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Gupta R, Min CW, Son S, Lee GH, Jang JW, Kwon SW, Park SR, Kim ST. Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against Xanthomonas oryzae pv. oryzae. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:105-114. [PMID: 34979446 DOI: 10.1016/j.plaphy.2021.12.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 proteins. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase 1 (OsArg 1) in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type. In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to wild-type. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of OsARG1 in plant defense against Xoo.
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Affiliation(s)
- Ravi Gupta
- College of General Education, Kookmin University, Seoul, 02707, South Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea
| | - Seungmin Son
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Gi Hyun Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea
| | - Soon Wook Kwon
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea.
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, South Korea.
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Wu G, Zhang Y, Wang B, Li K, Lou Y, Zhao Y, Liu F. Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction. RICE (NEW YORK, N.Y.) 2021; 14:57. [PMID: 34176023 PMCID: PMC8236019 DOI: 10.1186/s12284-021-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/11/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. RESULTS Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. CONCLUSION Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.
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Affiliation(s)
- Guichun Wu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yuqiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, P. R. China
| | - Bo Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Kaihuai Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Yuanlai Lou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yancun Zhao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
| | - Fengquan Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
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Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
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Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
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Vo KTX, Rahman MM, Rahman MM, Trinh KTT, Kim ST, Jeon JS. Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update. RICE (NEW YORK, N.Y.) 2021; 14:30. [PMID: 33721115 PMCID: PMC7960847 DOI: 10.1186/s12284-021-00461-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/28/2021] [Indexed: 05/19/2023]
Abstract
Biotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mizanor Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Kieu Thi Thuy Trinh
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463 South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
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Sahoo S, Sanghamitra P, Nanda N, Pawar S, Pandit E, Bastia R, Muduli KC, Pradhan SK. Association of molecular markers with physio-biochemical traits related to seed vigour in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1989-2003. [PMID: 33088044 PMCID: PMC7548267 DOI: 10.1007/s12298-020-00879-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/18/2020] [Accepted: 09/01/2020] [Indexed: 05/08/2023]
Abstract
Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content, superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R2 value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R2 value will be useful for improvement of seed vigour in rice.
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Affiliation(s)
- Swastideepa Sahoo
- Department of Seed Technology, College of Agriculture, OUAT, Bhubaneswar, 751003 Odisha India
| | | | - Nibedita Nanda
- Department of Seed Technology, College of Agriculture, OUAT, Bhubaneswar, 751003 Odisha India
| | - Swapnil Pawar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Ramakrushna Bastia
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | - Kumuda Chandra Muduli
- Department of Seed Technology, College of Agriculture, OUAT, Bhubaneswar, 751003 Odisha India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
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Zhu J, Zhu K, Li L, Li Z, Qin W, Park Y, He Y. Proteomics of the Honeydew from the Brown Planthopper and Green Rice Leafhopper Reveal They Are Rich in Proteins from Insects, Rice Plant and Bacteria. INSECTS 2020; 11:insects11090582. [PMID: 32882811 PMCID: PMC7564128 DOI: 10.3390/insects11090582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/26/2022]
Abstract
Honeydew is a watery fluid excreted by plant sap-feeding insects. It is a waste product for the insect hosts. However, it plays important roles for other organisms, such as serving as a nutritional source for beneficial insects and bacteria, as well as elicitors and effectors modulating plant responses. In this study, shotgun LC-MS/MS analyses were used to identify the proteins in the honeydew from two important rice hemipteran pests, the brown planthopper (Nilaparvata lugens, BPH) and green rice leafhopper (Nephotettix cincticeps, GRH). A total of 277 and 210 proteins annotated to insect proteins were identified in the BPH and GRH honeydews, respectively. These included saliva proteins that may have similar functions as the saliva proteins, such as calcium-binding proteins and apolipophorin, involved in rice plant defenses. Additionally, a total of 52 and 32 Oryza proteins were identified in the BPH and GRH honeydews, respectively, some of which are involved in the plant immune system, such as Pathogen-Related Protein 10, ascorbate peroxidase, thioredoxin and glutaredoxin. Coincidently, 570 and 494 bacteria proteins were identified from the BPH and GRH honeydews, respectively, which included several well-known proteins involved in the plant immune system: elongation factor Tu, flagellin, GroEL and cold-shock proteins. The results of our study indicate that the insect honeydew is a complex fluid cocktail that contains abundant proteins from insects, plants and microbes, which may be involved in the multitrophic interactions of plants-insects-microbes.
