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Lai T, Yu Q, Pan J, Wang J, Tang Z, Bai X, Shi L, Zhou T. The Identification and Comparative Analysis of Non-Coding RNAs in Spores and Mycelia of Penicillium expansum. J Fungi (Basel) 2023; 9:999. [PMID: 37888255 PMCID: PMC10607695 DOI: 10.3390/jof9100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Penicillium expansum is the most popular post-harvest pathogen and causes blue mold disease in pome fruit and leads to significant economic losses worldwide every year. However, the fundamental regulation mechanisms of growth in P. expansum are unclear. Recently, non-coding RNAs (ncRNAs) have attracted more attention due to critical roles in normalizing gene expression and maintaining cellular genotypes in organisms. However, the research related to ncRNAs in P. expansum have not been reported. Therefore, to provide an overview of ncRNAs on composition, distribution, expression changes, and potential targets in the growth process, a comparative transcriptomic analysis was performed on spores and mycelia of P. expansum in the present study. A total of 2595 novel mRNAs, 3362 long non-coding RNAs (lncRNAs), 10 novel microRNAs (miRNAs), 86 novel small interfering RNAs (siRNAs), and 11,238 circular RNAs (circRNAs) were predicted and quantified. Of these, 1482 novel mRNAs, 5987 known mRNAs, 2047 lncRNAs, 40 miRNAs, 38 novel siRNAs, and 9235 circRNAs were differentially expressed (DE) in response to the different development stages. Afterward, the involved functions and pathways of DE RNAs were revealed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database enrichment analysis. The interaction networks between mRNAs, lncRNAs, and miRNAs were also predicted based on their correlation coefficient of expression profiles. Among them, it was found that miR168 family members may play important roles in fungal growth due to their central location in the network. These findings will contribute to a better understanding on regulation machinery at the RNA level on fungal growth and provide a theoretical basis to develop novel control strategies against P. expansum.
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Affiliation(s)
- Tongfei Lai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Qinru Yu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Pan
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Zhenxing Tang
- School of Culinary Arts, Tourism College of Zhejiang, Hangzhou 311231, China;
| | - Xuelian Bai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Lue Shi
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Ting Zhou
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
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Jiang C, Li Z, Zheng L, Yu Y, Niu D. Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions. MOLECULAR PLANT PATHOLOGY 2023; 24:999-1013. [PMID: 37026481 PMCID: PMC10346379 DOI: 10.1111/mpp.13329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.
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Affiliation(s)
- Chun‐Hao Jiang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zi‐Jie Li
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Li‐Yu Zheng
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Yi‐Yang Yu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dong‐Dong Niu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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Macharia TN, Duong TA, Moleleki LN. In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins. BMC Genomics 2023; 24:296. [PMID: 37264326 DOI: 10.1186/s12864-023-09366-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/07/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Plant-parasitic nematodes (PPNs) that cause most damage include root-knot nematodes (RKNs) which are a major impediment to crop production. Root-knot nematodes, like other parasites, secrete proteins which are required for parasite proliferation and survival within the host during the infection process. RESULTS Here, we used various computational tools to predict and identify classically and non-classically secreted proteins encoded in the Meloidogyne javanica genome. Furthermore, functional annotation analysis was performed using various integrated bioinformatic tools to determine the biological significance of the predicted secretome. In total, 7,458 proteins were identified as secreted ones. A large percentage of this secretome is comprised of small proteins of ≤ 300 aa sequence length. Functional analyses showed that M. javanica secretome comprises cell wall degrading enzymes for facilitating nematode invasion, and migration by disintegrating the complex plant cell wall components. In addition, peptidases and peptidase inhibitors are an important category of M. javanica secretome involved in compatible host-nematode interactions. CONCLUSION This study identifies the putative secretome encoded in the M. javanica genome. Future experimental validation analyses can greatly benefit from this global analysis of M. javanica secretome. Equally, our analyses will advance knowledge of the interaction between plants and nematodes.
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Affiliation(s)
- Teresia Nyambura Macharia
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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Islam W, Idrees A, Waheed A, Zeng F. Plant responses to drought stress: microRNAs in action. ENVIRONMENTAL RESEARCH 2022; 215:114282. [PMID: 36122702 DOI: 10.1016/j.envres.2022.114282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Atif Idrees
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Abdul Waheed
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Islam W, Naveed H, Idress A, Ishaq DU, Kurfi BG, Zeng F. Plant responses to metals stress: microRNAs in focus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69197-69212. [PMID: 35951237 DOI: 10.1007/s11356-022-22451-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Metal toxicity can largely affect the growth and yield of numerous plant species. Plants have developed specific mechanisms to withstand the varying amounts of metals. One approach involves utilization of microRNAs (miRNAs) that are known for cleaving transcripts or inhibiting translation to mediate post-transcriptional control. Use of transcription factors (TFs) or gene regulation in metal detoxification largely depends on metal-responsive miRNAs. Moreover, systemic signals and physiological processes for plants response to metal toxicities are likewise controlled by miRNAs. Therefore, it is necessary to understand miRNAs and their regulatory networks in relation to metal stress. The miRNA-based approach can be important to produce metal-tolerant plant species. Here, we have reviewed the importance of plant miRNAs and their role in mitigating metal toxicities. The current review also discusses the specific advances that have occurred as a result of the identification and validation of several metal stress-responsive miRNAs.
