in Regulating the Production of Antimicrobial Peptides in Response to Escherichia coli and Candida albicans Infections. Int J Mol Sci 2020; 21:ijms21051878. [PMID: 32182940 PMCID: PMC7084639 DOI: 10.3390/ijms21051878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/19/2020] [Accepted: 03/07/2020] [Indexed: 12/20/2022] Open
Abstract
Spätzle family proteins activate the Toll pathway and induce antimicrobial peptide (AMP) production against microbial infections. However, the functional importance of Tmspätzle4 (TmSpz4) in the immune response of Tenebrio molitor has not been reported. Therefore, here, we have identified and functionally characterized the role of TmSpz4 against bacterial and fungal infections. We showed that TmSpz4 expression was significantly induced in hemocytes at 6 h post-injection with Escherichia coli, Staphylococcus aureus, and Candida albicans. TmSpz4 knock-down significantly reduced larval survival against E. coli and C. albicans. To understand the reason for the survivability difference, the role of TmSpz4 in AMP production was examined in TmSpz4-silenced larvae following microbe injection. The AMPs that are active against Gram-negative bacteria, including TmTenecin-2, TmTenecin-4, TmAttacin-1a, TmDefensin-2, and TmCecropin-2, were significantly downregulated in response to E. coli in TmSpz4-silenced larvae. Similarly, the expression of TmTenecin-1, TmTenecin-3, TmThaumatin-like protein-1 and -2, TmDefensin-1, TmDefensin-2, and TmCecropin-2 were downregulated in response to C. albicans in TmSpz4-silenced larvae. In addition, the transcription factor NF-κB (TmDorX1 and TmDorX2) expression was significantly suppression in TmSpz4-silenced larvae. In conclusion, these results suggest that TmSpz4 plays a key role in regulating immune responses of T. molitor against to E. coli and C. albicans.
Collapse
|
33
|
Keshavarz M, Jo YH, Patnaik BB, Park KB, Ko HJ, Kim CE, Edosa TT, Lee YS, Han YS. TmRelish is required for regulating the antimicrobial responses to Escherichia coli and Staphylococcus aureus in Tenebrio molitor. Sci Rep 2020; 10:4258. [PMID: 32144366 PMCID: PMC7060202 DOI: 10.1038/s41598-020-61157-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/18/2020] [Indexed: 11/09/2022] Open
Abstract
Relish, a transcription factor, is a critical downstream component of the immune deficiency (Imd) pathway and regulates host defense against bacterial infection by mediating antimicrobial peptide (AMP) synthesis. Understanding the immunological function of the mealworm beetle, Tenebrio molitor Relish (TmRelish) will be instructive in understanding insect immunity. In the present study, full-length ORF of TmRelish was retrieved from T. molitor-expressed sequence tags and RNA-seq database. The predicted TmRelish amino acid sequence contained an N-terminal Rel-homology domain; an Ig-like, plexin, and transcription factor domain; ankyrin repeat motifs; a nuclear localization signal; and a C-terminal death domain and shared the highly conserved structure of the Relish proteins of other insect species. TmRelish mRNA was detected in all developmental stages of the insect; however, the highest levels were detected in the larval gut tissue and adult hemocytes. TmRelish mRNA level was upregulated in the fat body, hemocyte, and gut tissue 9 h after infection of T. molitor larvae by the gram-negative bacteria, Escherichia coli. Furthermore, TmRelish knockdown led to significantly higher mortality of the E. coli-infected larvae, and significantly lower mortality of larvae infected with Staphylococcus aureus or Candida albicans. To elucidate the possible cause of mortality, we measured AMP transcription in the fat body, hemocytes, gut, and Malpighian tubules (MTs) of T. molitor larvae. TmRelish knockdown suppressed the expression of nine AMP genes in the larval fat body and gut tissue during E. coli infection, suggesting that TmRelish positively regulates AMP expression in both immune-related tissues, in response to E. coli challenge. Furthermore, negative regulation of some AMPs by TmRelish in the MTs, gut and hemocytes in response to C. albicans infection suggests a crosstalk between the Toll and Imd pathways.