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Affiliation(s)
- Jinghua Zhu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (K.Z.); (L.L.); (Z.L.); (W.Q.)
| | - Kunmiao Zhu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (K.Z.); (L.L.); (Z.L.); (W.Q.)
| | - Liang Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (K.Z.); (L.L.); (Z.L.); (W.Q.)
| | - Zengxin Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (K.Z.); (L.L.); (Z.L.); (W.Q.)
| | - Weiwei Qin
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (K.Z.); (L.L.); (Z.L.); (W.Q.)
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA;
| | - Yueping He
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (K.Z.); (L.L.); (Z.L.); (W.Q.)
- Correspondence: ; Tel.: +86-13554408979
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Sruthilaxmi CB, Babu S. Proteome Responses to Individual Pathogens and Abiotic Conditions in Rice Seedlings. PHYTOPATHOLOGY 2020; 110:1326-1341. [PMID: 32175828 DOI: 10.1094/phyto-11-19-0425-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice plants under field conditions experience various biotic and abiotic stresses and are adapted to survive using a molecular cross-talk of genes and their protein products based on the severity of a given stress. Seedlings of cultivated variety ASD16 (resistant to fungal disease, blast; tolerant to abiotic stress, salinity) were subjected to salt, drought, high temperature and low temperature stress as well as infection by Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (causing reemerging diseases such as sheath blight and leaf blight), respectively, the sheath blight and bacterial leaf blight pathogens. Leaf proteome was analyzed using two-dimensional electrophoresis and differentially expressed proteins were identified using mass spectrometry. In addition to many other differentially expressed proteins, acidic endochitinase was found to be upregulated during fungal infection and drought treatment, and a germin-like protein upregulated during fungal infection and high temperature stress. These two proteins were further validated at the gene expression level using reverse transcription-PCR in dual stress experiments. Pot culture plants were subjected to fungal infection followed by drought and drought followed by fungal infection to validate chitinase gene expression. Similarly, plants subjected to fungal infections followed by high temperature stress and vice versa were used to validate the expression of germin-like protein-coding gene. The results of the present study indicate that chitinase and germin-like protein are potential targets for further exploration to develop rice plants resistant or tolerant to biotic and abiotic stresses.
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Affiliation(s)
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore 632014, India
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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Chen J, Ullah H, Tu X, Zhang Z. Understanding the genetic mechanism of resistance in aphid-treated alfalfa ( Medicago sativa L.) through proteomic analysis. 3 Biotech 2019; 9:241. [PMID: 31168434 DOI: 10.1007/s13205-019-1755-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023] Open
Abstract
To minimize dependency on chemical pesticides, plant breeders are trying to emphasize on important agricultural pests for the development of pest resistant cultivars. However, the molecular approach and associated genetic tools conferring resistance have not been widely studied. In the current study, proteomic analysis of two of the alfalfa cultivars viz. a resistant (R) (Zhongmu-1) and a susceptible (S) (WL343), with (+ A) and without (- A) aphids rearing were carried out. Results indicated that 325 differentially expressed proteins (DEPs) up-regulated while 319 down-regulated with a pattern of R + A/R - A plants, whereas 371 up- and 583 down-regulated DEPs were identified in the S + A/S - A plants. Total number of DEPs found in (S + A/S - A) was around 19.7% greater than that of (R + A/R - A), whereas, the down-regulated DEPs of susceptible variety was 11.6% higher than the resistant cultivar. Applying the KEGG analysis, 96 and 142 DEPs were portrayed to 15 and 10 substantively augmented pathways for Zhongmu-1 and WL343, respectively. We also found that two of the shared pathways (carbon metabolism and pyruvate metabolism) are linking to important traits conferring resistance in alfalfa. Most importantly, the specific role of linoleic acid metabolism was found to be associated with jasmonic acid, flavonoid biosynthesis, and terpenoid backbone biosynthesis that might have been associated with the insect-resistant material synthesis in the resistant alfalfa cultivar. Our study suggested that both alfalfa cultivars (R, S) could govern protein expression through carbon and pyruvate metabolism. But only the resistant alfalfa cultivar (Zhongmu-1) can tune protein expression via linoleic acid metabolism and terpenoid backbone biosynthesis to induce the defensive protein expressions (e.g., jasmonic acid and flavonoid biosynthesis along with terpenoid backbone biosynthesis), to enhance plant defense capacity.
