1
|
Padilla-Padilla EA, De la Rosa C, Aragón W, Ávila-Sandoval AK, Torres M, Dorantes-Acosta AE, Arteaga-Vázquez MA, Formey D, Serrano M. Identification of Arabidopsis thaliana small RNAs responsive to the fungal pathogen Botrytis cinerea at an early stage of interaction. PLoS One 2024; 19:e0304790. [PMID: 38875250 PMCID: PMC11178217 DOI: 10.1371/journal.pone.0304790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/19/2024] [Indexed: 06/16/2024] Open
Abstract
In plants, small RNAs (sRNAs), mainly microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been described as key regulators of plant development, growth, and abiotic and biotic responses. Despite reports indicating the involvement of certain sRNAs in regulating the interaction between Botrytis cinerea (a major necrotrophic fungal phytopathogen) and host plants, there remains a lack of analysis regarding the potential regulatory roles of plant sRNAs during early stages of the interaction despite early immune responses observed then during infection. We present the first transcriptome-wide analysis of small RNA expression on the early interaction between the necrotrophic fungus Botrytis cinerea and the model plant Arabidopsis thaliana. We found that evolutionary conserved A. thaliana miRNAs were the sRNAs that accumulated the most in the presence of B. cinerea. The upregulation of miR167, miR159 and miR319 was of particular interest because these, together with their target transcripts, are involved in the fine regulation of the plant hormone signaling pathways. We also describe that miR173, which triggers the production of secondary siRNAs from TAS1 and TAS2 loci, as well as secondary siRNAs derived from these loci, is upregulated in response to B. cinerea. Thus, at an early stage of the interaction there are transcriptional changes of sRNA-guided silencing pathway genes and of a subset of sRNAs that targeted genes from the PPR gene superfamily, and these may be important mechanisms regulating the interaction between A. thaliana and B. cinerea. This work provides the basis for a better understanding of the regulation mediated by sRNAs during early B. cinerea-plant interaction and may help in the development of more effective strategies for its control.
Collapse
Affiliation(s)
- Emir Alejandro Padilla-Padilla
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Ciudad Universitaria, Coyoacán, Ciudad de México
| | - Carlos De la Rosa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Wendy Aragón
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Chiapas, México
| | - Ana Karen Ávila-Sandoval
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Torres
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ana Elena Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, México
| | - Mario A Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, México
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
2
|
Rodrigues JCM, Carrijo J, Anjos RM, Cunha NB, Grynberg P, Aragão FJL, Vianna GR. The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development. Transgenic Res 2024:10.1007/s11248-024-00387-9. [PMID: 38856866 DOI: 10.1007/s11248-024-00387-9] [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: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Plants evolved, over millions of years, complex defense systems against pathogens. Once infected, the interaction between pathogen effector molecules and host receptors triggers plant immune responses, which include apoptosis, systemic immune response, among others. An important protein family responsible for pathogen effector recognition is the nucleotide binding site-leucine repeat rich (NBS-LRR) proteins. The NBS-LRR gene family is the largest disease resistance gene class in plants. These proteins are widely distributed in vascular plants and have a complex multigenic cluster distribution in plant genomes. To counteract the genetic load of such a large gene family on fitness cost, plants evolved a mechanism using post transcriptional gene silencing induced by small RNAs, particularly microRNAs. For the NBS-LRR gene family, the small RNAs involved in this silencing mechanism are mainly the microRNA482/2118 superfamily. This suppression mechanism is relieved upon pathogen infection, thus allowing increased NBS-LRR expression and triggering plant immunity. In this review, we will discuss the biogenesis of microRNAs and secondary RNAs involved in this silencing mechanism, biochemical and structural features of NBS-LRR proteins in response to pathogen effectors and the evolution of microRNA-based silencing mechanism with a focus on the miR482/2118 family. Furthermore, the biotechnological manipulation of microRNA expression, using both transgenic or genome editing approaches to improve cultivated plants will be discussed, with a focus on the miR482/2118 family in soybean.
Collapse
Affiliation(s)
- J C M Rodrigues
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
| | - J Carrijo
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - R M Anjos
- University of Brasília, Brasília, Brazil
| | - N B Cunha
- University of Brasília, Brasília, Brazil
| | - P Grynberg
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - F J L Aragão
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - G R Vianna
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| |
Collapse
|
3
|
Silvestri A, Bansal C, Rubio-Somoza I. After silencing suppression: miRNA targets strike back. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00119-5. [PMID: 38811245 DOI: 10.1016/j.tplants.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024]
Abstract
Within the continuous tug-of-war between plants and microbes, RNA silencing stands out as a key battleground. Pathogens, in their quest to colonize host plants, have evolved a diverse arsenal of silencing suppressors as a common strategy to undermine the host's RNA silencing-based defenses. When RNA silencing malfunctions in the host, genes that are usually targeted and silenced by microRNAs (miRNAs) become active and can contribute to the reprogramming of host cells, providing an additional defense mechanism. A growing body of evidence suggests that miRNAs may act as intracellular sensors to enable a rapid response to pathogen threats. Herein we review how plant miRNA targets play a crucial role in immune responses against different pathogens.
Collapse
Affiliation(s)
- Alessandro Silvestri
- Molecular Reprogramming and Evolution Laboratory, Centre for Research in Agricultural Genomics, 08193 Barcelona, Spain
| | - Chandni Bansal
- Molecular Reprogramming and Evolution Laboratory, Centre for Research in Agricultural Genomics, 08193 Barcelona, Spain
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution Laboratory, Centre for Research in Agricultural Genomics, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08001, Spain.
| |
Collapse
|
4
|
Ledford WC, Silvestri A, Fiorilli V, Roth R, Rubio-Somoza I, Lanfranco L. A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis. THE NEW PHYTOLOGIST 2024; 242:1534-1544. [PMID: 37985403 DOI: 10.1111/nph.19394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/15/2023] [Indexed: 11/22/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.
Collapse
Affiliation(s)
- William Conrad Ledford
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Alessandro Silvestri
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08001, Spain
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| |
Collapse
|
5
|
Asadi M, Millar AA. Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111993. [PMID: 38266718 DOI: 10.1016/j.plantsci.2024.111993] [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: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.
Collapse
Affiliation(s)
- Mohsen Asadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Agricultural Science, Technical and Vocational University (TVU), Tehran, Iran
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australia; ARC Training Centre for Accelerated Future Crop development, ANU, Canberra, Australia.
| |
Collapse
|
6
|
Mierziak J, Wojtasik W. Epigenetic weapons of plants against fungal pathogens. BMC PLANT BIOLOGY 2024; 24:175. [PMID: 38443788 PMCID: PMC10916060 DOI: 10.1186/s12870-024-04829-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.
Collapse
Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland.
| |
Collapse
|
7
|
Zhang JH, Wei HB, Hong YH, Yang RR, Meng J, Luan YS. The lncRNA20718-miR6022-RLPs module regulates tomato resistance to Phytophthora infestans. PLANT CELL REPORTS 2024; 43:57. [PMID: 38319523 DOI: 10.1007/s00299-024-03161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
KEY MESSAGE Sl-lncRNA20718 acts as an eTM of Sl-miR6022 regulating its expression thereby affecting SlRLP6/10 expression. SlRLP6/10 regulate PRs expression, ROS accumulation, and JA/ET content thereby affecting tomato resistance to P. infestans. Tomato (Solanum lycopersicum) is an important horticultural and cash crop whose yield and quality can be severely affected by Phytophthora infestans (P. infestans). Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are widely involved in plant defense responses against pathogens. The involvement of Sl-lncRNA20718 and Sl-miR6022 in tomato resistance to P. infestans as well as the targeting of Sl-miR6022 to receptor-like protein genes (RLPs) were predicted in our previous study. However, uncertainty exists regarding their potential interaction as well as the molecular processes regulating tomato resistance. Here, we found that Sl-lncRNA20718 and Sl-miR6022 are positive and negative regulators of tomato resistance to P. infestans by gain- and loss-of-function experiments, respectively. Overexpression of Sl-lncRNA20718 decreased the expression of Sl-miR6022, induced the expression of PRs, reduced the diameter of lesions (DOLs), thereby enhanced disease resistance. A six-point mutation in the binding region of Sl-lncRNA20718 to Sl-miR6022 disabled the interaction, indicating that Sl-lncRNA20718 acts as an endogenous target mimic (eTM) of Sl-miR6022. We demonstrated that Sl-miR6022 cleaves SlRLP6/10. Overexpression of Sl-miR6022 decreases the expression levels of SlRLP6/10, induces the accumulation of reactive oxygen species (ROS) and reduces the content of JA and ET, thus inhibiting tomato resistance to P. infestans. In conclusion, our study provides detailed information on the lncRNA20718-miR6022-RLPs module regulating tomato resistance to P. infestans by affecting the expression of disease resistance-related genes, the accumulation of ROS and the phytohormone levels, providing a new reference for tomato disease resistance breeding.
