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Dhiman V, Biswas S, Shekhawat RS, Sadhukhan A, Yadav P. In silico characterization of five novel disease-resistance proteins in Oryza sativa sp. japonica against bacterial leaf blight and rice blast diseases. 3 Biotech 2024; 14:48. [PMID: 38268986 PMCID: PMC10803709 DOI: 10.1007/s13205-023-03893-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/16/2023] [Indexed: 01/26/2024] Open
Abstract
In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (M. oryzae), respectively. In silico modeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins and submitted to ModelArchive for future use. An in-silico annotation indicated that the five proteins functioned in signal transduction pathways as kinases, phospholipases, transcription factors, and DNA-modifying enzymes. The proteins were localized in the nucleus and plasma membrane. Phylogenetic analysis showed the evolutionary relation of the five proteins with disease-resistance proteins (XA21, OsTRX1, PLD, and HKD-motif-containing proteins). This indicates similar disease-resistant properties between five unknown proteins and their evolutionary-related proteins. Furthermore, gene expression profiling of these proteins using public microarray data showed their differential expression under Xoo and M. oryzae infection. This study provides an insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will assist rice breeders in improving crop yield to address future food security through molecular breeding and biotechnology. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03893-5.
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Affiliation(s)
- Vedikaa Dhiman
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
| | - Soham Biswas
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana India
| | - Rajveer Singh Shekhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
| | - Ayan Sadhukhan
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, 342030 Rajasthan India
- School of Artificial Intelligence and Data Science, Indian Institute of Technology, Jodhpur, Rajasthan India
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Silva-Sanzana C, Gangas MV, Zavala D, Blanco-Herrera F. A Recipe for Success: Three Key Strategies Used by Aphids and Pseudomonas syringae to Colonize the Phyllosphere. Microb Ecol 2023; 85:1-8. [PMID: 35039905 PMCID: PMC9849291 DOI: 10.1007/s00248-022-01965-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Aphids and Pseudomonas syringae are a permanent challenge for agriculture, causing severe losses to the crop industry worldwide. Despite the obvious phylogenetic distance between them, both have become predominant colonizers of the plant kingdom. In this study, we reviewed three key steps of spread and colonization that aphids and P. syringae have mastered to successfully colonize the phyllosphere. These steps involve (i) plant-to-plant movement for locating new nutritional sources, (ii) disruption and modification of the apoplast to facilitate nutrient acquisition, and (iii) suppression of host defenses through effector proteins. In addition, we will provide insights about the direct interaction between aphids and P. syringae and how this yet underrated phenomenon could bring new ecological implications for both organisms beyond their pathogenicity.
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Affiliation(s)
- Christian Silva-Sanzana
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Maria Victoria Gangas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Diego Zavala
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), ANID, Santiago, Chile
| | - Francisca Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile.
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), ANID, Santiago, Chile.
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Chandrakanth R, Sunil L, Sadashivaiah L, Devaki NS. In silico modelling and characterization of eight blast resistance proteins in resistant and susceptible rice cultivars. J Genet Eng Biotechnol 2020; 18:75. [PMID: 33237489 DOI: 10.1186/s43141-020-00076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/22/2020] [Indexed: 11/10/2022]
Abstract
Background Nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes are the largest class of plant resistance genes which play an important role in the plant defense response. These genes are better conserved than others and function as a recognition-based immune system in plants through their encoded proteins. Results Here, we report the effect of Magnaporthe oryzae, the rice blast pathogen inoculation in resistant BR2655 and susceptible HR12 rice cultivars. Transcriptomic profiling was carried out to analyze differential gene expression in these two cultivars. A total of eight NBS-LRR uncharacterized resistance proteins (RP1, RP2, RP3, RP4, RP5, RP6, RP7, and RP8) were selected in these two cultivars for in silico modeling. Modeller 9.22 and SWISS-MODEL servers were used for the homology modeling of eight RPs. ProFunc server was utilized for the prediction of secondary structure and function. The CDvist Web server and Interpro scan server detected the motif and domains in eight RPs. Ramachandran plot of eight RPs confirmed that the modeled structures occupied favorable positions. Conclusions From the present study, computational analysis of these eight RPs may afford insights into their role, function, and valuable resource for studying the intricate details of the plant defense mechanism. Furthermore, the identification of resistance proteins is useful for the development of molecular markers linked to resistance genes. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-020-00076-0.