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Affiliation(s)
- Jun Chen
- 1State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Hidayat Ullah
- 1State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
- 2Department of Agriculture, The University of Swabi, Anbar, Swabi, Khyber Pakhtunkhwa 23561 Pakistan
| | - Xiongbing Tu
- 1State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Zehua Zhang
- 1State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
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10
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Identification of Two Novel Wheat Drought Tolerance-Related Proteins by Comparative Proteomic Analysis Combined with Virus-Induced Gene Silencing. Int J Mol Sci 2018; 19:ijms19124020. [PMID: 30545152 PMCID: PMC6321273 DOI: 10.3390/ijms19124020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023] Open
Abstract
Drought is a major adversity that limits crop yields. Further exploration of wheat drought tolerance-related genes is critical for the genetic improvement of drought tolerance in this crop. Here, comparative proteomic analysis of two wheat varieties, XN979 and LA379, with contrasting drought tolerance was conducted to screen for drought tolerance-related proteins/genes. Virus-induced gene silencing (VIGS) technology was used to verify the functions of candidate proteins. A total of 335 differentially abundant proteins (DAPs) were exclusively identified in the drought-tolerant variety XN979. Most DAPs were mainly involved in photosynthesis, carbon fixation, glyoxylate and dicarboxylate metabolism, and several other pathways. Two DAPs (W5DYH0 and W5ERN8), dubbed TaDrSR1 and TaDrSR2, respectively, were selected for further functional analysis using VIGS. The relative electrolyte leakage rate and malonaldehyde content increased significantly, while the relative water content and proline content significantly decreased in the TaDrSR1- and TaDrSR2-knock-down plants compared to that in non-knocked-down plants under drought stress conditions. TaDrSR1- and TaDrSR2-knock-down plants exhibited more severe drooping and wilting phenotypes than non-knocked-down plants under drought stress conditions, suggesting that the former were more sensitive to drought stress. These results indicate that TaDrSR1 and TaDrSR2 potentially play vital roles in conferring drought tolerance in common wheat.
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Wang A, Shu X, Niu X, Zhao W, Ai P, Li P, Zheng A. Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection. PLoS One 2018; 13:e0202309. [PMID: 30372430 PMCID: PMC6205584 DOI: 10.1371/journal.pone.0202309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/09/2018] [Indexed: 01/29/2023] Open
Abstract
The biotrophic soil-borne fungus Tilletia horrida causes rice kernel smut, an important disease affecting the production of rice male sterile lines in most hybrid rice growing regions of the world. There are no successful ways of controlling this disease and there has been little study of mechanisms of resistance to T. horrida. Based on transcriptional data of different infection time points, we found 23, 782 and 23, 718 differentially expressed genes (fragments per kilobase of transcript sequence per million, FPKM >1) in Jiangcheng 3A (resistant to T. horrida) and 9311A (susceptible to T. horrida), respectively. In order to illuminate the differential responses of the two rice male sterile lines to T. horrida, we identified gene co-expression modules using the method of weighted gene co-expression network analysis (WGCNA) and compared the different biological functions of gene co-expression networks in key modules at different infection time points. The results indicated that gene co-expression networks in the two rice genotypes were different and that genes contained in some modules of the two groups may play important roles in resistance to T. horrida, such as DTH8 and OsHop/Sti1a. Furthermore, these results provide a global view of the responses of two different phenotypes to T. horrida, and assist our understanding of the regulation of expression changes after T. horrida infection.
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Affiliation(s)
- Aijun Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Xinyue Shu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Xianyu Niu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Wenjuan Zhao
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Peng Ai
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Aiping Zheng
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
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Zhang J, Zhao W, Fu R, Fu C, Wang L, Liu H, Li S, Deng Q, Wang S, Zhu J, Liang Y, Li P, Zheng A. Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection. Funct Integr Genomics 2018; 18:545-557. [PMID: 29730773 PMCID: PMC6097106 DOI: 10.1007/s10142-018-0607-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 12/16/2022]
Abstract
Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA). We compared the different genes assigned to each module and the biological interpretations of gene co-expression networks at early and later modules in the two rice genotypes to reveal differential responses to AG1 IA. Our results show that different changes occurred in the two rice genotypes and that the modules in the two groups contain a number of candidate genes possibly involved in pathogenesis, such as the VQ protein. Furthermore, these gene co-expression networks provide comprehensive transcriptional information regarding gene expression in rice in response to AG1 IA. The co-expression networks derived from our data offer ideas for follow-up experimentation that will help advance our understanding of the translational regulation of rice gene expression changes in response to AG1 IA.