Collapse
Affiliation(s)
- Jia-Hui Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Hong-Bo Wei
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Hui Hong
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Rui-Rui Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Shi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| |
Collapse
|
8
|
de Oliveira Cabral SK, de Freitas MB, Stadnik MJ, Kulcheski FR. Emerging roles of plant microRNAs during Colletotrichum spp. infection. PLANTA 2024; 259:48. [PMID: 38285194 DOI: 10.1007/s00425-023-04318-6] [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: 07/10/2023] [Accepted: 12/23/2023] [Indexed: 01/30/2024]
Abstract
MAIN CONCLUSION This review provides valuable insights into plant molecular regulatory mechanisms during fungus attacks, highlighting potential miRNA candidates for future disease management. Plant defense responses to biotic stress involve intricate regulatory mechanisms, including post-transcriptional regulation of genes mediated by microRNAs (miRNAs). These small RNAs play a vital role in the plant's innate immune system, defending against viral, bacterial, and fungal attacks. Among the plant pathogenic fungi, Colletotrichum spp. are notorious for causing anthracnose, a devastating disease affecting economically important crops worldwide. Understanding the molecular machinery underlying the plant immune response to Colletotrichum spp. is crucial for developing tools to reduce production losses. In this comprehensive review, we examine the current understanding of miRNAs associated with plant defense against Colletotrichum spp. We summarize the modulation patterns of miRNAs and their respective target genes. Depending on the function of their targets, miRNAs can either contribute to host resistance or susceptibility. We explore the multifaceted roles of miRNAs during Colletotrichum infection, including their involvement in R-gene-dependent immune system responses, hormone-dependent defense mechanisms, secondary metabolic pathways, methylation regulation, and biosynthesis of other classes of small RNAs. Furthermore, we employ an integrative approach to correlate the identified miRNAs with various strategies and distinct phases of fungal infection. This study provides valuable insights into the current understanding of plant miRNAs and their regulatory mechanisms during fungus attacks.
Collapse
Affiliation(s)
- Sarah Kirchhofer de Oliveira Cabral
- Group of Plant Molecular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
- Post-Graduation Program in Cell and Developmental Biology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Mateus Brusco de Freitas
- Laboratory of Plant Pathology, Center of Agricultural Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Marciel João Stadnik
- Laboratory of Plant Pathology, Center of Agricultural Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Franceli Rodrigues Kulcheski
- Group of Plant Molecular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianópolis, Brazil.
- Post-Graduation Program in Cell and Developmental Biology, Federal University of Santa Catarina, Florianópolis, Brazil.
| |
Collapse
|
9
|
Ormancey M, Guillotin B, Ribeyre C, Medina C, Jariais N, San Clemente H, Thuleau P, Plaza S, Beck M, Combier J. Immune-enhancing miPEPs reduce plant diseases and offer new solutions in agriculture. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:13-15. [PMID: 37864306 PMCID: PMC10753997 DOI: 10.1111/pbi.14187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/22/2023]
Affiliation(s)
- Mélanie Ormancey
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
- Present address:
Epigenetics and Plant Development, Centre for Research in Agricultural Genomics (CRAG)UABBarcelonaSpain
| | - Bruno Guillotin
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
- Micropep TechnologiesAuzeville‐TolosaneFrance
- Present address:
The Department of Biology, The Center for Genomics and Systems BiologyNew York UniversityNew YorkUSA
| | | | | | - Nathanael Jariais
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
| | - Patrice Thuleau
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
| | - Serge Plaza
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
| | | | - Jean‐Philippe Combier
- Laboratoire de Recherche en Sciences VégétalesCNRS/UPSAuzeville‐TolosaneFrance
- Micropep TechnologiesAuzeville‐TolosaneFrance
| |
Collapse
|
10
|
Mmbando GS. The recent relationship between ultraviolet-B radiation and biotic resistance in plants: a novel non-chemical strategy for managing biotic stresses. PLANT SIGNALING & BEHAVIOR 2023; 18:2191463. [PMID: 36934364 PMCID: PMC10730183 DOI: 10.1080/15592324.2023.2191463] [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: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Ultraviolet-B radiation (UVB; 280-315 nm) is a significant environmental factor that alters plant development, changes interactions between species, and reduces the prevalence of pests and diseases. While UVB radiation has negative effects on plant growth and performance at higher doses, at lower and ambient doses, UVB radiation acts as a non-chemical method for managing biotic stresses by having positive effects on disease resistance and genes that protect plants from pests. Understanding the recent relationship between UVB radiation and plants' biotic stresses is crucial for the development of crops that are resistant to UVB and biotic stresses. However, little is known about the recent interactions between UVB radiation and biotic stresses in plants. This review discusses the most recent connections between UVB radiation and biotic stresses in crops, including how UVB radiation affects a plant's resistance to disease and pests. The interaction of UVB radiation with pathogens and herbivores has been the subject of the most extensive research of these. This review also discusses additional potential strategies for conferring multiple UVB-biotic stress resistance in crop plants, such as controlling growth inhibition, miRNA 396 and 398 modulations, and MAP kinase. This study provides crucial knowledge and methods for scientists looking to develop multiple resistant crops that will improve global food security.
Collapse
Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma (UDOM), Dodoma, Tanzania
| |
Collapse
|
11
|
Si X, Liu H, Cheng X, Xu C, Han Z, Dai Z, Wang R, Pan C, Lu G. Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum. Int J Biol Macromol 2023; 253:126891. [PMID: 37709224 DOI: 10.1016/j.ijbiomac.2023.126891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.
Collapse
Affiliation(s)
- Xiuyang Si
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongyan Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi Cheng
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chengcui Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanghui Han
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhongren Dai
- Branch Academy of Horticultural Research, Harbin Academy of Agricultural Sciences, Harbin 150029, China
| | - Rongqing Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Changtian Pan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China
| | - Gang Lu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
12
|
Javed M, Reddy B, Sheoran N, Ganesan P, Kumar A. Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction. Gene 2023; 886:147718. [PMID: 37595851 DOI: 10.1016/j.gene.2023.147718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
The plant pathogen Magnaporthe oryzae poses a significant threat to global food security, and its management through the cultivation of resistant varieties and crop husbandry practices, including fungicidal sprays, has proven to be inadequate. To address this issue, we conducted small-RNA sequencing to identify the roles of miRNAs and their target genes in both resistant (PB1637) and susceptible (PB1) rice genotypes. We confirmed the expression of differentially expressed miRNAs using stem-loop qRT-PCR analysis and correlated them with rice patho-phenotypic and physio-biochemical responses. Our findings revealed several noteworthy differences between the resistant and susceptible genotypes. The resistant genotype exhibited reduced levels of total chlorophyll and carotenoids compared to the susceptible genotype. However, it showed increased levels of total protein, callose, H2O2, antioxidants, flavonoids, and total polyphenols. Additionally, among the defense-associated enzymes, guaiacol peroxidase and polyphenol oxidase responses were higher in the susceptible genotypes. In our comparative analysis, we identified 27 up-regulated and 43 down-regulated miRNAs in the resistant genotype, while the susceptible genotype exhibited 44 up-regulated and 62 down-regulated miRNAs. Furthermore, we discovered eight up-regulated and five down-regulated miRNAs shared between the resistant and susceptible genotypes. Notably, we also identified six novel miRNAs in the resistant genotype and eight novel miRNAs in the susceptible genotype. These novel miRNAs, namely Chr8_26996, Chr12_40110, and Chr12_41899, were found to negatively correlate with the expression of predicted target genes, including Cyt-P450 monooxygenase, serine carboxypeptidase, and zinc finger A20 domain-containing stress-associated protein, respectively. The results of our study on miRNA and transcriptional responses provide valuable insights for the development of future rice lines that are resistant to blast disease. By understanding the roles of specific miRNAs and their target genes in conferring resistance, we can enhance breeding strategies and improve crop management practices to ensure global food security.