Collapse
Affiliation(s)
- Maryam Keshavarz
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yong Hun Jo
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Bharat Bhusan Patnaik
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.,Department of Biotechnology, Trident Academy of Technology (TAT), F2-A, Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha, 751024, India
| | - Ki Beom Park
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hye Jin Ko
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chang Eun Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tariku Tesfaye Edosa
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yong Seok Lee
- School of Biotechnology and Life Sciences, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 31538, South Korea
| | - Yeon Soo Han
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| |
Collapse
|
34
|
Edosa TT, Jo YH, Keshavarz M, Park KB, Cho JH, Bae YM, Kim B, Lee YS, Han YS. TmAtg6 Plays an Important Role in Anti-Microbial Defense Against Listeria monocytogenes in the Mealworm, Tenebrio molitor. Int J Mol Sci 2020; 21:ijms21041232. [PMID: 32059408 PMCID: PMC7072900 DOI: 10.3390/ijms21041232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/17/2020] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Autophagy-related gene-6 (Beclin-1 in mammals) plays a pivotal role in autophagy and is involved in autophagosome formation and autolysosome maturation. In this study, we identified and characterized the autophagy-related gene-6 from Tenebrio molitor (TmAtg6) and analyzed its functional role in the survival of the insect against infection. The expression of TmAtg6 was studied using qRT-PCR for the assessment of the transcript levels at various developmental stages in the different tissues. The results showed that TmAtg6 was highly expressed at the 6-day-old pupal stage. Tissue-specific expression studies revealed that TmAtg6 was highly expressed in the hemocytes of late larvae. The induction patterns of TmAtg6 in different tissues of T. molitor larvae were analyzed by injecting Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, or Candida albicans. The intracellular Gram-positive bacteria, L. monocytogenes, solely induced the expression of TmAtg6 in hemocytes at 9 h-post-injection, whilst in the fat body and gut, bimodal expression times were observed. RNAi-mediated knockdown of the TmAtg6 transcripts, followed by a challenge with microbes, showed a significant reduction in larval survival rate against L. monocytogenes. Taken together, our results suggest that TmAtg6 plays an essential role in anti-microbial defense against intracellular bacteria.
Collapse
Affiliation(s)
- Tariku Tesfaye Edosa
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Yong Hun Jo
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Maryam Keshavarz
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Ki Beom Park
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Jun Ho Cho
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Young Min Bae
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Bobae Kim
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan City 31538, Korea;
| | - Yeon Soo Han
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (K.B.P.); (J.H.C.); (Y.M.B.); (B.K.)
- Correspondence: ; Tel.: +82-62-530-2072
| |
Collapse
|
35
|
Edosa TT, Jo YH, Keshavarz M, Bae YM, Kim DH, Lee YS, Han YS. TmSpz6 Is Essential for Regulating the Immune Response to Escherichia Coli and Staphylococcus Aureus Infection in Tenebrio Molitor. INSECTS 2020; 11:insects11020105. [PMID: 32033290 PMCID: PMC7074004 DOI: 10.3390/insects11020105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 12/20/2022]
Abstract
Spätzle is an extracellular protein that activates the Toll receptor during embryogenesis and immune responses in Drosophila. However, the functions of the spätzle proteins in the innate immune response against bacteria or fungi in T. molitor are not well understood. Therefore, in this study, the open reading frame (ORF) of TmSpz6 was identified and its function in the response to bacterial and fungal infections in T. molitor was investigated using RNAi. The highest expression of TmSpz6 was in prepupae, and 3- and 6-day-old pupae, while remarkable expression was also observed in other stages. The tissue-specific expression analysis showed that TmSpz6 expression was highest in the hemocytes of larvae. TmSpz6 expression was highly induced when challenged with Escherichia coli, Staphylococcus aureus, or Candida albicans at 6 h post-injection; however, TmSpz6-silenced larvae were significantly more susceptible to only E. coli and S. aureus infection. The antimicrobial peptides (AMPs) gene expression analysis results show that TmSpz6 mainly positively regulated the expression of TmTencin-2 and -3 in response to E. coli and S. aureus infection. Collectively, these results suggest that TmSpz6 plays an important role in regulating AMP expression and increases the survival of T. molitor against E. coli and S. aureus.