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Affiliation(s)
- Jinfeng Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenjuan Zhao
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Rong Fu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Chenglin Fu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lingxia Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Huainian Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Shuangcheng Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Qiming Deng
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Shiquan Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jun Zhu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yueyang Liang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Ping Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
| | - Aiping Zheng
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130 China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, 611130 China
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13
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MEENA RK, PULLAIAHGARI D, GUDIPALLI P. Proteomic analysis of heterotic seed germination in maize using F1 hybrid DHM 117 and its parental inbreds. Turk J Biol 2018; 42:345-363. [PMID: 30814898 PMCID: PMC6392162 DOI: 10.3906/biy-1803-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
A number of differentially expressed proteins (DEPs) were identified in comparative two-dimensional gel electrophoresis analysis of dry and 24-h water-imbibed seeds of maize F1 hybrid DHM 117 (BML 6 × BML 7) and its parental inbreds. Of the DEPs, 53.4% (86/161) in dry seeds and 58% (127/219) in water-imbibed seeds exhibited a nonadditive pattern in the F1 hybrid as compared to parental inbreds. A total of 30 DEPs were categorized into different biological processes, most of which were related to metabolism and energy (34%), followed by storage proteins (27%), stress response (23%), transcription and translation (7%), cell cycle (3%), and hormone biosynthesis (3%). The transcript accumulation pattern of 8 selected genes corresponding to DEPs was examined using qRTPCR. Interestingly, LEA protein Rab28 showed higher accumulation in dry seeds at both protein and transcript levels, whereas indole3-acetaldehyde oxidase showed lower accumulation in water-imbibed seeds of the F1 hybrid than the female parent at the protein level. Thus, the DEPs particularly involved in metabolic and energy processes, as well as hormone biosynthesis in the F 1 hybrid, might be responsible for heterotic seed germination in the F1 hybrid. The DEPs identified in this study provide a scope for improving the seed germination trait of agricultural crops.
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Affiliation(s)
- Rajesh Kumar MEENA
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
,
Gachibowli, Hyderabad, Telangana
,
India
| | - Durgeshwar PULLAIAHGARI
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
,
Gachibowli, Hyderabad, Telangana
,
India
| | - Padmaja GUDIPALLI
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
,
Gachibowli, Hyderabad, Telangana
,
India
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14
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Rampuria S, Bag P, Rogan CJ, Sharma A, Gassmann W, Kirti PB. Pathogen-induced AdDjSKI of the wild peanut, Arachis diogoi, potentiates tolerance of multiple stresses in E. coli and tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:62-74. [PMID: 29807607 DOI: 10.1016/j.plantsci.2018.03.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/25/2018] [Accepted: 03/31/2018] [Indexed: 06/08/2023]
Abstract
A gene encoding a serine-rich DnaJIII protein called AdDjSKI that has a 4Fe-4S cluster domain was found to be differentially upregulated in the wild peanut, Arachis diogoi in its resistance responses against the late leaf spot causing fungal pathogen Phaeoisariopsis personata when compared with the cultivated peanut, Arachis hypogaea. AdDjSKI is induced in multiple stress conditions in A. diogoi. Recombinant E. coli cells expressing AdDjSKI showed better growth kinetics when compared with vector control cells under salinity, osmotic, acidic and alkaline stress conditions. Overexpression of this type three J-protein potentiates not only abiotic stress tolerance in Nicotiana tabacum var. Samsun, but also enhances its disease resistance against the phytopathogenic fungi Phytophthora parasitica pv nicotianae and Sclerotinia sclerotiorum. In the present study we show transcriptional upregulation of APX, Mn-SOD and HSP70 under heat stress and increased transcripts of PR genes in response to fungal infection. This transmembrane-domain-containing J protein displays punctate localization in chloroplasts. AdDjSKI appears to ensure proper folding of proteins associated with the photosynthetic machinery under stress.