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Rampino P, De Pascali M, De Caroli M, Luvisi A, De Bellis L, Piro G, Perrotta C. Td4IN2: A drought-responsive durum wheat (Triticum durum Desf.) gene coding for a resistance like protein with serine/threonine protein kinase, nucleotide binding site and leucine rich domains. Plant Physiol Biochem 2017; 120:223-231. [PMID: 29065389 DOI: 10.1016/j.plaphy.2017.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/01/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
Wheat, the main food source for a third of world population, appears strongly under threat because of predicted increasing temperatures coupled to drought. Plant complex molecular response to drought stress relies on the gene network controlling cell reactions to abiotic stress. In the natural environment, plants are subjected to the combination of abiotic and biotic stresses. Also the response of plants to biotic stress, to cope with pathogens, involves the activation of a molecular network. Investigations on combination of abiotic and biotic stresses indicate the existence of cross-talk between the two networks and a kind of overlapping can be hypothesized. In this work we describe the isolation and characterization of a drought-related durum wheat (Triticum durum Desf.) gene, identified in a previous study, coding for a protein combining features of NBS-LRR type resistance protein with a S/TPK domain, involved in drought stress response. This is one of the few examples reported where all three domains are present in a single protein and, to our knowledge, it is the first report on a gene specifically induced by drought stress and drought-related conditions, with this particular structure.
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Affiliation(s)
- Patrizia Rampino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy.
| | - Mariarosaria De Pascali
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Monica De Caroli
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Andrea Luvisi
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Luigi De Bellis
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Gabriella Piro
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
| | - Carla Perrotta
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy
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Garner CM, Kim SH, Spears BJ, Gassmann W. Express yourself: Transcriptional regulation of plant innate immunity. Semin Cell Dev Biol 2016; 56:150-162. [PMID: 27174437 DOI: 10.1016/j.semcdb.2016.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
The plant immune system is a complex network of components that function together to sense the presence and activity of potential biotic threats, and integrate these signals into an appropriate output, namely the transcription of genes that activate an immune response that is commensurate with the perceived threat. Given the variety of biotic threats a plant must face the immune response must be plastic, but because an immune response is costly to the plant in terms of energy expenditure and development it must also be under tight control. To meet these needs transcriptional control is exercised at multiple levels. In this article we will review some of the latest developments in understanding how the plant immune response is regulated at the level of transcription. New roles are being discovered for the long-studied WRKY and TGA transcription factor families, while additional critical defense functions are being attributed to TCPs and other transcription factors. Dynamically controlling access to DNA through post-translational modification of histones is emerging as an essential component of priming, maintaining, attenuating, and repressing transcription in response to biotic stress. Unsurprisingly, the plant's transcriptional response is targeted by pathogen effectors, and in turn resistance proteins stand guard over and participate in transcriptional regulation. Together, these multiple layers lead to the observed complexity of the plant transcriptional immune response, with different transcription factors or chromatin components playing a prominent role depending on the plant-pathogen interaction being studied.
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Affiliation(s)
- Christopher M Garner
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Sang Hee Kim
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Benjamin J Spears
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Walter Gassmann
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA; C.S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
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Boyle PC, Schwizer S, Hind SR, Kraus CM, De la Torre Diaz S, He B, Martin GB. Detecting N-myristoylation and S-acylation of host and pathogen proteins in plants using click chemistry. Plant Methods 2016; 12:38. [PMID: 27493678 PMCID: PMC4972946 DOI: 10.1186/s13007-016-0138-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/20/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND The plant plasma membrane is a key battleground in the war between plants and their pathogens. Plants detect the presence of pathogens at the plasma membrane using sensor proteins, many of which are targeted to this lipophilic locale by way of fatty acid modifications. Pathogens secrete effector proteins into the plant cell to suppress the plant's defense mechanisms. These effectors are able to access and interfere with the surveillance machinery at the plant plasma membrane by hijacking the host's fatty acylation apparatus. Despite the important involvement of protein fatty acylation in both plant immunity and pathogen virulence mechanisms, relatively little is known about the role of this modification during plant-pathogen interactions. This dearth in our understanding is due largely to the lack of methods to monitor protein fatty acid modifications in the plant cell. RESULTS We describe a rapid method to detect two major forms of fatty acylation, N-myristoylation and S-acylation, of candidate proteins using alkyne fatty acid analogs coupled with click chemistry. We applied our approach to confirm and decisively demonstrate that the archetypal pattern recognition receptor FLS2, the well-characterized pathogen effector AvrPto, and one of the best-studied intracellular resistance proteins, Pto, all undergo plant-mediated fatty acylation. In addition to providing a means to readily determine fatty acylation, particularly myristoylation, of candidate proteins, this method is amenable to a variety of expression systems. We demonstrate this using both Arabidopsis protoplasts and stable transgenic Arabidopsis plants and we leverage Agrobacterium-mediated transient expression in Nicotiana benthamiana leaves as a means for high-throughput evaluation of candidate proteins. CONCLUSIONS Protein fatty acylation is a targeting tactic employed by both plants and their pathogens. The metabolic labeling approach leveraging alkyne fatty acid analogs and click chemistry described here has the potential to provide mechanistic details of the molecular tactics used at the host plasma membrane in the battle between plants and pathogens.
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Affiliation(s)
- Patrick C. Boyle
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
- Monsanto Company, St. Louis, MO 63141 USA
| | - Simon Schwizer
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Sarah R. Hind
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
| | - Christine M. Kraus
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | | | - Bin He
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 USA
- College of Pharmacy, Guiyang Medical University, Guiyang, 550004 Guizhou China
| | - Gregory B. Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
- Plant Pathology and Plant–Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
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