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Affiliation(s)
- Waqar Islam
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Hassan Naveed
- College of Life Sciences, Leshan Normal University, Sichuan, 614004, China
| | - Atif Idress
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Daha Umar Ishaq
- Centre of Mitochondrial Biology & Medicine, Xian Joiotong University, Xi'An, 710049, China
- Department of Biochemistry, Faculty of Basic Medical Sciences, Bayero University, Kano, 700241, Nigeria
| | - Binta G Kurfi
- Department of Biochemistry, Faculty of Basic Medical Sciences, Bayero University, Kano, 700241, Nigeria
| | - Fanjiang Zeng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China.
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MicroRNAs Mediated Plant Responses to Salt Stress. Cells 2022; 11:cells11182806. [PMID: 36139379 PMCID: PMC9496875 DOI: 10.3390/cells11182806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/17/2022] Open
Abstract
One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.
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MicroRNA Mediated Plant Responses to Nutrient Stress. Int J Mol Sci 2022; 23:ijms23052562. [PMID: 35269700 PMCID: PMC8910084 DOI: 10.3390/ijms23052562] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023] Open
Abstract
To complete their life cycles, plants require several minerals that are found in soil. Plant growth and development can be affected by nutrient shortages or high nutrient availability. Several adaptations and evolutionary changes have enabled plants to cope with inappropriate growth conditions and low or high nutrient levels. MicroRNAs (miRNAs) have been recognized for transcript cleavage and translational reduction, and can be used for post-transcriptional regulation. Aside from regulating plant growth and development, miRNAs play a crucial role in regulating plant’s adaptations to adverse environmental conditions. Additionally, miRNAs are involved in plants’ sensory functions, nutrient uptake, long-distance root transport, and physiological functions related to nutrients. It may be possible to develop crops that can be cultivated in soils that are either deficient in nutrients or have extreme nutrient supplies by understanding how plant miRNAs are associated with nutrient stress. In this review, an overview is presented regarding recent advances in the understanding of plants’ responses to nitrogen, phosphorus, potassium, sulfur, copper, iron, boron, magnesium, manganese, zinc, and calcium deficiencies via miRNA regulation. We conclude with future research directions emphasizing the modification of crops for improving future food security.
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Hu J, Li W, Qiao X, Li W, Xie K, Wang Y, Huang B, Zhao Q, Liu L, Fan X. Characterization of microRNA Profiles in Pasteurella multocida-Infected Rabbits and Identification of miR-29-5p as a Regulator of Antibacterial Immune Response. Front Vet Sci 2021; 8:746638. [PMID: 34869721 PMCID: PMC8635715 DOI: 10.3389/fvets.2021.746638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Pasteurella multocida is the pathogenic agent for a variety of severe diseases in livestock, including rabbits. MicroRNAs (miRNAs) participate in the immune response to the pathogen. Distinct miRNA expression patterns were explored in rabbit lung by small-RNA deep sequencing to assess dysregulated miRNAs during P. multocida infection. Totally, 571 miRNAs were screened, of which, 62 were novel, and 32 exhibited differential expression (DE). Of the 32 known DE-miRNAs, 13 and 15 occurred at 1 day and 3 days post-infection (dpi); and ocu-miR-107-3p and ocu-miR-29b-5p were shared between the two time points. Moreover, 7,345 non-redundant target genes were predicted for the 32 DE-miRNAs. Putative target genes were enriched in diverse GO and KEGG pathways and might be crucial for disease resistance. Interestingly, upregulation of ocu-miR-29-5p suppresses P. multocida propagation and downregulates expression of epithelial membrane protein-2 (EMP2) and T-box 4 (TBX4) genes by binding to their 3′ untranslated region in RK13 cells. Thus, ocu-miR-29-5p may indirectly inhibit P. multocida invasion by modulating genes related to the host immune response, such as EMP2 and TBX4.