Collapse
Affiliation(s)
- Mohammed Javed
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, Postal Code: 110012, India
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, Postal Code: 110012, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, Postal Code: 110012, India
| | - Prakash Ganesan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, Postal Code: 110012, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, Postal Code: 110012, India.
| |
Collapse
|
13
|
Hasan MN, Mosharaf MP, Uddin KS, Das KR, Sultana N, Noorunnahar M, Naim D, Mollah MNH. Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea ( Vigna unguiculata (L.) Walp.). BIOMED RESEARCH INTERNATIONAL 2023; 2023:8832406. [PMID: 38046903 PMCID: PMC10691899 DOI: 10.1155/2023/8832406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.
Collapse
Affiliation(s)
- Mohammad Nazmol Hasan
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Parvez Mosharaf
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Khandoker Saif Uddin
- Department of Quantitative Science (Statistics), International University of Business Agriculture and Technology (IUBAT), Uttara, Bangladesh
| | - Keya Rani Das
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nasrin Sultana
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mst. Noorunnahar
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Yang X, Fu T, Yu R, Zhang L, Yang Y, Xiao D, Wang Y, Wang Y, Wang Y. miR159a modulates poplar resistance against different fungi and bacteria. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107899. [PMID: 37494825 DOI: 10.1016/j.plaphy.2023.107899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/14/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Trees are inevitably attacked by different kinds of pathogens in their life. However, little is known about the regulatory factors in poplar response to different pathogen infections. MicroRNA159 (miR159) is a highly conserved microRNA (miRNA) in plants and regulates plant development and stress responses. Here, transgenic poplar overexpressing pto-miR159a (OX-159) showed antagonistic regulation mode to poplar stem disease caused by fungi Cytospora chrysosperma and bacteria Lonsdalea populi. OX-159 lines exhibited a higher susceptibility after inoculation with bacterium L. populi, whereas enhanced disease resistance to necrotrophic fungi C. chrysosperma compared with wild-type (WT) poplars. Intriguingly, further disease assay found that OX159 line rendered the poplar susceptible to hemi-biotrophic fungi Colletotrichum gloeosporioide, exhibiting larger necrosis and lower ROS accumulation than WT lines. Transcriptome analyses revealed that more down-regulated differentially expressed genes with disease-resistant domains in OX-159 line compared with WT line. Moreover, the central mediator NPR1 of salicylic acid (SA) pathway showed a decrease in expression level, while jasmonic acid/ethylene (JA/ET) signal pathway marker genes ERF, as well as PR3, MPK3, and MPK6 genes showed an increase level in OX159-2 and OX159-5 compared with WT lines. Further spatio-temporal expression analysis revealed JA/ET signaling was involved in the dynamic response process to C. gloeosporioides in WT and OX159 lines. These results demonstrate that overexpression of pto-miR159a resulted in the crosstalk changes of the downstream hub genes, thereby controlling the disease resistance of poplars, which provides clues for understanding pto-miR159a role in coordinating poplar-pathogen interactions.
Collapse
Affiliation(s)
- Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tiantian Fu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruen Yu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lichun Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Forestry Investigation and Planning Institute of Liaoning Province, Liaoning, 110122, China
| | - Yuzhang Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Dandan Xiao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - YuanYuan Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Yonglin Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
16
|
Arora S, Singh AK, Chaudhary B. Coordination of floral and fiber development in cotton (Gossypium) by hormone- and flavonoid-signalling associated regulatory miRNAs. PLANT MOLECULAR BIOLOGY 2023; 112:1-18. [PMID: 37067671 DOI: 10.1007/s11103-023-01341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/16/2023] [Indexed: 05/09/2023]
Abstract
Various plant development activities and stress responses are tightly regulated by various microRNAs (miRNA) and their target genes, or transcription factors in a spatiotemporal manner. Here, to exemplify how flowering-associated regulatory miRNAs synchronize their expression dynamics during floral and fiber development in cotton, constitutive expression diminution transgenic lines of auxin-signaling regulatory Gh-miR167 (35S-MIM167) were developed through target mimicry approach. 'Moderate' (58% to 80%)- and 'high' (> 80%)-Gh-miR167 diminution mimic lines showed dosage-dependent developmental deformities in anther development, pollen maturation, and fruit (= boll) formation. Cross pollination of 'moderate' 35S-MIM167 mimic lines with wild type (WT) plant partially restored boll formation and emergence of fiber initials on the ovule surface. Gh-miR167 diminution favored organ-specific transcription biases in miR159, miR166 as well as miR160, miR164, and miR172 along with their target genes during anther and petal development, respectively. Similarly, accumulative effect of percent Gh-miR167 diminution, cross regulation of its target ARF6/8 genes, and temporal mis-expression of hormone signaling- and flavonoid biosynthesis-associated regulatory miRNAs at early fiber initiation stage caused irregular fiber formation. Spatial and temporal transcription proportions of regulatory miRNAs were also found crucial for the execution of hormone- and flavonoid-dependent progression of floral and fiber development. These observations discover how assorted regulatory genetic circuits get organized in response to Gh-miR167 diminution and converge upon ensuing episodes of floral and fiber development in cotton.
Collapse
Affiliation(s)
- Sakshi Arora
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Amarjeet Kumar Singh
- Center for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India.
| |
Collapse
|
17
|
Yan J, Qiu R, Wang K, Liu Y, Zhang W. Enhancing alfalfa resistance to Spodoptera herbivory by sequestering microRNA396 expression. PLANT CELL REPORTS 2023; 42:805-819. [PMID: 36757447 DOI: 10.1007/s00299-023-02993-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
KEY MESSAGE Sequestering microRNA396 by overexpression of MIM396 enhanced alfalfa resistance to Spodoptera litura larvae, which may be due to increased lignin content and enhanced low-molecular weight flavonoids and glucosinolates biosynthesis. Alfalfa (Medicago sativa), the most important leguminous forage crop, suffers from the outbreak of defoliator insects, especially Spodoptera litura, resulting in heavy losses in yield and forage quality. Here, we found that the expression of alfalfa microRNA396 (miR396) precursor genes and mature miR396 was significantly up-regulated in wounding treatment that simulates feeding injury by defoliator insects. To verify the function of miR396 in alfalfa resistance to insect, we generated MIM396 transgenic alfalfa plants with significantly down-regulated miR396 expression by Agrobacterium-mediated genetic transformation. The MIM396 transgenic alfalfa plants exhibited improved resistance to Spodoptera litura larvae with increased lignin content but decreased JA accumulation. Most of the miR396 putative target GRF genes were up-regulated in MIM396 transgenic lines, and responded to the wounding treatment. By RNA sequencing analysis, we found that the differentially expressed genes related to insect resistance between WT and MIM396 transgenic plants mainly clustered in biosynthesis pathways in lignin, flavonoids and glucosinolates. In addition to the phenotype of enhanced insect resistance, MIM396 transgenic plants also displayed reduced biomass yield and forage quality. Our results broaden the function of miR396 in alfalfa and provide genetic resources for studying alfalfa insect resistance.
Collapse
Affiliation(s)
- Jianping Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rumeng Qiu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kexin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
18
|
Rego ECS, Pinheiro TDM, Fonseca FCDA, Gomes TG, Costa EDC, Bastos LS, Alves GSC, Cotta MG, Amorim EP, Ferreira CF, Togawa RC, Costa MMDC, Grynberg P, Miller RNG. Characterization of microRNAs and Target Genes in Musa acuminata subsp. burmannicoides, var. Calcutta 4 during Interaction with Pseudocercospora musae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1473. [PMID: 37050099 PMCID: PMC10097032 DOI: 10.3390/plants12071473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Endogenous microRNAs (miRNAs) are small non-coding RNAs that perform post-transcriptional regulatory roles across diverse cellular processes, including defence responses to biotic stresses. Pseudocercospora musae, the causal agent of Sigatoka leaf spot disease in banana (Musa spp.), is an important fungal pathogen of the plant. Illumina HiSeq 2500 sequencing of small RNA libraries derived from leaf material in Musa acuminata subsp. burmannicoides, var. Calcutta 4 (resistant) after inoculation with fungal conidiospores and equivalent non-inoculated controls revealed 202 conserved miRNAs from 30 miR-families together with 24 predicted novel miRNAs. Conserved members included those from families miRNA156, miRNA166, miRNA171, miRNA396, miRNA167, miRNA172, miRNA160, miRNA164, miRNA168, miRNA159, miRNA169, miRNA393, miRNA535, miRNA482, miRNA2118, and miRNA397, all known to be involved in plant immune responses. Gene ontology (GO) analysis of gene targets indicated molecular activity terms related to defence responses that included nucleotide binding, oxidoreductase activity, and protein kinase activity. Biological process terms associated with defence included response to hormone and response to oxidative stress. DNA binding and transcription factor activity also indicated the involvement of miRNA target genes in the regulation of gene expression during defence responses. sRNA-seq expression data for miRNAs and RNAseq data for target genes were validated using stem-loop quantitative real-time PCR (qRT-PCR). For the 11 conserved miRNAs selected based on family abundance and known involvement in plant defence responses, the data revealed a frequent negative correlation of expression between miRNAs and target host genes. This examination provides novel information on miRNA-mediated host defence responses, applicable in genetic engineering for the control of Sigatoka leaf spot disease.