Collapse
Affiliation(s)
- Tariku Tesfaye Edosa
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (Y.M.B.); (D.H.K.)
- Ethiopian Institute of Agricultural Research, Ambo Agricultural Research Center, Ambo 37, Ethiopia
| | - Yong Hun Jo
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (Y.M.B.); (D.H.K.)
| | - Maryam Keshavarz
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (Y.M.B.); (D.H.K.)
| | - Young Min Bae
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (Y.M.B.); (D.H.K.)
| | - Dong Hyun Kim
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (Y.M.B.); (D.H.K.)
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Korea;
| | - Yeon Soo Han
- Department of Applied Biology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.E.); (Y.H.J.); (M.K.); (Y.M.B.); (D.H.K.)
- Correspondence: ; Tel.: +82-62-530-2072
| |
Collapse
|
36
|
Scherbakova A, Rykova V, Danilova K, Solovyev A, Egorova D. Extracellular RNA Isolation from Biofilm Matrix of Pseudomonas aeruginosa. Bio Protoc 2020. [DOI: 10.21769/bioprotoc.3810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
37
|
Lugassi N, Yadav BS, Egbaria A, Wolf D, Kelly G, Neuhaus E, Raveh E, Carmi N, Granot D. Expression of Arabidopsis Hexokinase in Tobacco Guard Cells Increases Water-Use Efficiency and Confers Tolerance to Drought and Salt Stress. PLANTS (BASEL, SWITZERLAND) 2019; 8:E613. [PMID: 31888275 PMCID: PMC6963886 DOI: 10.3390/plants8120613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 11/17/2022]
Abstract
Abiotic stresses such as drought and saline water impose major limitations on plant growth. Modulation of stomatal behavior may help plants cope with such stresses by reducing both water loss and salt uptake. Hexokinase (HXK) is a sugar-phosphorylating enzyme involved in guard cells' sugar-sensing, mediating stomatal closure and coordinating photosynthesis with transpiration. We generated transgenic tobacco lines expressing the Arabidopsis hexokinase1 (AtHXK1) under the guard cell-specific promoter KST1 and examined those plants using growth room and greenhouse experiments. The expression of AtHXK1 in tobacco guard cells reduced stomatal conductance and transpiration by about 25% with no negative effects on photosynthesis or growth, leading to increased water-use efficiency. In addition, these plants exhibited tolerance to drought and salt stress due to their lower transpiration rate, indicating that improved stomatal function has the potential to improve plant performance under stress conditions.
Collapse
Affiliation(s)
- Nitsan Lugassi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| | - Brijesh Singh Yadav
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| | - Aiman Egbaria
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| | - Dalia Wolf
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| | - Gilor Kelly
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| | - Efrat Neuhaus
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Gilat Research Center, Negev, Israel; (E.N.); (E.R.)
| | - Eran Raveh
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Gilat Research Center, Negev, Israel; (E.N.); (E.R.)
| | - Nir Carmi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| | - David Granot
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel; (N.L.); (B.S.Y.); (A.E.); (D.W.); (G.K.); (N.C.)