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Affiliation(s)
- Jiaqing Hu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Wenqiang Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Xibo Qiao
- Shandong New Hexin Technology Co. Ltd., Taian, China
| | - Wenjie Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Kerui Xie
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Yanyan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Bing Huang
- Shandong Provincial Key Laboratory of Poultry Disease Diagnose and Immune, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qiaoya Zhao
- Shandong Provincial Key Laboratory of Poultry Disease Diagnose and Immune, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lei Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Xinzhong Fan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
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Shaw RK, Shen Y, Wang J, Sheng X, Zhao Z, Yu H, Gu H. Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L. FRONTIERS IN PLANT SCIENCE 2021; 12:742553. [PMID: 34938304 PMCID: PMC8687090 DOI: 10.3389/fpls.2021.742553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Brassica oleracea is one of the most important species of the Brassicaceae family encompassing several economically important vegetables produced and consumed worldwide. But its sustainability is challenged by a range of pathogens, among which black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the most serious and destructive seed borne bacterial disease, causing huge yield losses. Host-plant resistance could act as the most effective and efficient solution to curb black rot disease for sustainable production of B. oleracea. Recently, 'omics' technologies have emerged as promising tools to understand the host-pathogen interactions, thereby gaining a deeper insight into the resistance mechanisms. In this review, we have summarized the recent achievements made in the emerging omics technologies to tackle the black rot challenge in B. oleracea. With an integrated approach of the omics technologies such as genomics, proteomics, transcriptomics, and metabolomics, it would allow better understanding of the complex molecular mechanisms underlying black rot resistance. Due to the availability of sequencing data, genomics and transcriptomics have progressed as expected for black rot resistance, however, other omics approaches like proteomics and metabolomics are lagging behind, necessitating a holistic and targeted approach to address the complex questions of Xcc-Brassica interactions. Genomic studies revealed that the black rot resistance is a complex trait and is mostly controlled by quantitative trait locus (QTL) with minor effects. Transcriptomic analysis divulged the genes related to photosynthesis, glucosinolate biosynthesis and catabolism, phenylpropanoid biosynthesis pathway, ROS scavenging, calcium signalling, hormonal synthesis and signalling pathway are being differentially expressed upon Xcc infection. Comparative proteomic analysis in relation to susceptible and/or resistance interactions with Xcc identified the involvement of proteins related to photosynthesis, protein biosynthesis, processing and degradation, energy metabolism, innate immunity, redox homeostasis, and defence response and signalling pathways in Xcc-Brassica interaction. Specifically, most of the studies focused on the regulation of the photosynthesis-related proteins as a resistance response in both early and later stages of infection. Metabolomic studies suggested that glucosinolates (GSLs), especially aliphatic and indolic GSLs, its subsequent hydrolysis products, and defensive metabolites synthesized by jasmonic acid (JA)-mediated phenylpropanoid biosynthesis pathway are involved in disease resistance mechanisms against Xcc in Brassica species. Multi-omics analysis showed that JA signalling pathway is regulating resistance against hemibiotrophic pathogen like Xcc. So, the bonhomie between omics technologies and plant breeding is going to trigger major breakthroughs in the field of crop improvement by developing superior cultivars with broad-spectrum resistance. If multi-omics tools are implemented at the right scale, we may be able to achieve the maximum benefits from the minimum. In this review, we have also discussed the challenges, future prospects, and the way forward in the application of omics technologies to accelerate the breeding of B. oleracea for disease resistance. A deeper insight about the current knowledge on omics can offer promising results in the breeding of high-quality disease-resistant crops.
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Affiliation(s)
| | | | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Qi S, Zhang S, Islam MM, El-Sappah AH, Zhang F, Liang Y. Natural Resources Resistance to Tomato Spotted Wilt Virus (TSWV) in Tomato ( Solanum lycopersicum). Int J Mol Sci 2021; 22:ijms222010978. [PMID: 34681638 PMCID: PMC8538096 DOI: 10.3390/ijms222010978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
Tomato spotted wilt virus (TSWV) is one of the most destructive diseases affecting tomato (Solanum lycopersicum) cultivation and production worldwide. As defenses against TSWV, natural resistance genes have been identified in tomato, including Sw-1a, Sw-1b, sw-2, sw-3, sw-4, Sw-5, Sw-6, and Sw-7. However, only Sw-5 exhibits a high level of resistance to the TSWV. Thus, it has been cloned and widely used in the breeding of tomato with resistance to the disease. Due to the global spread of TSWV, resistance induced by Sw-5 decreases over time and can be overcome or broken by a high concentration of TSWV. How to utilize other resistance genes and identify novel resistance resources are key approaches for breeding tomato with resistance to TSWV. In this review, the characteristics of natural resistance genes, natural resistance resources, molecular markers for assisted selection, and methods for evaluating resistance to TSWV are summarized. The aim is to provide a theoretical basis for identifying, utilizing resistance genes, and developing tomato varieties that are resistant to TSWV.
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Affiliation(s)
- Shiming Qi
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Shijie Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Md. Monirul Islam
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Ahmed H. El-Sappah
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Fei Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
| | - Yan Liang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (S.Q.); (S.Z.); (M.M.I.); (A.H.E.-S.); (F.Z.)
- State Agriculture Ministry Laboratory of Northwest Horticultural Plant Germplasm Resources & Genetic Improvement, Northwest A&F University, Xianyang 712100, China
- Correspondence: ; Tel.: +86-29-8708-2613
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Hu J, Li W, Huang B, Zhao Q, Fan X. The Profiles of Long Non-coding RNA and mRNA Transcriptome Reveals the Genes and Pathway Potentially Involved in Pasteurella multocida Infection of New Zealand Rabbits. Front Vet Sci 2021; 8:591273. [PMID: 34026883 PMCID: PMC8131872 DOI: 10.3389/fvets.2021.591273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/19/2021] [Indexed: 12/22/2022] Open
Abstract
Infection with Pasteurella multocida (P. multocida) causes severe epidemic diseases in rabbits and is responsible for the pronounced economic losses in the livestock industry. Long non-coding RNAs (lncRNAs) have been proven to exert vital functions in regulating the host immune responses to bacterial attacks. However, little is known about how lncRNAs participate in the rabbit's immune response against P. multocida infection in the lungs. LncRNA and mRNA expression profiles were analyzed by transcriptomics and bioinformatics during P. multocida infection. A total of 336 lncRNAs and 7,014 mRNAs were differentially regulated at 1 day and 3 days post infection (dpi). Nearly 80% of the differentially expressed lncRNAs exhibited an increased expression at 3 dpi suggesting that the P. multocida genes are responsible for regulation. Moreover, GO and KEGG enriched analysis indicated that the immune-related pathways including pattern recognition receptors (PRRs), cytokines, and chemokines were significantly enriched at 3 dpi. These results indicate that the dysregulated immune-related genes may play crucial roles in defending against P. multocida attacks. Overall, these results advance our cognition of the role of lncRNAs and mRNAs in modulating the rabbit's innate immune response against P. multocida attacks, which will offer a valuable clue for further studies into exploring P. multocida-related diseases in human.