Collapse
Affiliation(s)
| | | | | | - Taísa Godoy Gomes
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Erica de Castro Costa
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Lucas Santos Bastos
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | | | - Michelle Guitton Cotta
- Instituto de Ciências Biológicas, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | | | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, Brasília 70770-917, DF, Brazil
| | - Marcos Mota Do Carmo Costa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, Brasília 70770-917, DF, Brazil
| | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, Brasília 70770-917, DF, Brazil
| | | |
Collapse
|
19
|
Wang S, Wang X, Chen J. Identification of miRNAs Involved in Maize-Induced Systemic Resistance Primed by Trichoderma harzianum T28 against Cochliobolus heterostrophus. J Fungi (Basel) 2023; 9:jof9020278. [PMID: 36836392 PMCID: PMC9964586 DOI: 10.3390/jof9020278] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
microRNAs (miRNAs) are known to play important roles in the immune response to pathogen infection in different plants. Further, Trichoderma strains are able to activate plant defense responses against pathogen attacks. However, little is known about the involvement of miRNAs in the defense response primed by Trichoderma strains. To explore the miRNAs sensitive to priming by Trichoderma, we studied the small RNAs and transcriptome changes in maize leaves that were systemically induced by seed treatment with Trichoderma harzianum (strain T28) against Cochliobolus heterostrophus (C. heterostrophus) infection in leaves. Through analysis of the sequencing data, 38 differentially expressed miRNAs (DEMs) and 824 differentially expressed genes (DEGs) were identified. GO and KEGG analyses of DEGs demonstrated that genes involved in the plant hormone signal transduction pathway and oxidation-reduction process were significantly enriched. In addition, 15 miRNA-mRNA interaction pairs were identified through the combined analysis of DEMs and DEGs. These pairs were supposed to play roles in the maize resistance primed by T. harzianum T28 to C. heterostrophus, in which miR390, miR169j, miR408b, miR395a/p, and novel miRNA (miRn5231) were more involved in the induction of maize resistance. This study provided valuable information for understanding the regulatory role of miRNA in the T. harzianum primed defense response.
Collapse
Affiliation(s)
- Shaoqing Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xinhua Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Ministry of Agriculture Key Laboratory of Urban Agriculture (South), Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Correspondence:
| |
Collapse
|
20
|
Halder K, Chaudhuri A, Abdin MZ, Datta A. Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant. Int J Mol Sci 2023; 24:ijms24043143. [PMID: 36834556 PMCID: PMC9966754 DOI: 10.3390/ijms24043143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.
Collapse
Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Correspondence: (A.C.); (A.D.); Tel.: +91-1126742750 or +91-1126735119 (A.D.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Correspondence: (A.C.); (A.D.); Tel.: +91-1126742750 or +91-1126735119 (A.D.)
| |
Collapse
|
21
|
Luo M, Sun X, Xu M, Tian Z. Identification of miRNAs Involving Potato- Phytophthora infestans Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:461. [PMID: 36771544 PMCID: PMC9921761 DOI: 10.3390/plants12030461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
sRNAs (small RNAs) play an important role in regulation of plant immunity against a variety of pathogens. In this study, sRNA sequencing analysis was performed to identify miRNAs (microRNAs) during the interaction of potato and Phytophthora infestans. Totally, 171 potato miRNAs were identified, 43 of which were annotated in the miRNA database and 128 were assigned as novel miRNAs in this study. Those potato miRNAs may target 878 potato genes and half of them encode resistance proteins. Fifty-three potato miRNAs may target 194 P. infestans genes. Three potato miRNAs (novel 72, 133, and 140) were predicted to have targets only in the P. infestans genome. miRNAs transient expression and P. infestans inoculation assay showed that miR396, miR166, miR6149-5P, novel133, or novel140 promoted P. infestans colonization, while miR394 inhibited colonization on Nicotiana benthamiana leaves. An artificial miRNA target (amiRNA) degradation experiment demonstrated that miR394 could target both potato gene (PGSC0003DMG400034305) and P. infestans genes. miR396 targets the multicystatin gene (PGSC0003DMG400026899) and miR6149-5p could shear the galactose oxidase F-box protein gene CPR30 (PGSC0003DMG400021641). This study provides new information on the aspect of cross-kingdom immune regulation in potato-P. infestans interaction at the sRNAs regulation level.
Collapse
Affiliation(s)
- Ming Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
| | - Xinyuan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan 430070, China
| | - Meng Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan 430070, China
- Hubei Hongshan Laboratory (HZAU), Wuhan 430070, China
| |
Collapse
|
22
|
He R, Tang Y, Wang D. Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit. PLANTS (BASEL, SWITZERLAND) 2023; 12:411. [PMID: 36679124 PMCID: PMC9866404 DOI: 10.3390/plants12020411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Non-coding RNAs play vital roles in the diverse biological processes of plants, and they are becoming key topics in horticulture research. In particular, miRNAs and long non-coding RNAs (lncRNAs) are receiving increased attention in fruit crops. Recent studies in horticulture research provide both genetic and molecular evidence that miRNAs and lncRNAs regulate biological function and stress responses during fruit development. Here, we summarize multiple regulatory modules of miRNAs and lncRNAs and their biological roles in fruit sets and stress responses, which would guide the development of molecular breeding techniques on horticultural crops.
Collapse
Affiliation(s)
- Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yajun Tang
- Shandong Laboratory of Advanced Agricultural Sciences, Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang 330031, China
| |
Collapse
|
23
|
Yu Y, Zhang T, Sun J, Jing T, Shen Y, Zhang K, Chen Y, Ding D, Wang G, Yang J, Tang J, Shi Z, Wang D, Gou M. Evolutionary characterization of miR396s in Poaceae exemplified by their genetic effects in wheat and maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111465. [PMID: 36155239 DOI: 10.1016/j.plantsci.2022.111465] [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: 07/24/2022] [Revised: 09/01/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
MiR396s play important roles in regulating plant growth and stress response, and great potential for crop yield promotion was anticipated. For more comprehensive and precise understanding of miR396s in Poaceae, we analyzed the phylogenetic linkage, gene expression, and chromosomal distribution of miR396s in this study. Although the mature miR396s' sequences were mostly conserved, differential expression patterns and chromosomal distribution were found among Poaceae species including the major cereal crops rice, wheat, and maize. Consistently, in comparison with rice, wheat and maize plants transformed with the target mimicry construct of miR396 (MIM396) exhibited differential effects on grain size and disease resistance. While the TaMIM396 plants showed increased grain size, panicle length and sensitivity to B. graminis, the ZmMIM396 plants didn't show obvious changes in grain size and disease resistance. In Addition, several GROWTH-REGULATING FACTOR (GRF) genes in wheat and maize were repressed by miR396s, which could be reversed by MIM396, confirming the conserved regulatory roles of miR396 on GRFs. While providing new solution to enhance grain yield in wheat and revealing potential regulatory variations of miR396s in controlling grain size and disease resistance in different crops, this study gives clues to further explore miR396s' functions in other Poaceae species.