| |
Collapse
|
38
|
TmDorX2 positively regulates antimicrobial peptides in Tenebrio molitor gut, fat body, and hemocytes in response to bacterial and fungal infection. Sci Rep 2019; 9:16878. [PMID: 31728023 PMCID: PMC6856108 DOI: 10.1038/s41598-019-53497-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022] Open
Abstract
Dorsal, a member of the nuclear factor-kappa B (NF-κB) family of transcription factors, is a critical downstream component of the Toll pathway that regulates the expression of antimicrobial peptides (AMPs) against pathogen invasion. In this study, the full-length ORF of Dorsal was identified from the RNA-seq database of the mealworm beetle Tenebrio molitor (TmDorX2). The ORF of TmDorX2 was 1,482 bp in length, encoding a polypeptide of 493 amino acid residues. TmDorX2 contains a conserved Rel homology domain (RHD) and an immunoglobulin-like, plexins, and transcription factors (IPT) domain. TmDorX2 mRNA was detected in all developmental stages, with the highest levels observed in 3-day-old adults. TmDorX2 transcripts were highly expressed in the adult Malpighian tubules (MT) and the larval fat body and MT tissues. After challenging the larvae with Staphylococcus aureus and Escherichia coli, the TmDorX2 mRNA levels were upregulated 6 and 9 h post infection in the whole body, fat body, and hemocytes. Upon Candida albicans challenge, the TmDorX2 mRNA expression were found highest at 9 h post-infection in the fat body. In addition, TmDorX2-knockdown larvae exposed to E. coli, S. aureus, or C. albicans challenge showed a significantly increased mortality rate. Furthermore, the expression of 11 AMP genes was downregulated in the gut and fat body of dsTmDorX2-injected larvae upon E. coli challenge. After C. albicans and S. aureus challenge of dsTmDorX2-injected larvae, the expression of 11 and 10 AMPs was downregulated in the gut and fat body, respectively. Intriguingly, the expression of antifungal transcripts TmTenecin-3 and TmThaumatin-like protein-1 and -2 was greatly decreased in TmDorX2-silenced larvae in response to C. albicans challenge, suggesting that TmDorX2 regulates antifungal AMPs in the gut in response to C. albicans infection. The AMP expression profiles in the fat body, hemocytes, gut, and MTs suggest that TmDorX2 might have an important role in promoting the survival of T. molitor larvae against all mentioned pathogens.
Collapse
|
39
|
Patnaik BB, Kim BB, Jo YH, Bang IS. Molecular Cloning and Expression Analysis of Three Suppressors of Cytokine Signaling Genes ( SOCS5, SOCS6, SOCS7) in the Mealworm Beetle Tenebrio molitor. INSECTS 2019; 10:insects10030076. [PMID: 30884777 PMCID: PMC6468919 DOI: 10.3390/insects10030076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/06/2019] [Accepted: 03/09/2019] [Indexed: 12/28/2022]
Abstract
Suppressors of cytokine signaling (SOCS) influence cytokine and growth factor signaling by negatively regulating the Janus kinase (JAK)-signal transducers and activators of transcription (STAT) pathway to maintain homeostasis during immune responses. However, functional characterization of SOCS family members in invertebrates is limited. Here, we identified and evaluated three SOCS genes (type I sub-family) in the mealworm beetle Tenebrio molitor. The full-length open reading frames (ORFs) of TmSOCS5, TmSOCS6, and TmSOCS7 comprised of 1389, 897, and 1458 nucleotides, encoding polypeptides of 462, 297, and 485 amino acids, respectively. The SH2 and SOCS box domains of the TmSOCS C-terminal region were highly conserved. Phylogenetic analysis revealed that these SOCS genes were clustered within the type I subfamily that exhibits the highest amino acid identity with Tribolium castaneum SOCS genes. Contrary to TmSOCS7 expression, the expression levels of TmSOCS5 and TmSOCS6 were lower in the larval, pupal, and adult stages. In larvae and adults, the expression levels of TmSOCS5 and TmSOCS6 were highest in the hemocytes and ovaries, respectively. SOCS transcripts were also highly upregulated in the hemocytes of T. molitor larvae within 3–6 h post-infection with the fungus Candida albicans. Collectively, these results provide valuable information regarding the involvement of TmSOCS type-I subfamily in the host immune response of insects.
Collapse
Affiliation(s)
- Bharat Bhusan Patnaik
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea.