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Affiliation(s)
- Sakshi Rampuria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Pushan Bag
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Conner J Rogan
- Division of Biological Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Akanksha Sharma
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Walter Gassmann
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - P B Kirti
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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15
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Garcia-Seco D, Chiapello M, Bracale M, Pesce C, Bagnaresi P, Dubois E, Moulin L, Vannini C, Koebnik R. Transcriptome and proteome analysis reveal new insight into proximal and distal responses of wheat to foliar infection by Xanthomonas translucens. Sci Rep 2017; 7:10157. [PMID: 28860643 PMCID: PMC5579275 DOI: 10.1038/s41598-017-10568-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
The molecular details of local plant response against Xanthomonas translucens infection is largely unknown. Moreover, there is no knowledge about effects of the pathogen on the root's transcriptome and proteome. Therefore, we investigated the global gene and protein expression changes both in leaves and roots of wheat (Triticum aestivum) 24 h post leaf infection of X. translucens. This simultaneous analysis allowed us to obtain insight into possible metabolic rearrangements in above- and belowground tissues and to identify common responses as well as specific alterations. At the site of infection, we observed the implication of various components of the recognition, signaling, and amplification mechanisms in plant response to the pathogen. Moreover, data indicate a massive down-regulation of photosynthesis and confirm the chloroplast as crucial signaling hub during pathogen attack. Notably, roots responded as well to foliar attack and their response significantly differed from that locally triggered in infected leaves. Data indicate that roots as a site of energy production and synthesis of various secondary metabolites may actively influence the composition and colonisation level of root-associated microbes. Finally, our results emphasize the accumulation of jasmonic acid, pipecolic acid and/or the downstream mediator of hydrogen peroxide as long distal signals from infected leaves to roots.
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Affiliation(s)
- D Garcia-Seco
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France.
| | - M Chiapello
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - M Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - C Pesce
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
- Université catholique de Louvain, Earth and Life Institute, Applied Microbiology Phytopathology, Louvain-la-Neuve, Belgium
| | - P Bagnaresi
- Council for agricultural research and economics (CREA) - Genomics Research Centre, via San Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - E Dubois
- CNRS, Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier Cedex 34, France
| | - L Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - C Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy.
| | - R Koebnik
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
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16
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Comparative analysis of constitutive proteome between resistant and susceptible tomato genotypes regarding to late blight. Funct Integr Genomics 2017; 18:11-21. [DOI: 10.1007/s10142-017-0570-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/18/2017] [Accepted: 08/23/2017] [Indexed: 01/07/2023]
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17
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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18
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Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
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Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
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19
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Dantas GC, Martins PMM, Martins DAB, Gomes E, Ferreira H. A protein expression system for tandem affinity purification in Xanthomonas citri subsp. citri. Braz J Microbiol 2016; 47:518-26. [PMID: 26991273 PMCID: PMC4874617 DOI: 10.1016/j.bjm.2016.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/23/2015] [Indexed: 11/30/2022] Open
Abstract
Citrus canker, caused by the Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), is one of the most devastating diseases to affect citrus crops. There is no treatment for citrus canker; effective control against the spread of Xac is usually achieved by the elimination of affected plants along with that of asymptomatic neighbors. An in depth understanding of the pathogen is the keystone for understanding of the disease; to this effect we are committed to the development of strategies to ease the study of Xac. Genome sequencing and annotation of Xac revealed that ∼37% of the genome is composed of hypothetical ORFs. To start a systematic characterization of novel factors encoded by Xac, we constructed integrative-vectors for protein expression specific to this bacterium. The vectors allow for the production of TAP-tagged proteins in Xac under the regulation of the xylose promoter. In this study, we show that a TAP-expression vector, integrated into the amy locus of Xac, does not compromise its virulence. Furthermore, our results also demonstrate that the polypeptide TAP can be overproduced in Xac and purified from the soluble phase of cell extracts. Our results substantiate the use of our vectors for protein expression in Xac thus contributing a novel tool for the characterization of proteins and protein complexes generated by this bacterium in vivo.
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Affiliation(s)
- Giordanni C Dantas
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Paula M M Martins
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Daniela A B Martins
- Depto. de Bioquímica e Tecnologia Química, Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Eleni Gomes
- Depto. de Biologia, Universidade Estadual Paulista, São Jose do Rio Preto, SP, Brazil
| | - Henrique Ferreira
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil.