Collapse
Affiliation(s)
- Yanwen Yu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Tongxiang Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingfan Sun
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Teng Jing
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanjie Shen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kunpu Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yan Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Ding
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou, Henan 450002, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
24
|
Nair MM, Kumar SHK, Jyothsna S, Sundaram KT, Manjunatha C, Sivasamy M, Alagu M. Stem and leaf rust-induced miRNAome in bread wheat near-isogenic lines and their comparative analysis. Appl Microbiol Biotechnol 2022; 106:8211-8232. [PMID: 36385566 DOI: 10.1007/s00253-022-12268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
Abstract
Wheat rusts remain a major threat to global wheat production and food security. The R-gene-mediated resistance has been employed as an efficient approach to develop rust-resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel molecular players, including non-coding RNAs for plant response. This study identified microRNAs associated with Sr36 and Lr45 disease resistance genes in response to stem and leaf rust, respectively. Here, small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem and leaf rust pathotypes. microRNA mining in stem rust-inoculated cultivars revealed a total of distinct 26 known and 7 novel miRNAs, and leaf rust libraries culminated with 22 known and 4 novel miRNAs. The comparative analysis between two disease sets provides a better understanding of altered miRNA profiles associated with respective R-genes and infections. Temporal differential expression pattern of miRNAs pinpoints their role during the progress of infection. Differential expression pattern of miRNAs among various treatments as well as time-course expression of miRNAs revealed stem and leaf rust-responsive miRNAs and their possible role in balancing disease resistance/susceptibility. Disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 from different subgenome origins might serve as a potential link between stem and leaf rust defence mechanisms downstream to respective R-genes. The outcome from the analysis of microRNA dynamics among two rust diseases and further characterization of identified microRNAs can contribute to significant novel insights on wheat-rust interactions and rust management. KEY POINTS: • Identification and comparative analysis of stem and leaf rust-responsive miRNAs. • Chromosomal location and functional prediction of miRNAs. • Time-course expression analysis of pathogen-responsive miRNAs.
Collapse
Affiliation(s)
- Minu M Nair
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Jyothsna
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South Asia Hub, Patancheru, 502324, Telangana, India
| | - C Manjunatha
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560024, Karnataka, India
| | - M Sivasamy
- ICAR-Indian Agricultural, Research Institute, Regional Station, Wellington, 643231, Tamil Nadu, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India.
| |
Collapse
|
25
|
Wang L, Calabria J, Chen HW, Somssich M. The Arabidopsis thaliana-Fusarium oxysporum strain 5176 pathosystem: an overview. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6052-6067. [PMID: 35709954 PMCID: PMC9578349 DOI: 10.1093/jxb/erac263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Fusarium oxysporum is a soil-borne fungal pathogen of several major food crops. Research on understanding the molecular details of fungal infection and the plant's defense mechanisms against this pathogen has long focused mainly on the tomato-infecting F. oxysporum strains and their specific host plant. However, in recent years, the Arabidopsis thaliana-Fusarium oxysporum strain 5176 (Fo5176) pathosystem has additionally been established to study this plant-pathogen interaction with all the molecular biology, genetic, and genomic tools available for the A. thaliana model system. Work on this system has since produced several new insights, especially with regards to the role of phytohormones involved in the plant's defense response, and the receptor proteins and peptide ligands involved in pathogen detection. Furthermore, work with the pathogenic strain Fo5176 and the related endophytic strain Fo47 has demonstrated the suitability of this system for comparative studies of the plant's specific responses to general microbe- or pathogen-associated molecular patterns. In this review, we highlight the advantages of this specific pathosystem, summarize the advances made in studying the molecular details of this plant-fungus interaction, and point out open questions that remain to be answered.
Collapse
Affiliation(s)
- Liu Wang
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jacob Calabria
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hsiang-Wen Chen
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | | |
Collapse
|
26
|
Val-Torregrosa B, Bundó M, Mallavarapu MD, Chiou TJ, Flors V, San Segundo B. Loss-of-function of NITROGEN LIMITATION ADAPTATION confers disease resistance in Arabidopsis by modulating hormone signaling and camalexin content. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111374. [PMID: 35839945 DOI: 10.1016/j.plantsci.2022.111374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Phosphorus is an important macronutrient required for plant growth and development. It is absorbed by the roots in the form of inorganic phosphate (Pi). Under Pi limiting conditions, plants activate the Phosphate Starvation Response (PSR) system to enhance Pi acquisition. The NITROGEN LIMITATION ADAPTION (NLA) gene is a component of the Arabidopsis PSR, and its expression is post-transcriptionally regulated by miR827. We show that loss-of-function of NLA and MIR827 overexpression increases Pi level and enhances resistance to infection by the fungal pathogen Plectosphaerella cucumerina in Arabidopsis. Upon pathogen infection, high Pi plants (e.g. nla plants and wild type plants grown under high Pi supply) showed enhanced callose deposition. High Pi plants also exhibited superinduction of camalexin biosynthesis genes which is consistent with increased levels of camalexin during pathogen infection. Pathogen infection and treatment with fungal elicitors, triggered up-regulation of MIR827 and down-regulation of NLA expression. Under non-infection conditions, the nla plants showed increased levels of SA and JA compared with wild type plants, their levels further increasing upon pathogen infection. Overall, the outcomes of this study suggest that NLA plays a role in Arabidopsis immunity, while supporting convergence between Pi signaling and immune signaling in Arabidopsis.
Collapse
Affiliation(s)
- Beatriz Val-Torregrosa
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Carrer de la Vall Moronta, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Carrer de la Vall Moronta, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Mani Deepika Mallavarapu
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Carrer de la Vall Moronta, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, 128 Academia Road, Nankang, 115 Taipei, Taiwan
| | - Victor Flors
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Superior de Tecnología y Ciencias Experimentales, Universitat Jaume I, Castellón 12071, Spain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Carrer de la Vall Moronta, Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), Serrano, 117, 28010 Madrid, Spain.
| |
Collapse
|
27
|
Zheng Z, Xu Z, Cai C, Liao Y, Yang C, Du X, Huang R, Deng Y. Circulating exosome miRNA, is it the novel nutrient molecule through cross-kingdom regulation mediated by food chain transmission from microalgae to bivalve? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 43:101004. [PMID: 35644102 DOI: 10.1016/j.cbd.2022.101004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/10/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. Plant-derived miRNAs are highly enriched in animal haemolymph and regulate mammalian gene expression. However, evidence for food-derived miRNAs in Mollusca species is lacking. In this study, we fed the microalga Nannochloropsis oculata to the pearl oyster Pinctada fucata martensii and detected dietary miRNAs in exosomes isolated from the haemolymph by RNA-seq. In total, 273 endogenous miRNAs were identified in all biological replicates. We identified 23 microalgae-derived miRNAs in the exosomes of pearl oyster haemolymph. Most microalgae-derived miRNAs showed high expression levels in both exosomes and microalgae and exhibited apparent variation among individuals. These food-derived miRNAs were predicted to participate in endocytosis, apoptosis, signal transduction, energy metabolism, and biomineralization by targeting multiple genes. These findings demonstrated the cross-kingdom transport of miRNAs from microalgae to bivalves and provide insights into novel nutrient transmission through the food chain.
Collapse
Affiliation(s)
- Zhe Zheng
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Zhijie Xu
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China
| | - Caixia Cai
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China
| | - Yongshan Liao
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China
| | - Chuangye Yang
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Xiaodong Du
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China
| | - Ronglian Huang
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Yuewen Deng
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China.
| |
Collapse
|
28
|
Dey S, Sarkar A, Chowdhury S, Singh R, Mukherjee A, Ghosh Z, Kundu P. Heightened miR6024-NLR interactions facilitate necrotrophic pathogenesis in tomato. PLANT MOLECULAR BIOLOGY 2022; 109:717-739. [PMID: 35499677 DOI: 10.1007/s11103-022-01270-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
miR6024 acts as a negative regulator of R genes, hence of Tomato plant immunity, and facilitates disease by the necrotrophic pathogen A. solani. Plant resistance genes or Nucleotide-binding leucine-rich repeat (NLR) genes, integral components of plant disease stress-signaling are targeted by variable groups of miRNAs. However, the significance of miRNA-mediated regulation of NLRs during a pathogen stress response, specifically for necrotrophic fungus, is poorly understood. A thorough examination of Tomato NLRs and miRNAs could map substantial interactions of which half the annotated NLRs were targets of Solanaceae-specific and conserved miRNAs, at the NB subdomain. The Solanaceae-specific miR6024 and its NLR targets analysed in different phytopathogenic stresses revealed differential and mutually antagonistic regulation. Interestingly, miR6024-targeted cleavage of a target NLR also triggered the generation of secondary phased siRNAs which could potentially amplify the defense signal. RNA-seq analysis of leaf tissues from miR6024 overexpressing Tomato plants evidenced a perturbation in the defense transcriptome with the transgenics showing unwarranted immune response-related genes' expression with or without infection with necrotrophic Alternaria solani, though no adverse effect could be observed in the growth and development of the transgenic plants. Transgenic plants exhibited constitutive downregulation of the target NLRs, aggravated disease phenotype with an enhanced lesion, greater ROS generation and hypersusceptibility to A. solani infection, thus establishing that miR6024 negatively impacts plant immune response during necrotrophic pathogenesis. Limited knowledge about the outcome of NLR-miRNA interaction during necrotrophic pathogenesis is a hindrance to the deployment of miRNAs in crop improvement programs. With the elucidation of the necrotrophic disease-synergistic role played by miR6024, it becomes a potent candidate for biotechnological manipulation for the rapid development of pathogen-tolerant solanaceous plants.