- School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandrasekharpur, Bhubaneswar, Odisha 751024, India.
| | - Bo Bae Kim
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea.
| | - Yong Hun Jo
- Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea.
| | - In Seok Bang
- Department of Biological Science and the Research Institute for Basic Sciences, Hoseo University, Asan 31499, Korea.
| |
Collapse
|
40
|
Effects of diethylcarbamazine and ivermectin treatment on Brugia malayi gene expression in infected gerbils ( Meriones unguiculatus). ACTA ACUST UNITED AC 2019; 5. [PMID: 33777408 PMCID: PMC7994942 DOI: 10.1017/pao.2019.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lymphatic filariasis (LF) threatens nearly 20% of the world’s population and has handicapped one-third of the 120 million people currently infected. Current control and elimination programs for LF rely on mass drug administration of albendazole plus diethylcarbamazine (DEC) or ivermectin. Only the mechanism of action of albendazole is well understood. To gain a better insight into antifilarial drug action in vivo, we treated gerbils harbouring patent Brugia malayi infections with 6 mg kg−1 DEC, 0.15 mg kg−1 ivermectin or 1 mg kg−1 albendazole. Treatments had no effect on the numbers of worms present in the peritoneal cavity of treated animals, so effects on gene expression were a direct result of the drug and not complicated by dying parasites. Adults and microfilariae were collected 1 and 7 days post-treatment and RNA isolated for transcriptomic analysis. The experiment was repeated three times. Ivermectin treatment produced the most differentially expressed genes (DEGs), 113. DEC treatment yielded 61 DEGs. Albendazole treatment resulted in little change in gene expression, with only 6 genes affected. In total, nearly 200 DEGs were identified with little overlap between treatment groups, suggesting that these drugs may interfere in different ways with processes important for parasite survival, development, and reproduction.
Collapse
|
41
|
Shi R, Lewis RS, Panthee DR. Filter paper-based spin column method for cost-efficient DNA or RNA purification. PLoS One 2018; 13:e0203011. [PMID: 30532193 PMCID: PMC6286138 DOI: 10.1371/journal.pone.0203011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/16/2018] [Indexed: 11/19/2022] Open
Abstract
We describe herein a method of recharging used commercial spin columns or assembling homemade spin columns using filter paper as binding material for cost-effective, low throughput nucleic acid purification. The efficiency of filter paper-based spin columns was evaluated for purification of nucleic acids from various sources. Following protocols of commercial kits, we found filter paper to be a useful binding material for purification of nucleic acids, including plant genomic DNA, plant total RNA, PCR products, and DNA from agarose gels. However, filter paper has a weak binding affinity to plasmid DNA in tested miniprep protocols. Protocols for the use of filter paper recharged spin columns or homemade spin columns for low throughput purification of plant genomic DNA and total RNA with unused commercial kit buffers or less expensive homemade buffers are presented.
Collapse
Affiliation(s)
- Rui Shi
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research & Extension Center, Mills River, NC, United States of America
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, United States of America
| | - Ramsey S. Lewis
- Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, United States of America
| | - Dilip R. Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research & Extension Center, Mills River, NC, United States of America
| |
Collapse
|
42
|
Henríquez-Valencia C, Arenas-M A, Medina J, Canales J. Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:470. [PMID: 29692794 PMCID: PMC5902692 DOI: 10.3389/fpls.2018.00470] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/26/2018] [Indexed: 05/10/2023]
Abstract
Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.
Collapse
Affiliation(s)
- Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Anita Arenas-M
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias, Universidad Austral de Chile, Valdivia, Chile
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Santiago, Chile
- *Correspondence: Javier Canales,
| |
Collapse
|
43
|
Kelly G, Sade N, Doron-Faigenboim A, Lerner S, Shatil-Cohen A, Yeselson Y, Egbaria A, Kottapalli J, Schaffer AA, Moshelion M, Granot D. Sugar and hexokinase suppress expression of PIP aquaporins and reduce leaf hydraulics that preserves leaf water potential. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:325-339. [PMID: 28390076 DOI: 10.1111/tpj.13568] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 05/27/2023]
Abstract
Sugars affect central aspects of plant physiology, including photosynthesis, stomatal behavior and the loss of water through the stomata. Yet, the potential effects of sugars on plant aquaporins (AQPs) and water conductance have not been examined. We used database and transcriptional analyses, as well as cellular and whole-plant functional techniques to examine the link between sugar-related genes and AQPs. Database analyses revealed a high level of correlation between the expression of AQPs and that of sugar-related genes, including the Arabidopsis hexokinases 1 (AtHXK1). Increased expression of AtHXK1, as well as the addition of its primary substrate, glucose (Glc), repressed the expression of 10 AQPs from the plasma membrane-intrinsic proteins (PIP) subfamily (PIP-AQPs) and induced the expression of two stress-related PIP-AQPs. The osmotic water permeability of mesophyll protoplasts of AtHXK1-expressing plants and the leaf hydraulic conductance of those plants were significantly reduced, in line with the decreased expression of PIP-AQPs. Conversely, hxk1 mutants demonstrated a higher level of hydraulic conductance, with increased water potential in their leaves. In addition, the presence of Glc reduced leaf water potential, as compared with an osmotic control, indicating that Glc reduces the movement of water from the xylem into the mesophyll. The production of sugars entails a significant loss of water and these results suggest that sugars and AtHXK1 affect the expression of AQP genes and reduce leaf water conductance, to coordinate sugar levels with the loss of water through transpiration.