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Affiliation(s)
- Jiaqing Hu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Wenqiang Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Bing Huang
- Shandong Provincial Key Laboratory of Poultry Disease Diagnose and Immune, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qiaoya Zhao
- Shandong Provincial Key Laboratory of Poultry Disease Diagnose and Immune, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinzhong Fan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
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12
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Alshehri B. Plant-derived xenomiRs and cancer: Cross-kingdom gene regulation. Saudi J Biol Sci 2021; 28:2408-2422. [PMID: 33911956 PMCID: PMC8071896 DOI: 10.1016/j.sjbs.2021.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/18/2022] Open
Abstract
Exosomal microRNAs (miRNAs) critically regulate several major intracellular and metabolic activities, including cancer evolution. Currently, increasing evidence indicates that exosome harbor and transport these miRNAs from donor cells to neighboring and distantly related recipient cells, often in a cross-species manner. Several studies have reported that plant-based miRNAs can be absorbed into the serum of humans, where they hinder the expression of human disease-related genes. Moreover, few recent studies have demonstrated the role of these xenomiRs in cancer development and progression. However, the cross-kingdom gene regulation hypothesis remains highly debatable, and many follow up studies fail to reproduce the same. There are reports that show no effect of plant-derived miRNAs on mammalian cancers. The foremost cause of this controversy remains the lack of reproducibility of the results. Here, we reassess the latest developments in the field of cross-kingdom transference of miRNAs, emphasizing on the role of the diet-based xenomiRs on cancer progression.
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Affiliation(s)
- Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia
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13
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Mahesh HB, Shirke MD, Wang GL, Gowda M. In planta transcriptome analysis reveals tissue-specific expression of pathogenicity genes and microRNAs during rice-Magnaporthe interactions. Genomics 2020; 113:265-275. [PMID: 33326830 DOI: 10.1016/j.ygeno.2020.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
Transcriptional re-programming in host and pathogen upon leaf and neck infection is an evolving area of research for the rice blast community. Analysis of in planta rice transcriptome in leaf and neck tissues revealed tissue-specific and infection-specific expression of rice and Magnaporthe oryzae genes in host and pathogen. The glycosyl hydrolase, isocitrate lyase, cupin domain containing protein, TF2, CMPG1, CHIT17 and OsCML14 genes were uniquely expressed in leaf infection. Genes like cytochrome P450, inhibitor I family protein, GSTU6, abscisic stress ripening, and cupin domain containing protein were up-regulated during neck infection. In our microRNA sequencing study, Osa-miR166n-3p was highly expressed in upon Magnaporthe leaf infection, whereas osa-miR1661-3p, osa-miR166n-3p and osa-miR159b were overexpressed in neck infection. Here we report several transcripts being targeted by up and down regulated microRNAs during infection. The putative genes expressed upon infection in leaf and neck could be used in understanding the dual-epidemics of blast disease.
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Affiliation(s)
- H B Mahesh
- Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru 560065, India; Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru 560065, India; Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India.
| | - Meghana Deepak Shirke
- Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India
| | - Guo-Liang Wang
- Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru 560065, India
| | - Malali Gowda
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus 43210, USA; Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India.
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14
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Qasim M, Xiao H, He K, Omar MAA, Liu F, Ahmed S, Li F. Genetic engineering and bacterial pathogenesis against the vectorial capacity of mosquitoes. Microb Pathog 2020; 147:104391. [PMID: 32679245 DOI: 10.1016/j.micpath.2020.104391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/05/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022]
Abstract
Mosquitoes are the main vector of multiple diseases worldwide and transmit viral (malaria, chikungunya, encephalitis, yellow fever, as well as dengue fever), as well as bacterial diseases (tularemia). To manage the outbreak of mosquito populations, various management programs include the application of chemicals, followed by biological and genetic control. Here we aimed to focus on the role of bacterial pathogenesis and molecular tactics for the management of mosquitoes and their vectorial capacity. Bacterial pathogenesis and molecular manipulations have a substantial impact on the biology of mosquitoes, and both strategies change the gene expression and regulation of disease vectors. The strategy for genetic modification is also proved to be excellent for the management of mosquitoes, which halt the development of population via incompatibility of different sex. Therefore, the purpose of the present discussion is to illustrate the impact of both approaches against the vectorial capacity of mosquitoes. Moreover, it could be helpful to understand the relationship of insect-pathogen and to manage various insect vectors as well as diseases.