Collapse
Affiliation(s)
- Sayani Dey
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Arijita Sarkar
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Shreya Chowdhury
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Raghuvir Singh
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Mukherjee
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Pallob Kundu
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
| |
Collapse
|
29
|
Tian J, Zhang G, Zhang F, Ma J, Wen C, Li H. Genome-Wide Identification of Powdery Mildew Responsive Long Non-Coding RNAs in Cucurbita pepo. Front Genet 2022; 13:933022. [PMID: 35846119 PMCID: PMC9283782 DOI: 10.3389/fgene.2022.933022] [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: 04/30/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Cucurbita pepo L. is an essential economic vegetable crop worldwide, and its production is severely affected by powdery mildew (PM). However, our understanding of the molecular mechanism of PM resistance in C. pepo is very limited. Long non-coding RNAs (lncRNAs) play an important role in regulating plant responses to biotic stress. Here, we systematically identified 2,363 reliably expressed lncRNAs from the leaves of PM-susceptible (PS) and PM-resistant (PR) C. pepo. The C. pepo lncRNAs are shorter in length and expressed at a lower level than the protein-coding transcripts. Among the 2,363 lncRNAs, a total of 113 and 146 PM-responsive lncRNAs were identified in PS and PR, respectively. Six PM-responsive lncRNAs were predicted as potential precursors of microRNAs (miRNAs). In addition, 58 PM-responsive lncRNAs were predicted as targets of miRNAs and one PM-responsive lncRNA was predicted as an endogenous target mimic (eTM). Furthermore, a total of 5,200 potential cis target genes and 5,625 potential trans target genes were predicted for PM-responsive lncRNAs. Functional enrichment analysis showed that these potential target genes are involved in different biological processes, such as the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway. Taken together, this study provides a comprehensive view of C. pepo lncRNAs and explores the putative functions of PM-responsive lncRNAs, thus laying the foundation for further study of the regulatory mechanisms of lncRNAs responding to PM.
Collapse
Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jian Ma
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| |
Collapse
|
30
|
Val‐Torregrosa B, Bundó M, Martín‐Cardoso H, Bach‐Pages M, Chiou T, Flors V, Segundo BS. Phosphate-induced resistance to pathogen infection in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:452-469. [PMID: 35061924 PMCID: PMC9303409 DOI: 10.1111/tpj.15680] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 12/30/2021] [Accepted: 01/17/2022] [Indexed: 05/12/2023]
Abstract
In nature, plants are concurrently exposed to a number of abiotic and biotic stresses. Our understanding of convergence points between responses to combined biotic/abiotic stress pathways remains, however, rudimentary. Here we show that MIR399 overexpression, loss-of-function of PHOSPHATE2 (PHO2), or treatment with high phosphate (Pi) levels is accompanied by an increase in Pi content and accumulation of reactive oxygen species (ROS) in Arabidopsis thaliana. High Pi plants (e.g., miR399 overexpressors, pho2 mutants, and plants grown under high Pi supply) exhibited resistance to infection by necrotrophic and hemibiotrophic fungal pathogens. In the absence of pathogen infection, the expression levels of genes in the salicylic acid (SA)- and jasmonic acid (JA)-dependent signaling pathways were higher in high Pi plants compared to wild-type plants grown under control conditions, which is consistent with increased levels of SA and JA in non-infected high Pi plants. During infection, an opposite regulation in the two branches of the JA pathway (ERF1/PDF1.2 and MYC2/VSP2) occurs in high Pi plants. Thus, while pathogen infection induces PDF1.2 expression in miR399 OE and pho2 plants, VSP2 expression is downregulated by pathogen infection in these plants. This study supports the notion that Pi accumulation promotes resistance to infection by fungal pathogens in Arabidopsis, while providing a basis to better understand interactions between Pi signaling and hormonal signaling pathways for modulation of plant immune responses.
Collapse
Affiliation(s)
- Beatriz Val‐Torregrosa
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Héctor Martín‐Cardoso
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Marcel Bach‐Pages
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
| | - Tzyy‐Jen Chiou
- Agricultural Biotechnology Research Center, Academia SinicaTaipei 115Taiwan
| | - Victor Flors
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Superior de Tecnología y Ciencias ExperimentalesUniversitat Jaume ICastellóSpain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)BarcelonaSpain
- Consejo Superior de Investigaciones Científicas (CSIC)BarcelonaSpain
| |
Collapse
|
31
|
|
32
|
An J, Liu Y, Han J, He C, Chen M, Zhu X, Hu W, Song W, Hu J, Guan Y. Transcriptional multiomics reveals the mechanism of seed deterioration in Nicotiana tabacum L. and Oryza sativa L. J Adv Res 2022; 42:163-176. [PMID: 36513411 PMCID: PMC9788960 DOI: 10.1016/j.jare.2022.03.009] [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: 01/20/2022] [Revised: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Mature seeds deteriorate gradually and die eventually during long-term storage. Controlled deterioration is often used to accelerate the seed deterioration rate to assess the seed vigor and physiological quality of seed lots. OBJECTIVES Although it is well known that the process of seed deterioration produced by controlled deterioration is distinct from that caused by long-term storage, the differences in transcriptional levels have not been reported. Clarifying the mechanism of seed deterioration is critical for identifying, conserving and utilizing germplasm resources. METHODS Tobacco (Nicotiana tabacum L.) seeds were studied thoroughly using transcriptome, small RNA, and degradome sequencing after long-term storage (LS) and controlled deterioration (CD). Co-expression trend analysis identified transcripts involved in tobacco seed deterioration, while phylogenetic analysis helped to uncover comparable targets in rice (Oryza sativa L.) for further verification and utilization. RESULTS In LS and CD, a total of 2,112 genes and 164 miRNAs were differentially expressed, including 20 interaction miRNA-mRNA pairs with contrasting expression. Transcriptional multiomics found that the main causes of LS were plant hormone signal transduction and protein processing in the endoplasmic reticulum, whereas the primary cause of CD was nucleotide excision repair dysfunction. The homeostatic balance of RNA degradation and the spliceosome occurred in both modes of seed deterioration. Additionally, co-expression trend analysis identified two coherent pairs, nta-miR160b-NtARF18 and nta-miR396c-NtMBD10, as being significant in LS and CD, respectively. For utilization, rice homologous targets OsARF18 and OsMBD707 were verified to play similar roles in LS and CD, respectively. CONCLUSION This study demonstrated the transcriptional mechanism of tobacco and key genes in seed deterioration. And the application of key genes in rice also verified the feasibility of the multiomics method, guiding the identification of candidate genes to precisely delay seed deterioration in other species of seed research.