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20
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Agrawal L, Gupta S, Mishra SK, Pandey G, Kumar S, Chauhan PS, Chakrabarty D, Nautiyal CS. Elucidation of Complex Nature of PEG Induced Drought-Stress Response in Rice Root Using Comparative Proteomics Approach. FRONTIERS IN PLANT SCIENCE 2016; 7:1466. [PMID: 27746797 PMCID: PMC5040710 DOI: 10.3389/fpls.2016.01466] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/14/2016] [Indexed: 05/22/2023]
Abstract
Along with many adaptive strategies, dynamic changes in protein abundance seem to be the common strategy to cope up with abiotic stresses which can be best explored through proteomics. Understanding of drought response is the key to decipher regulatory mechanism of better adaptation. Rice (Oryza sativa L.) proteome represents a phenomenal source of proteins that govern traits of agronomic importance, such as drought tolerance. In this study, a comparison of root cytoplasmic proteome was done for a drought tolerant rice (Heena) cultivar in PEG induced drought conditions. A total of 510 protein spots were observed by PDQuest analysis and 125 differentially regulated spots were subjected for MALDI-TOF MS-MS analysis out of which 102 protein spots identified which further led to identification of 78 proteins with a significant score. These 78 differentially expressed proteins appeared to be involved in different biological pathways. The largest percentage of identified proteins was involved in bioenergy and metabolism (29%) and mainly consists of malate dehydrogenase, succinyl-CoA, putative acetyl-CoA synthetase, and pyruvate dehydrogenase etc. This was followed by proteins related to cell defense and rescue (22%) such as monodehydroascorbate reductase and stress-induced protein sti1, then by protein biogenesis and storage class (21%) e.g. putative thiamine biosynthesis protein, putative beta-alanine synthase, and cysteine synthase. Further, cell signaling (9%) proteins like actin and prolyl endopeptidase, and proteins with miscellaneous function (19%) like Sgt1 and some hypothetical proteins were also represented a large contribution toward drought regulatory mechanism in rice. We propose that protein biogenesis, cell defense, and superior homeostasis may render better drought-adaptation. These findings might expedite the functional determination of the drought-responsive proteins and their prioritization as potential molecular targets for perfect adaptation.
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A single gene all3940 (Dps) overexpression in Anabaena sp. PCC 7120 confers multiple abiotic stress tolerance via proteomic alterations. Funct Integr Genomics 2015; 16:67-78. [DOI: 10.1007/s10142-015-0467-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022]
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Fagundes D, Bohn B, Cabreira C, Leipelt F, Dias N, Bodanese-Zanettini MH, Cagliari A. Caspases in plants: metacaspase gene family in plant stress responses. Funct Integr Genomics 2015; 15:639-49. [PMID: 26277721 DOI: 10.1007/s10142-015-0459-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 12/26/2022]
Abstract
Programmed cell death (PCD) is an ordered cell suicide that removes unwanted or damaged cells, playing a role in defense to environmental stresses and pathogen invasion. PCD is component of the life cycle of plants, occurring throughout development from embryogenesis to the death. Metacaspases are cysteine proteases present in plants, fungi, and protists. In certain plant-pathogen interactions, the PCD seems to be mediated by metacaspases. We adopted a comparative genomic approach to identify genes coding for the metacaspases in Viridiplantae. We observed that the metacaspase was divided into types I and II, based on their protein structure. The type I has a metacaspase domain at the C-terminus region, presenting or not a zinc finger motif in the N-terminus region and a prodomain rich in proline. Metacaspase type II does not feature the prodomain and the zinc finger, but has a linker between caspase-like catalytic domains of 20 kDa (p20) and 10 kDa (p10). A high conservation was observed in the zinc finger domain (type I proteins) and in p20 and p10 subunits (types I and II proteins). The phylogeny showed that the metacaspases are divided into three principal groups: type I with and without zinc finger domain and type II metacaspases. The algae and moss are presented as outgroup, suggesting that these three classes of metacaspases originated in the early stages of Viridiplantae, being the absence of the zinc finger domain the ancient condition. The study of metacaspase can clarify their assignment and involvement in plant PCD mechanisms.
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Affiliation(s)
- David Fagundes
- Universidade Estadual do Rio Grande do Sul (UERGS), CEP 96816-50, Santa Cruz do Sul, RS, Brazil.
| | - Bianca Bohn
- Universidade Estadual do Rio Grande do Sul (UERGS), CEP 96816-50, Santa Cruz do Sul, RS, Brazil.
| | - Caroline Cabreira
- Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
| | - Fábio Leipelt
- Universidade Estadual do Rio Grande do Sul (UERGS), CEP 96816-50, Santa Cruz do Sul, RS, Brazil.
| | - Nathalia Dias
- Universidade Estadual do Rio Grande do Sul (UERGS), CEP 96816-50, Santa Cruz do Sul, RS, Brazil.
| | | | - Alexandro Cagliari
- Universidade Estadual do Rio Grande do Sul (UERGS), CEP 96816-50, Santa Cruz do Sul, RS, Brazil.
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