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Affiliation(s)
- Muhammad Qasim
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Huamei Xiao
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China; College of Life Sciences and Resource Environment, Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, Yichun University, Yichun, 336000, China
| | - Kang He
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mohamed A A Omar
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Feiling Liu
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Sohail Ahmed
- Department of Entomology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Fei Li
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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15
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Leitão AL, Costa MC, Gabriel AF, Enguita FJ. Interspecies Communication in Holobionts by Non-Coding RNA Exchange. Int J Mol Sci 2020; 21:ijms21072333. [PMID: 32230931 PMCID: PMC7177868 DOI: 10.3390/ijms21072333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.
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Affiliation(s)
- Ana Lúcia Leitão
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal;
- MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.C.); (A.F.G.)
- Correspondence: ; Tel.: +351-217999480
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16
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Xu X, Zhong C, Tan M, Song Y, Qi X, Xu Q, Chen X. Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing. Front Genet 2020; 11:246. [PMID: 32273882 PMCID: PMC7113371 DOI: 10.3389/fgene.2020.00246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/02/2020] [Indexed: 01/04/2023] Open
Abstract
Powdery mildew (PM) is a prevalent disease known to limit cucumber production worldwide. MicroRNAs (miRNAs) are single-stranded molecules that regulate host defense responses through posttranscriptional gene regulation. However, which specific miRNAs are involved and how they regulate cucumber PM resistance remain elusive. A PM-resistant single-segment substitution line, SSSL508-28, was developed previously using marker-assisted backcrossing of the PM-susceptible cucumber inbred D8 line. In this study, we applied small RNA and degradome sequencing to identify PM-responsive miRNAs and their target genes in the D8 and SSSL508-28 lines. The deep sequencing resulted in the identification of 156 known and 147 novel miRNAs. Among them, 32 and six differentially expressed miRNAs (DEMs) were detected in D8 and SSSL508-28, respectively. The positive correlation between DEMs measured by small RNA sequencing and stem-loop quantitative real-time reverse transcription-polymerase chain reaction confirmed the accuracy of the observed miRNA abundances. The 32 DEMs identified in the PM-susceptible D8 were all upregulated, whereas four of the six DEMs identified in the PM-resistant SSSL508-28 were downregulated. Using in silico and degradome sequencing approaches, 517 and 20 target genes were predicted for the D8 and SSSL508-28 DEMs, respectively. Comparison of the DEM expression profiles with the corresponding mRNA expression profiles obtained in a previous study with the same experimental design identified 60 and three target genes in D8 and SSSL508-28, respectively, which exhibited inverse expression patterns with their respective miRNAs. In particular, five DEMs were located in the substituted segment that contained two upregulated DEMs, Csa-miR172c-3p and Csa-miR395a-3p, in D8 and two downregulated DEMs, Csa-miR395d-3p and Csa-miR398b-3p, in SSSL508-28. One gene encoding L-aspartate oxidase, which was targeted by Csa-miR162a, was also located on the same segment and was specifically downregulated in PM-inoculated D8 leaves. Our results will facilitate the future use of miRNAs in breeding cucumber varieties with enhanced resistance to PM.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Cailian Zhong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Min Tan
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ya Song
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China
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17
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Islam W, Noman A, Naveed H, Alamri SA, Hashem M, Huang Z, Chen HYH. Plant-insect vector-virus interactions under environmental change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 701:135044. [PMID: 31726403 DOI: 10.1016/j.scitotenv.2019.135044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Insects play an important role in the spread of viruses from infected plants to healthy hosts through a variety of transmission strategies. Environmental factors continuously influence virus transmission and result in the establishment of infection or disease. Plant virus diseases become epidemic when viruses successfully dominate the surrounding ecosystem. Plant-insect vector-virus interactions influence each other; pushing each other for their benefit and survival. These interactions are modulated through environmental factors, though environmental influences are not readily predictable. This review focuses on exploiting the diverse relationships, embedded in the plant-insect vector-virus triangle by highlighting recent research findings. We examined the interactions between viruses, insect vectors, and host plants, and explored how these interactions affect their behavior.
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Affiliation(s)
- Waqar Islam
- College of Geographical Sciences, Fujian Normal University, Fuzhou, Fujian 350007, China; Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, Sichuan 614004, China
| | - Saad A Alamri
- King Khalid University, Faculty of Science, Biological Science Department, P.O. Box 10255, Abha 61321, Saudi Arabia; Prince Sultan Ben Abdulaziz Center for Environmental and Tourism Research and Studies, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Hashem
- King Khalid University, Faculty of Science, Biological Science Department, P.O. Box 10255, Abha 61321, Saudi Arabia; Assiut University, Faculty of Science, Botany Department, Assiut 71516, Egypt
| | - Zhiqun Huang
- College of Geographical Sciences, Fujian Normal University, Fuzhou, Fujian 350007, China; Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China.
| | - Han Y H Chen
- College of Geographical Sciences, Fujian Normal University, Fuzhou, Fujian 350007, China; Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Faculty of Natural Resources Management, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada.