Collapse
Affiliation(s)
- Jianyu An
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Yihan Liu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Jiajun Han
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Can He
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Min Chen
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Xiaobo Zhu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Weimin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Wenjian Song
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Jin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Yajing Guan
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China,Corresponding author.
| |
Collapse
|
33
|
Comprehensive Identification and Profiling of miRNAs Involved in Terpenoid Synthesis of Gleditsia sinensis Lam. FORESTS 2022. [DOI: 10.3390/f13010108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gleditsia sinensis Lam. is a tree with worldwide distribution and important economic and medicinal values; its pods contain terpenoids including gleditsioside, thiamine, and brassinosteroids. However, thus far, there are few studies on the terpenoid regulation of G. sinensis at the molecular level. microRNA (miRNA) is a class of small RNAs with conserved and crucial roles in the regulation of diverse biological processes during plant growth and development. To identify the miRNAs of G. sinensis and evaluate their involvement in terpenoid synthesis, this investigation quantified the content changes in saponins in pods at three developmental stages: May (pod-setting stage), July (elongation stage), and September (browning stage), and then we performed genome-wide miRNA profiles during the three development stages of the G. sinensis pods. A total of 351 conserved miRNAs belonging to 216 families were identified, among which 36 conserved miRNAs exist specifically in legumes. Through target analysis, 708 unigenes were predicted to be candidate targets of 37 differentially expressed miRNAs. The targets of miR838-3p and miR2093-5p were involved in the derived branches of monoterpenes and gleditsioside, in brassinosteroid biosynthesis (BRB), and in indole alkaloid biosynthesis (IAB). Intriguingly, the targets of miR829-3p.1 were predicted to take part in thiamine biosynthesis, and the targets of miR4414b and miR5037a were involved in the main process of cytokinin synthesis. The corresponding targets participated in BRB, IAB, and terpenoid backbone biosynthesis, which were enriched significantly, suggesting that miR2093-5p, miR4414b, miR5037a, miR829-3p.1, and miR838-3p play indispensable roles in the regulation of triterpenoid saponin and monoterpenoid biosynthesis. To date, this is the first report of miRNA identification in G. sinensis and miRNA expression profiles at different developmental stages of G. sinensis pods, which provides a basis for further uncovering the molecular regulation of terpenoid synthesis in G. sinensis and new insights into the role of miRNAs in legumes.
Collapse
|
34
|
Liu Z, Sun Z, Zeng C, Dong X, Li M, Liu Z, Yan M. The elemental defense effect of cadmium on Alternaria brassicicola in Brassica juncea. BMC PLANT BIOLOGY 2022; 22:17. [PMID: 34986803 PMCID: PMC8729108 DOI: 10.1186/s12870-021-03398-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/10/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND The elemental defense hypothesis states a new defensive strategy that hyperaccumulators defense against herbivores or pathogens attacks by accumulating heavy metals. Brassica juncea has an excellent ability of cadmium (Cd) accumulation. However, the elemental defense effect and its regulation mechanism in B. juncea remain unclear. RESULTS In this study, we profiled the elemental defense effect and the molecular regulatory mechanism in Cd-accumulated B. juncea after Alternaria brassicicola infection. B. juncea treated with 180 mg Kg- 1 DW CdCl2 2.5H2O exhibited obvious elemental defense effect after 72 h of infection with A. brassicicola. The expression of some defense-related genes including BjNPR1, BjPR12, BjPR2, and stress-related miRNAs (miR156, miR397, miR398a, miR398b/c, miR408, miR395a, miR395b, miR396a, and miR396b) were remarkably elevated during elemental defense in B. juncea. CONCLUSIONS The results indicate that Cd-accumulated B. juncea may defend against pathogens by coordinating salicylic acid (SA) and jasmonic acid (JA) mediated systemic acquired resistance (SAR) and elemental defense in a synergistic joint effect. Furthermore, the expression of miRNAs related to heavy metal stress response and disease resistance may regulate the balance between pathogen defense and heavy metal stress-responsive in B. juncea. The findings provide experimental evidence for the elemental defense hypothesis in plants from the perspectives of phytohormones, defense-related genes, and miRNAs.
Collapse
Affiliation(s)
- Zhe Liu
- Hunan Provincial Key Laboratory of Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Zhenzhen Sun
- Hunan Provincial Key Laboratory of Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Chaozhen Zeng
- Hunan Provincial Key Laboratory of Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Xujie Dong
- Hunan Provincial Key Laboratory of Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zhixiang Liu
- Hunan Provincial Key Laboratory of Forestry Biotechnology, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China.
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Hunan University of Science and Technology, Xiangtan, 411201, China.
| |
Collapse
|
35
|
Analyses of Lysin-motif Receptor-like Kinase ( LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study. Cells 2021; 11:cells11010037. [PMID: 35011598 PMCID: PMC8750388 DOI: 10.3390/cells11010037] [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: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.
Collapse
|
36
|
Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
Collapse
Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
| |
Collapse
|
37
|
Unravelling the Initial Triggers of Botrytis cinerea Infection: First Description of Its Surfactome. J Fungi (Basel) 2021; 7:jof7121021. [PMID: 34947003 PMCID: PMC8708654 DOI: 10.3390/jof7121021] [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: 11/04/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
Botrytis cinerea is a critically important phytopathogenic fungus, causing devastating crop losses; signal transduction cascades mediate the “dialogue” among the fungus, plant, and environment. Surface proteins play important roles as front-line receptors. We report the first description of the surfactome of a filamentous fungus. To obtain a complete view of these cascades during infection of B. cinerea, its surfactome has been described by optimization of the “shaving” process and LC–MS/MS at two different infection stages, and with both rapid and late responses to environmental changes. The best results were obtained using PBS buffer in the “shaving” protocol. The surfactome obtained comprises 1010 identified proteins. These have been categorized by gene ontology and protein–protein interactions to reveal new potential pathogenicity/virulence factors. From these data, the percentage of total proteins predicted for the genome of the fungus represented by proteins identified in this and other proteomics studies is calculated at 54%, a big increase over the previous 12%. The new data may be crucial for understanding better its biological activity and pathogenicity. Given its extensive exposure to plants and environmental conditions, the surfactome presents innumerable opportunities for interactions between the fungus and external elements, which should offer the best targets for fungicide development.
Collapse
|
38
|
Xu J, Xian Q, Zhang N, Wang K, Zhou X, Li Y, Dong J, Chen X. Identification of miRNA-Target Gene Pairs Responsive to Fusarium Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles. Biomolecules 2021; 11:biom11111620. [PMID: 34827618 PMCID: PMC8615934 DOI: 10.3390/biom11111620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium wilt (FW) of cucumber (Cucumis sativus L.) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to FW remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar 'Rijiecheng', which is resistant to FW. The integrated analysis identified FW-responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that JRL3 (Csa2G362470), which is targeted by miR319a, and BEE1 (Csa1G024150), DAHP1 (Csa2G369040), and PERK2 (Csa4G642480), which are targeted by miR6300, are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that miR319a-JRL3, miR6300-BEE1, miR6300-DAHP1 and miR6300-PERK2 regulate cucumber defenses against FW, and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to FW.
Collapse
Affiliation(s)
- Jun Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Qianqian Xian
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Ningyuan Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Ke Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Xin Zhou
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Yansong Li
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Jingping Dong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300192, China
- Correspondence:
| |
Collapse
|
39
|
Wu F, Xu J, Gao T, Huang D, Jin W. Molecular mechanism of modulating miR482b level in tomato with botrytis cinerea infection. BMC PLANT BIOLOGY 2021; 21:496. [PMID: 34706648 PMCID: PMC8555085 DOI: 10.1186/s12870-021-03203-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato. RESULTS First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3'-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing. CONCLUSIONS Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.
Collapse
Affiliation(s)
- Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jinfeng Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Tiantian Gao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Diao Huang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
| |
Collapse
|
40
|
Chandra S, Oh Y, Han H, Salinas N, Anciro A, Whitaker VM, Chacon JG, Fernandez G, Lee S. Comparative Transcriptome Analysis to Identify Candidate Genes for FaRCg1 Conferring Resistance Against Colletotrichum gloeosporioides in Cultivated Strawberry ( Fragaria × ananassa). Front Genet 2021; 12:730444. [PMID: 34504518 PMCID: PMC8422960 DOI: 10.3389/fgene.2021.730444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Colletotrichum crown rot (CCR) caused by Colletotrichum gloeosporioides is a serious threat to the cultivated strawberry (Fragaria × ananassa). Our previous study reported that a major locus, FaRCg1, increases resistance. However, the genomic structure of FaRCg1 and potential candidate genes associated with the resistance remained unknown. Here, we performed comparative transcriptome analyses of resistant 'Florida Elyana' and susceptible 'Strawberry Festival' after infection and identified candidate genes potentially involved in resistance. In 'Florida Elyana', 6,099 genes were differentially expressed in response to C. gloeosporioides. Gene ontology analysis showed that the most upregulated genes were functionally associated with signaling pathways of plant defense responses. Three genes in the genomic region of FaRCg1 were highly upregulated: a von Willebrand Factor A domain-containing protein, a subtilisin-like protease, and a TIFY 11A-like protein. Subgenome-specific markers developed for the candidate genes were tested with a diverse panel of 219 accessions from University of Florida and North Carolina State University breeding programs. Significant and positive associations were found between the high-resolution melting (HRM) marker genotypes and CCR phenotypes. These newly developed subgenome-specific functional markers for FaRCg1 can facilitate development of resistant varieties through marker-assisted selection.