Collapse
Affiliation(s)
- Gilor Kelly
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Nir Sade
- The Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Adi Doron-Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Stephen Lerner
- The Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Arava Shatil-Cohen
- The Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Yelena Yeselson
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Aiman Egbaria
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Jayaram Kottapalli
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Arthur A Schaffer
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Menachem Moshelion
- The Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - David Granot
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| |
Collapse
|
44
|
Stein O, Avin-Wittenberg T, Krahnert I, Zemach H, Bogol V, Daron O, Aloni R, Fernie AR, Granot D. Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development. FRONTIERS IN PLANT SCIENCE 2017; 7:2047. [PMID: 28119723 PMCID: PMC5222831 DOI: 10.3389/fpls.2016.02047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/21/2016] [Indexed: 05/25/2023]
Abstract
Sucrose (a disaccharide made of glucose and fructose) is the primary carbon source transported to sink organs in many plants. Since fructose accounts for half of the hexoses used for metabolism in sink tissues, plant fructokinases (FRKs), the main fructose-phosphorylating enzymes, are likely to play a central role in plant development. However, to date, their specific functions have been the subject of only limited study. The Arabidopsis genome contains seven genes encoding six cytosolic FRKs and a single plastidic FRK. T-DNA knockout mutants for five of the seven FRKs were identified and used in this study. Single knockouts of the FRK mutants did not exhibit any unusual phenotype. Double-mutants of AtFRK6 (plastidic) and AtFRK7 showed normal growth in soil, but yielded dark, distorted seeds. The seed distortion could be complemented by expression of the well-characterized tomato SlFRK1, confirming that a lack of FRK activity was the primary cause of the seed phenotype. Seeds of the double-mutant germinated, but failed to establish on 1/2 MS plates. Seed establishment was made possible by the addition of glucose or sucrose, indicating reduced seed storage reserves. Metabolic profiling of the double-mutant seeds revealed decreased TCA cycle metabolites and reduced fatty acid metabolism. Examination of the mutant embryo cells revealed smaller oil bodies, the primary storage reserve in Arabidopsis seeds. Quadruple and penta FRK mutants showed growth inhibition and leaf wilting. Anatomical analysis revealed smaller trachea elements and smaller xylem area, accompanied by necrosis around the cambium and the phloem. These results demonstrate overlapping and complementary roles of the plastidic AtFRK6 and the cytosolic AtFRK7 in seed storage accumulation, and the importance of AtFRKs for vascular development.
