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Talukdar S, Mal S, Kundu P. Physico-chemical features and functional relevance of tomato rhomboid proteases. Int J Biol Macromol 2024; 272:132681. [PMID: 38806088 DOI: 10.1016/j.ijbiomac.2024.132681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
In plants, regulated intramembrane proteolysis (RIP) is crucial for proper growth, development, and stress management. Rhomboid proteases (RPs) residing in the membrane play a vital role in orchestrating RIP. Although RPs can be found in most sequenced genomes, tomato rhomboids (SlRPs) have not yet been studied. Using alternative and comprehensive strategies, we found ten SlRPs encoded in the tomato genome. These SlRPs possess signature motifs and transmembrane domains, showing structural similarity to other members of the RP family. Also, SlRPs are genetically related to other known RPs of the Solanaceae family. Seven of the SlRPs retain serine-histidine catalytic dyads, making them proteolytically active, while three iRhoms lack the dyad and other structural motifs. Although SlRPs could have functional redundancy, their distribution and expression pattern indicate tissue specificity and responsiveness to specific external stimuli. The presence of development and stress-response-related cis-elements in the promoters of SlRPs supports this view. Furthermore, our strategically designed substrate-reporter assay shows that SlRPs have proteolytic activity similar to that of known RPs. This study provides a detailed understanding of all SlRPs and their physico-chemical features, shedding light on their involvement in physiological processes.
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Affiliation(s)
- Sushmita Talukdar
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India
| | - Sayan Mal
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India
| | - Pallob Kundu
- Department of Biological Sciences, Bose Institute, EN80, Sector V, Bidhannagar, Kolkata 700091, India.
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Misra V, Mall AK, Pandey H, Srivastava S, Sharma A. Advancements and prospects of CRISPR/Cas9 technologies for abiotic and biotic stresses in sugar beet. Front Genet 2023; 14:1235855. [PMID: 38028586 PMCID: PMC10665535 DOI: 10.3389/fgene.2023.1235855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Sugar beet is a crop with high sucrose content, known for sugar production and recently being considered as an emerging raw material for bioethanol production. This crop is also utilized as cattle feed, mainly when animal green fodder is scarce. Bioethanol and hydrogen gas production from this crop is an essential source of clean energy. Environmental stresses (abiotic/biotic) severely affect the productivity of this crop. Over the past few decades, the molecular mechanisms of biotic and abiotic stress responses in sugar beet have been investigated using next-generation sequencing, gene editing/silencing, and over-expression approaches. This information can be efficiently utilized through CRISPR/Cas 9 technology to mitigate the effects of abiotic and biotic stresses in sugar beet cultivation. This review highlights the potential use of CRISPR/Cas 9 technology for abiotic and biotic stress management in sugar beet. Beet genes known to be involved in response to alkaline, cold, and heavy metal stresses can be precisely modified via CRISPR/Cas 9 technology for enhancing sugar beet's resilience to abiotic stresses with minimal off-target effects. Similarly, CRISPR/Cas 9 technology can help generate insect-resistant sugar beet varieties by targeting susceptibility-related genes, whereas incorporating Cry1Ab and Cry1C genes may provide defense against lepidopteron insects. Overall, CRISPR/Cas 9 technology may help enhance sugar beet's adaptability to challenging environments, ensuring sustainable, high-yield production.
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Affiliation(s)
- Varucha Misra
- ICAR-Indian Institute of Sugarcane Research, Lucknow, India
| | - A. K. Mall
- ICAR-Indian Institute of Sugarcane Research, Lucknow, India
| | - Himanshu Pandey
- ICAR-Indian Institute of Sugarcane Research, Lucknow, India
- Khalsa College, Amritsar, India
| | | | - Avinash Sharma
- Faculty of Agricultural Sciences, Arunachal University of Studies, Namsai, India
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3
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Siddique S, Radakovic ZS, Hiltl C, Pellegrin C, Baum TJ, Beasley H, Bent AF, Chitambo O, Chopra D, Danchin EGJ, Grenier E, Habash SS, Hasan MS, Helder J, Hewezi T, Holbein J, Holterman M, Janakowski S, Koutsovoulos GD, Kranse OP, Lozano-Torres JL, Maier TR, Masonbrink RE, Mendy B, Riemer E, Sobczak M, Sonawala U, Sterken MG, Thorpe P, van Steenbrugge JJM, Zahid N, Grundler F, Eves-van den Akker S. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nat Commun 2022; 13:6190. [PMID: 36261416 PMCID: PMC9582021 DOI: 10.1038/s41467-022-33769-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.