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18
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Vincent D, Rafiqi M, Job D. The Multiple Facets of Plant-Fungal Interactions Revealed Through Plant and Fungal Secretomics. FRONTIERS IN PLANT SCIENCE 2020; 10:1626. [PMID: 31969889 PMCID: PMC6960344 DOI: 10.3389/fpls.2019.01626] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/19/2019] [Indexed: 05/14/2023]
Abstract
The plant secretome is usually considered in the frame of proteomics, aiming at characterizing extracellular proteins, their biological roles and the mechanisms accounting for their secretion in the extracellular space. In this review, we aim to highlight recent results pertaining to secretion through the conventional and unconventional protein secretion pathways notably those involving plant exosomes or extracellular vesicles. Furthermore, plants are well known to actively secrete a large array of different molecules from polymers (e.g. extracellular RNA and DNA) to small compounds (e.g. ATP, phytochemicals, secondary metabolites, phytohormones). All of these play pivotal roles in plant-fungi (or oomycetes) interactions, both for beneficial (mycorrhizal fungi) and deleterious outcomes (pathogens) for the plant. For instance, recent work reveals that such secretion of small molecules by roots is of paramount importance to sculpt the rhizospheric microbiota. Our aim in this review is to extend the definition of the plant and fungal secretomes to a broader sense to better understand the functioning of the plant/microorganisms holobiont. Fundamental perspectives will be brought to light along with the novel tools that should support establishing an environment-friendly and sustainable agriculture.
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Maryam Rafiqi
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Dominique Job
- CNRS/Université Claude Bernard Lyon 1/Institut National des Sciences Appliquées/Bayer CropScience Joint Laboratory (UMR 5240), Bayer CropScience, Lyon, France
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19
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Lin Y, Zhu S, Hu C, Wang J, Jiang P, Zhu L, Li Z, Wang S, Zhang Y, Xu X, Pan W. Cross-Species Suppression of Hepatoma Cell Growth and Migration by a Schistosoma japonicum MicroRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:400-412. [PMID: 31655260 PMCID: PMC6831938 DOI: 10.1016/j.omtn.2019.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/12/2019] [Accepted: 09/08/2019] [Indexed: 12/22/2022]
Abstract
Schistosoma japonicum eggs trapped in host liver secretes microRNA (miRNA)-containing extracellular vesicles (EVs) that can be transferred to host cells. Recent studies demonstrated that miRNAs derived from plants can modulate gene expression and phenotype of mammalian cells in a cross-kingdom manner. In this study, we identified a Schistosoma japonicum miRNA (e.g., Sja-miR-3096) that is present in the hepatocytes of mice infected with the parasite and has notable antitumor effects in both in vitro and in vivo models. The Sja-miR-3096 mimics suppressed cell proliferation and migration of both murine and human hepatoma cell lines by targeting phosphoinositide 3-kinase class II alpha (PIK3C2A). We generated a murine hepatoma cell line that stably expressed the pri-Sja-miR-3096 gene and demonstrated cross-species processing of the schistosome pri-miRNA to the mature Sja-miR-3096 in the mammalian cell. Importantly, inoculation of this cell line into the scapula and livers of mice led to a complete suppression of tumorigenesis of the hepatoma cells. Moreover, tumor weight was significantly reduced on intravenous administration of Sja-miR-3096 mimics. Thus, the schistosome miRNA-mediated antitumor activity occurs in host liver cells during schistosome infection, which may strengthen resistance of host to liver cancer, and discovery and development of such miRNAs may present promising interventions for cancer therapy.
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Affiliation(s)
- Yu Lin
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Shanli Zhu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Chao Hu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Jing Wang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Pengyue Jiang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Liufang Zhu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Zhengli Li
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Sai Wang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Yuanbin Zhang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Xindong Xu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Weiqing Pan
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China; Department of Tropical Diseases, Second Military Medical University, Shanghai, China.
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20
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de Vries S, de Vries J, Rose LE. The Elaboration of miRNA Regulation and Gene Regulatory Networks in Plant⁻Microbe Interactions. Genes (Basel) 2019; 10:genes10040310. [PMID: 31010062 PMCID: PMC6523410 DOI: 10.3390/genes10040310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plants are exposed to diverse abiotic and biotic stimuli. These require fast and specific integrated responses. Such responses are coordinated at the protein and transcript levels and are incorporated into larger regulatory networks. Here, we focus on the evolution of transcriptional regulatory networks involved in plant–pathogen interactions. We discuss the evolution of regulatory networks and their role in fine-tuning plant defense responses. Based on the observation that many of the cornerstones of immune signaling in angiosperms are also present in streptophyte algae, it is likely that some regulatory components also predate the origin of land plants. The degree of functional conservation of many of these ancient components has not been elucidated. However, ongoing functional analyses in bryophytes show that some components are conserved. Hence, some of these regulatory components and how they are wired may also trace back to the last common ancestor of land plants or earlier. Of course, an understanding of the similarities and differences during the evolution of plant defense networks cannot ignore the lineage-specific coevolution between plants and their pathogens. In this review, we specifically focus on the small RNA regulatory networks involved in fine-tuning of the strength and timing of defense responses and highlight examples of pathogen exploitation of the host RNA silencing system. These examples illustrate well how pathogens frequently target gene regulation and thereby alter immune responses on a larger scale. That this is effective is demonstrated by the diversity of pathogens from distinct kingdoms capable of manipulating the same gene regulatory networks, such as the RNA silencing machinery.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, 38106 Braunschweig, Germany.