Collapse
Affiliation(s)
- Ofer Stein
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
- Robert H. Smith Faculty of Agriculture, Institute of Plant Sciences and Genetics in Agriculture, Food and Environment, Hebrew University of JerusalemRehovot, Israel
| | - Tamar Avin-Wittenberg
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Department of Plant and Environmental Sciences, Hebrew University of JerusalemGivat Ram, Jerusalem, Israel
| | - Ina Krahnert
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Hanita Zemach
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
| | - Vlada Bogol
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
| | - Oksana Daron
- Department of Life Sciences, Ben-Gurion UniversityBeer-Sheva, Israel
| | - Roni Aloni
- Department of Plant Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - David Granot
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
| |
Collapse
|
45
|
Nwokeoji AO, Kilby PM, Portwood DE, Dickman MJ. RNASwift: A rapid, versatile RNA extraction method free from phenol and chloroform. Anal Biochem 2016; 512:36-46. [DOI: 10.1016/j.ab.2016.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022]
|
46
|
Lugassi N, Kelly G, Fidel L, Yaniv Y, Attia Z, Levi A, Alchanatis V, Moshelion M, Raveh E, Carmi N, Granot D. Expression of Arabidopsis Hexokinase in Citrus Guard Cells Controls Stomatal Aperture and Reduces Transpiration. FRONTIERS IN PLANT SCIENCE 2015; 6:1114. [PMID: 26734024 PMCID: PMC4679854 DOI: 10.3389/fpls.2015.01114] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/24/2015] [Indexed: 05/20/2023]
Abstract
Hexokinase (HXK) is a sugar-phosphorylating enzyme involved in sugar-sensing. It has recently been shown that HXK in guard cells mediates stomatal closure and coordinates photosynthesis with transpiration in the annual species tomato and Arabidopsis. To examine the role of HXK in the control of the stomatal movement of perennial plants, we generated citrus plants that express Arabidopsis HXK1 (AtHXK1) under KST1, a guard cell-specific promoter. The expression of KST1 in the guard cells of citrus plants has been verified using GFP as a reporter gene. The expression of AtHXK1 in the guard cells of citrus reduced stomatal conductance and transpiration with no negative effect on the rate of photosynthesis, leading to increased water-use efficiency. The effects of light intensity and humidity on stomatal behavior were examined in rooted leaves of the citrus plants. The optimal intensity of photosynthetically active radiation and lower humidity enhanced stomatal closure of AtHXK1-expressing leaves, supporting the role of sugar in the regulation of citrus stomata. These results suggest that HXK coordinates photosynthesis and transpiration and stimulates stomatal closure not only in annual species, but also in perennial species.
Collapse
Affiliation(s)
- Nitsan Lugassi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - Gilor Kelly
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - Lena Fidel
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - Yossi Yaniv
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - Ziv Attia
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
| | - Asher Levi
- Institute of Agricultural Engineering, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - Victor Alchanatis
- Institute of Agricultural Engineering, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
| | - Eran Raveh
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Gilat Research CenterNegev, Israel
| | - Nir Carmi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| | - David Granot
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani CenterBet Dagan, Israel
| |
Collapse
|
47
|
Barda O, Shalev O, Alster S, Buxdorf K, Gafni A, Levy M. Pseudozyma aphidis Induces Salicylic-Acid-Independent Resistance to Clavibacter michiganensis in Tomato Plants. PLANT DISEASE 2015; 99:621-626. [PMID: 30699688 DOI: 10.1094/pdis-04-14-0377-re] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The ability of plant pathogens to rapidly develop resistance to commonly used pesticides challenges efforts to maximize crop production. Fungal biocontrol agents have become an important alternative to chemical fungicides as a result of environmental concerns regarding conventional pesticides, including resistance issues. The complex mode of action of biocontrol agents reduces the likelihood that pathogens will develop resistance to them. We recently isolated a unique, biologically active isolate of the epiphytic fungus Pseudozyma aphidis. We show that the extracellular metabolites secreted by our P. aphidis isolate can inhibit Xanthomonas campestris pv. vesicatoria, X. campestris pv. campestris, Pseudomonas syringae pv. tomato, Erwinia amylovora, Clavibacter michiganensis, and Agrobacterium tumefaciens in vitro. Moreover, application of Pseudozyma aphidis spores on tomato plants in the greenhouse significantly reduced (by 60%) the incidence of bacterial wilt and canker disease caused by C. michiganensis subsp. michiganensis on those plants as well as disease severity by 35%. Furthermore, infected plants treated with P. aphidis were 25% taller than control infected plants. We found that P. aphidis activates PR1a-and other pathogenesis-related genes in tomato plants-and can trigger an induced-resistance response against C. michiganensis that proceeds in a salicylic-acid-independent manner, as shown using NahG-transgenic tomato plants.