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Affiliation(s)
- Shahid Siddique
- Department of Entomology and Nematology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Zoran S Radakovic
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
- P.H. Petersen Saatzucht Lundsgaard GmbH, D-24977, Grundhof, Germany
| | - Clarissa Hiltl
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Clement Pellegrin
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Helen Beasley
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Oliver Chitambo
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Divykriti Chopra
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Etienne G J Danchin
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Eric Grenier
- IGEPP, INRAE, Institut Agro, Université Rennes, 35650, Le Rheu, France
| | - Samer S Habash
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
- BASF Vegetable Seeds, Napoleonsweg 152, 6083, AB, Nunhem, The Netherlands
| | - M Shamim Hasan
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Johannes Helder
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Julia Holbein
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Martijn Holterman
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Solynta, Dreijenlaan 2, 6703, HA, Wageningen, The Netherlands
| | - Sławomir Janakowski
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | | | - Olaf P Kranse
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jose L Lozano-Torres
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Rick E Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA, 50010, USA
| | - Badou Mendy
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Esther Riemer
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany
| | - Mirosław Sobczak
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-787, Warsaw, Poland
| | - Unnati Sonawala
- The Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Peter Thorpe
- Mackenzie Institute for Early Diagnosis, School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Joris J M van Steenbrugge
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Nageena Zahid
- Institute for Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-University of Bonn, Meckenheimer Allee 168, D-53115, Bonn, Germany
| | - Florian Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert- Kreiten-Straße 13, D-53115, Bonn, Germany.
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Elkobrosy DH, Aseel DG, Hafez EE, El-Saedy MA, Al-Huqail AA, Ali HM, Jebril J, Shama S, Abdelsalam NR, Elnahal AS. Quantitative detection of induced systemic resistance genes of potato roots upon ethylene treatment and cyst nematode, Globodera rostochiensis, infection during plant–nematode interactions. Saudi J Biol Sci 2022; 29:3617-3625. [PMID: 35844398 PMCID: PMC9280246 DOI: 10.1016/j.sjbs.2022.02.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/13/2022] [Accepted: 02/27/2022] [Indexed: 11/02/2022] Open
Abstract
Potato cyst nematodes caused by Globodera rostochiensis, are quarantine-restricted pests causing significant yield losses to potato growers. The phytohormone ethylene play significant roles in various plant-pathogen interactions, however, the molecular knowledge of how ethylene influences potato–nematode interaction is still lacking. Precise detection of potato-induced genes is essential for recognizing plant-induced systemic resistance (ISR). Candidate genes or PR- proteins with putative functions in modulating the response to potato cyst nematode stress were selected and functionally characterized. Using real-time polymerase chain reaction (RT-PCR), we measured the quantified expression of four pathogenesis-related (PR) genes, PR2, PR3, peroxidase, and polyphenol oxidase. The activation of these genes is intermediate during the ISR signaling in the root tissues. Using different ethylene concentrations could detect and induce defense genes in infected potato roots compared to the control treatment. The observed differences in the gene expression of treated infected plants are because of different concentrations of ethylene treatment and pathogenicity. Besides, the overexpressed or suppressed of defense- related genes during developmental stages and pathogen infection. We concluded that ethylene treatments positively affected potato defensive genes expression levels against cyst nematode infection. The results emphasize the necessity of studying molecular signaling pathways controlling biotic stress responses. Understanding such mechanisms will be critical for the development of broad-spectrum and stress-tolerant crops in the future.
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Volk GM, Byrne PF, Coyne CJ, Flint-Garcia S, Reeves PA, Richards C. Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use. PLANTS (BASEL, SWITZERLAND) 2021; 10:2260. [PMID: 34834625 PMCID: PMC8619436 DOI: 10.3390/plants10112260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 05/17/2023]
Abstract
Plant genebanks provide genetic resources for breeding and research programs worldwide. These programs benefit from having access to high-quality, standardized phenotypic and genotypic data. Technological advances have made it possible to collect phenomic and genomic data for genebank collections, which, with the appropriate analytical tools, can directly inform breeding programs. We discuss the importance of considering genebank accession homogeneity and heterogeneity in data collection and documentation. Citing specific examples, we describe how well-documented genomic and phenomic data have met or could meet the needs of plant genetic resource managers and users. We explore future opportunities that may emerge from improved documentation and data integration among plant genetic resource information systems.
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Affiliation(s)
- Gayle M. Volk
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA; (P.A.R.); (C.R.)
| | - Patrick F. Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA;
| | - Clarice J. Coyne
- United States Department of Agriculture, Agricultural Research Service, Western Regional Plant Introduction Station, Pullman, WA 99164, USA;
| | - Sherry Flint-Garcia
- Plant Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Columbia, MO 65211, USA;
| | - Patrick A. Reeves
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA; (P.A.R.); (C.R.)
| | - Chris Richards
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA; (P.A.R.); (C.R.)
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