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
- CEPLAS-Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany.
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21
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Santos LS, Maximiano MR, Megias E, Pappas M, Ribeiro SG, Mehta A. Quantitative expression of microRNAs in Brassica oleracea infected with Xanthomonas campestris pv. campestris. Mol Biol Rep 2019; 46:3523-3529. [PMID: 30945070 DOI: 10.1007/s11033-019-04779-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/21/2019] [Indexed: 12/19/2022]
Abstract
Brassica oleracea var. capitata (cabbage) is an economically important crop affected by black rot disease caused by Xanthomonas campestris pv. campestris (Xcc). MicroRNAs (miRNAs) play an important role in plant defense modulation and therefore the analysis of these molecules can help better understand plant-pathogen interactions. In this study, we report the differential expression of four miRNAs that seem to participate in the plant response to Xcc infection. Northern Blot and RT-qPCR techniques were used to measure miRNA expression in resistant (União) and susceptible (Kenzan) cultivars. From 6 miRNAs analyzed, 4 were detected and differentially expressed, showing a down- and upregulated expression profile in susceptible and resistant cultivars, respectively. These results suggest that miR156, miR167, miR169, and miR390 could play a role in B. oleracea resistance enhancement against Xcc and could be explored as potential resistance markers in B. oleracea-Xcc interaction.
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Affiliation(s)
- Lucas Souza Santos
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
- Centro Universitário do Distrito Federal, SEP/SUL EQ 704/904 Conj.A, Brasília, DF, CEP 70390-045, Brazil
| | - Mariana Rocha Maximiano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
- Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n - Campus Universitário, Bairro São Pedro, Juiz de Fora, MG, CEP 36036-900, Brazil
| | - Esaú Megias
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
- Universidad de Cádiz, Calle Ancha, 16, 11001, Cádiz, Spain
| | - Marília Pappas
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
| | - Simone Graça Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil.
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Abstract
microRNA molecules have been shown to play various significant roles in many physiological and pathophysiological processes in living organisms. The tremendous interest in these molecules has led to the significant development and constant release of a number of computational tools useful for basic as well as advanced miRNA-related analyses. These approaches have various constantly evolving utilities, such as detection, target prediction, functional annotation, and many others. In this chapter, we provide an overview of several computational tools useful for broadly defined plant miRNA analysis.
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Affiliation(s)
- Anna Lukasik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
- Department of Plant Molecular Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Poland.
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23
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Islam W, Naveed H, Zaynab M, Huang Z, Chen HYH. Plant defense against virus diseases; growth hormones in highlights. PLANT SIGNALING & BEHAVIOR 2019; 14:1596719. [PMID: 30957658 PMCID: PMC6546145 DOI: 10.1080/15592324.2019.1596719] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 05/20/2023]
Abstract
Phytohormones are critical in various aspects of plant biology such as growth regulations and defense strategies against pathogens. Plant-virus interactions retard plant growth through rapid alterations in phytohormones and their signaling pathways. Recent research findings show evidence of how viruses impact upon modulation of various phytohormones affecting plant growth regulations. The opinion is getting stronger that virus-mediated phytohormone disruption and alteration weaken plant defense strategies through enhanced replication and systemic spread of viral particles. These hormones regulate plant-virus interactions in various ways that may involve antagonism and cross talk to modulate small RNA (sRNA) systems. The article aims to highlight the recent research findings elaborating the impact of viruses upon manipulation of phytohormones and virus biology.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Institute of Geography, Fujian Normal University, Fuzhou, China
| | - Hassan Naveed
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Madiha Zaynab
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Institute of Geography, Fujian Normal University, Fuzhou, China
- Zhiqun Huang Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Han Y. H. Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Institute of Geography, Fujian Normal University, Fuzhou, China
- Faculty of Natural Resources Management, Lakehead University, Ontario, Canada
- CONTACT Han Y. H. Chen Faculty of Natural Resources Management, Lakehead University, Ontario Canada
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24
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Islam W, Akutse KS, Qasim M, Khan KA, Ghramh HA, Idrees A, Latif S. Bemisia tabaci-mediated facilitation in diversity of begomoviruses: Evidence from recent molecular studies. Microb Pathog 2018; 123:162-168. [PMID: 30017827 DOI: 10.1016/j.micpath.2018.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 12/12/2022]
Abstract
Begomoviruses are considered as one of the most notorious plant viruses worldwide, which cause substantial economic losses to various field crops. Management of begomoviruses has become a challenge due to the continuous evolution and the emergence of new strains. Bemisia tabaci is globally known to be the key vector of begomoviruses, having relatively high reproductivity, fast dispersal ability, high survival rate due to its polyphagous nature and high resistance to various groups of insecticides. Continuous transmission of begomoviruses by the vector has led to the development and spread of epidemics of various diseases worldwide. In this review, we have critically analyzed the various dynamics which facilitate the diversity of begomoviruses through their vector. The interaction of begomovirus-whitefly leads to continuous research activities regarding management of both virus and its vector, thus opening exciting new horizons to formulate potential control strategies to ensure a disease-free cropping environment.