Collapse
Affiliation(s)
- Omer Barda
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Or Shalev
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shanee Alster
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Kobi Buxdorf
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aviva Gafni
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maggie Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
48
|
Whiteflies glycosylate salicylic acid and secrete the conjugate via their honeydew. J Chem Ecol 2015; 41:52-8. [PMID: 25563984 PMCID: PMC4303718 DOI: 10.1007/s10886-014-0543-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 12/30/2022]
Abstract
During insect feeding, a complex interaction takes place at the feeding site, with plants deciphering molecular information associated with the feeding herbivore, resulting in the upregulation of the appropriate defenses, and the herbivore avoiding or preventing these defenses from taking effect. Whiteflies can feed on plants without causing significant damage to mesophyll cells, making their detection extra challenging for the plant. However, whiteflies secrete honeydew that ends up on the plant surface at the feeding site and on distal plant parts below the feeding site. We reasoned that this honeydew, since it is largely of plant origin, may contain molecular information that alerts the plant, and we focused on the defense hormone salicylic acid (SA). First, we analyzed phloem sap from tomato plants, on which the whiteflies are feeding, and found that it contained salicylic acid (SA). Subsequently, we determined that in honeydew more than 80 % of SA was converted to its glycoside (SAG). When whiteflies were allowed to feed from an artificial diet spiked with labeled SA, labeled SAG also was produced. However, manually depositing honeydew on undamaged plants resulted still in a significant increase in endogenous free SA. Accordingly, transcript levels of PR1a, an SA marker gene, increased whereas those of PI-II, a jasmonate marker gene, decreased. Our results indicate that whiteflies manipulate the SA levels within their secretions, thus influencing the defense responses in those plant parts that come into contact with honeydew.
Collapse
|
49
|
Buxdorf K, Rahat I, Gafni A, Levy M. The epiphytic fungus Pseudozyma aphidis induces jasmonic acid- and salicylic acid/nonexpressor of PR1-independent local and systemic resistance. PLANT PHYSIOLOGY 2013; 161:2014-22. [PMID: 23388119 PMCID: PMC3613472 DOI: 10.1104/pp.112.212969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 02/02/2013] [Indexed: 05/07/2023]
Abstract
Pseudozyma spp. are yeast-like fungi, classified in the Ustilaginales, which are mostly epiphytic or saprophytic and are not pathogenic to plants. Several Pseudozyma species have been reported to exhibit biological activity against powdery mildews. However, previous studies have reported that Pseudozyma aphidis, which can colonize plant surfaces, is not associated with the collapse of powdery mildew colonies. In this report, we describe a novel P. aphidis strain and study its interactions with its plant host and the plant pathogen Botrytis cinerea. This isolate was found to secrete extracellular metabolites that inhibit various fungal pathogens in vitro and significantly reduce B. cinerea infection in vivo. Moreover, P. aphidis sensitized Arabidopsis (Arabidopsis thaliana) plants' defense machinery via local and systemic induction of pathogenesis-related1 (PR1) and plant defensin1.2 (PDF1.2) expression. P. aphidis also reduced B. cinerea infection, locally and systemically, in Arabidopsis mutants impaired in jasmonic acid (JA) or salicylic acid (SA) signaling. Thus, in addition to direct inhibition, P. aphidis may inhibit B. cinerea infection via induced resistance in a manner independent of SA, JA, and Nonexpressor of PR1 (NPR1). P. aphidis primed the plant defense machinery and induced stronger activation of PDF1.2 after B. cinerea infection. Finally, P. aphidis fully or partially reconstituted PR1 and PDF1.2 expression in npr1-1 mutant and in plants with the SA hydroxylase NahG transgene, but not in a jasmonate resistant1-1 mutant, after B. cinerea infection, suggesting that P. aphidis can bypass the SA/NPR1, but not JA, pathway to activate PR genes. Thus, either partial gene activation is sufficient to induce resistance, or the resistance is not directed solely through PR1 and PDF1.2 but probably through other pathogen-resistance genes or pathways as well.
Collapse
Affiliation(s)
| | | | | | - Maggie Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| |
Collapse
|