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Affiliation(s)
- Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan.
| | - Komivi Senyo Akutse
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - Muhammad Qasim
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Khalid Ali Khan
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Hamed A Ghramh
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Atif Idrees
- Institute of Beneficial Insects, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shahid Latif
- Department of Plant Pathology, Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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25
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Khalil F, Yueyu X, Naiyan X, Di L, Tayyab M, Hengbo W, Islam W, Rauf S, Pinghua C. Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding. Microb Pathog 2018; 120:187-197. [PMID: 29730517 DOI: 10.1016/j.micpath.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/26/2018] [Accepted: 05/02/2018] [Indexed: 12/28/2022]
Abstract
Sugarcane is an essential crop for sugar and biofuel. Globally, its production is severely affected by sugarcane yellow leaf disease (SCYLD) caused by Sugarcane Yellow Leaf Virus (SCYLV). Many aphid vectors are involved in the spread of the disease which reduced the effectiveness of cultural and chemical management. Empirical methods of plant breeding such as introgression from wild and cultivated germplasm were not possible or at least challenging due to the absence of resistance in cultivated and wild germplasm of sugarcane. RNA interference (RNAi) transformation is an effective method to create virus-resistant varieties. Nevertheless, limited progress has been made due to lack of comprehensive research program on SCYLV based on RNAi technique. In order to show improvement and to propose future strategies for the feasibility of the RNAi technique to cope SCYLV, genome-wide consensus sequences of SCYLV were analyzed through GenBank. The coverage rates of every consensus sequence in SCYLV isolates were calculated to evaluate their practicability. Our analysis showed that single consensus sequence from SCYLV could not work well for RNAi based sugarcane breeding programs. This may be due to high mutation rate and continuous recombination within and between various viral strains. Alternative multi-target RNAi strategy is suggested to combat several strains of the viruses and to reduce the silencing escape. The multi-target small interfering RNA (siRNA) can be used together to construct RNAi plant expression plasmid, and to transform sugarcane tissues to develop new sugarcane varieties resistant to SCYLV.
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Affiliation(s)
- Farghama Khalil
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xu Yueyu
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiao Naiyan
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Liu Di
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Muhammad Tayyab
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wang Hengbo
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Saeed Rauf
- University College of Agriculture, University of Sargodha, Pakistan
| | - Chen Pinghua
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; GMOs LAB of Quality Supervision Inspection &Testing Center for Sugarcane and Derived Products, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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26
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Islam W, Qasim M, Noman A, Adnan M, Tayyab M, Farooq TH, Wei H, Wang L. Plant microRNAs: Front line players against invading pathogens. Microb Pathog 2018. [PMID: 29524548 DOI: 10.1016/j.micpath.2018.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Plants are attacked by a large number of pathogens. To defend against these pathogens, plants activate or repress a vast array of genes. For genetic expression and reprogramming, host endogenous small RNAs (sRNAs) are the key factors. Among these sRNAs, microRNAs (miRNAs) mediate gene regulation through RNA silencing at the post-transcriptional level and play an essential role in the defense responses to biotic and abiotic stress. In the recent years, high-throughput sequencing has enabled the researchers to uncover the role of plant miRNAs during pathogen invasion. So here we have reviewed the recent research findings illustrating the plant miRNAs active involvement in various defense processes during fungal, bacterial, viral and nematode infections. However, rapid validation of direct targets of miRNAs is the dire need of time, which can be very helpful in improving the plant resistance against various pathogenic diseases.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Ali Noman
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Department of Botany, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Adnan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Tayyab
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Taimoor Hassan Farooq
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huang Wei
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
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27
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Islam W, Noman A, Qasim M, Wang L. Plant Responses to Pathogen Attack: Small RNAs in Focus. Int J Mol Sci 2018; 19:E515. [PMID: 29419801 PMCID: PMC5855737 DOI: 10.3390/ijms19020515] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 12/25/2022] Open
Abstract
Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38040, Pakistan.
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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28
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Islam W, Adnan M, Tayyab M, Hussain M, Islam SU. Phyto-metabolites; An Impregnable Shield against Plant Viruses. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Worldwide, economically important crops are under continuous threat from plant viruses as they reproduce within the host and spread via various biological and non biological means. The problem can be minimized via application of integrated management approaches involving utilization of resistant genotypes and reducing the insect vector population. But such strategies are rarely applied in developing countries and farmers prefer to use chemicals against all type of diseases. But increasing use of pesticides is a leading cause of disaster to our ecosystem so alternative means such as phyto-metabolites should be explored for eco friendly management of plant viruses. So here we have reviewed about different phyto-metabolites that can be effectively and potentially used against various plant virus diseases. We further explained about the various primary and secondary metabolites such as alkaloids, essential oils, flavonoids, polysaccharides and proteins. The review highlights the recent advances in the field of phyto-metabolites utilization against plant viruses and sums up via hoping through prospects that future drugs will be safer for human beings and our ecosystem.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Fujian Province Key Laboratory for Plant Viruses, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Muhammad Adnan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Muhammad Tayyab
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Mubasher Hussain
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Saif Ul Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Fujian Province Key Laboratory for Plant Viruses, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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