Collapse
Affiliation(s)
- Saket Chandra
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Youngjae Oh
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Hyeondae Han
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Natalia Salinas
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Ashlee Anciro
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Jose Guillermo Chacon
- Department of Horticultural Sciences, North Carolina State University, Raleigh, NC, United States
| | - Gina Fernandez
- Department of Horticultural Sciences, North Carolina State University, Raleigh, NC, United States
| | - Seonghee Lee
- Department of Horticultural Sciences, University of Florida-IFAS Gulf Coast Research and Education Center, Wimauma, FL, United States
| |
Collapse
|
41
|
Kunej U, Jakše J, Radišek S, Štajner N. Identification and Characterization of Verticillium nonalfalfae-Responsive MicroRNAs in the Roots of Resistant and Susceptible Hop Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:1883. [PMID: 34579416 PMCID: PMC8471970 DOI: 10.3390/plants10091883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
MicroRNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They can modulate various biological processes, including plant response and resistance to fungal pathogens. Hops are grown for use in the brewing industry and, recently, also for the pharmaceutical industry. Severe Verticillium wilt caused by the phytopathogenic fungus Verticillium nonalfalfae, is the main factor in yield loss in many crops, including hops (Humulus lupulus L.). In our study, we identified 56 known and 43 novel miRNAs and their expression patterns in the roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae. In response to inoculation with V. nonalfalfae, we found five known and two novel miRNAs that are differentially expressed in the susceptible cultivar and six known miRNAs in the resistant cultivar. Differentially expressed miRNAs target 49 transcripts involved in protein localization and pigment synthesis in the susceptible cultivar, whereas they are involved in transcription factor regulation and hormone signalling in the resistant cultivar. The results of our study suggest that the susceptible and resistant hop cultivars respond differently to V. nonalfalfae inoculation at the miRNA level and that miRNAs may contribute to the successful defence of the resistant cultivar.
Collapse
Affiliation(s)
- Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, 3310 Žalec, Slovenia;
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| |
Collapse
|
42
|
Campo S, Sánchez‐Sanuy F, Camargo‐Ramírez R, Gómez‐Ariza J, Baldrich P, Campos‐Soriano L, Soto‐Suárez M, San Segundo B. A novel Transposable element-derived microRNA participates in plant immunity to rice blast disease. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1798-1811. [PMID: 33780108 PMCID: PMC8428829 DOI: 10.1111/pbi.13592] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that direct post-transcriptional gene silencing in plant development and stress responses through cleavage or translational repression of target mRNAs. Here, we report the identification and functional characterization of a new member of the miR812 family in rice (named as miR812w) involved in disease resistance. miR812w is present in cultivated Oryza species, both japonica and indica subspecies, and wild rice species within the Oryza genus, but not in dicotyledonous species. miR812w is a 24nt-long that requires DCL3 for its biogenesis and is loaded into AGO4 proteins. Whereas overexpression of miR812w increased resistance to infection by the rice blast fungus Magnaporthe oryzae, CRISPR/Cas9-mediated MIR812w editing enhances disease susceptibility, supporting that miR812w plays a role in blast resistance. We show that miR812w derives from the Stowaway type of rice MITEs (Miniature Inverted-Repeat Transposable Elements). Moreover, miR812w directs DNA methylation in trans at target genes that have integrated a Stowaway MITE copy into their 3' or 5' untranslated region (ACO3, CIPK10, LRR genes), as well as in cis at the MIR812w locus. The target genes of miR812 were found to be hypo-methylated around the miR812 recognition site, their expression being up-regulated in transgene-free CRISPR/Cas9-edited miR812 plants. These findings further support that, in addition to post-transcriptional regulation of gene expression, miRNAs can exert their regulatory function at the transcriptional level. This relationship between miR812w and Stowaway MITEs integrated into multiple coding genes might eventually create a network for miR812w-mediated regulation of gene expression with implications in rice immunity.
Collapse
Affiliation(s)
- Sonia Campo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Ferran Sánchez‐Sanuy
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Rosany Camargo‐Ramírez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Jorge Gómez‐Ariza
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Donald Danforth Plant Science Center975 N Warson RoadSt. LouisMO63132USA
| | - Lidia Campos‐Soriano
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| | - Mauricio Soto‐Suárez
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
- Present address:
Corporación Colombiana de Investigación Agropecuaria. AGROSAVIAKm 14 vía Mosquera‐BogotáMosquera250047Colombia
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés)C/ de la Vall Moronta, CRAG BuildingBarcelona08193Spain
| |
Collapse
|
43
|
Regmi R, Newman TE, Kamphuis LG, Derbyshire MC. fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen. BMC PLANT BIOLOGY 2021; 21:366. [PMID: 34380425 PMCID: PMC8356391 DOI: 10.1186/s12870-021-03148-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Small RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. RESULTS We identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5'-RACE and RT-qPCR. CONCLUSIONS The findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.
Collapse
Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia.
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| |
Collapse
|
44
|
Cataloguing the small RNA content of honey using next generation sequencing. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 2:100014. [PMID: 35415639 PMCID: PMC8991712 DOI: 10.1016/j.fochms.2021.100014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022]
Abstract
Plant miRNAs are present in Australian polyfloral and Leptospermum scoparium honey. Sequencing shows that honey contains a diverse range of small, non-coding RNAs. Honey RNA comes from different phylogenies including invertebrates and prokaryotes. Unique small RNA profiles can provide insight into honey production conditions.
Honey adulteration is a problem that effects the global honey industry and specifically, has been discovered in the Australian market. Common methods of adulteration include dilution with sugar syrup substitutes and the mislabelling of the floral and geographic origin(s) of honey. Current authentication tools rely on the molecular variability between different honeys, identifying unique chemical profiles and/or DNA signatures characteristic of a particular honey. Honey is known to contain plant miRNAs derived from its floral source. To explore the composition and variability of honey RNA molecules, this is the first study to catalogue the small RNA content of Australian polyfloral table honey and New Zealand Leptospermum scoparium honey using next generation sequencing. The data shows that in addition to miRNAs, honey contains a variety of small non-coding RNAs including tRNA-derived fragments. Moreover, the honey small RNAs are derived from a range of phylogenetic sources, including from plant, invertebrate, and prokaryotic species. The data indicates that different honeys contain unique small RNA profiles, which suggests a novel avenue in developing molecular-based honey authentication tools.
Collapse
|
45
|
Song L, Fang Y, Chen L, Wang J, Chen X. Role of non-coding RNAs in plant immunity. PLANT COMMUNICATIONS 2021; 2:100180. [PMID: 34027394 PMCID: PMC8132121 DOI: 10.1016/j.xplc.2021.100180] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 05/06/2023]
Abstract
Crops are exposed to attacks by various pathogens that cause substantial yield losses and severely threaten food security. To cope with pathogenic infection, crops have elaborated strategies to enhance resistance against pathogens. In addition to the role of protein-coding genes as key regulators in plant immunity, accumulating evidence has demonstrated the importance of non-coding RNAs (ncRNAs) in the plant immune response. Here, we summarize the roles and molecular mechanisms of endogenous ncRNAs, especially microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), in plant immunity. We discuss the coordination between miRNAs and small interfering RNAs (siRNAs), between lncRNAs and miRNAs or siRNAs, and between circRNAs and miRNAs in the regulation of plant immune responses. We also address the role of cross-kingdom mobile small RNAs in plant-pathogen interactions. These insights improve our understanding of the mechanisms by which ncRNAs regulate plant immunity and can promote the development of better approaches for breeding disease-resistant crops.
Collapse
Affiliation(s)
- Li Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Yu Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Lin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
- Corresponding author
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
- Corresponding author
| |
Collapse
|
46
|
Yang X, Zhang L, Yang Y, Schmid M, Wang Y. miRNA Mediated Regulation and Interaction between Plants and Pathogens. Int J Mol Sci 2021; 22:ijms22062913. [PMID: 33805611 PMCID: PMC7999934 DOI: 10.3390/ijms22062913] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs.
Collapse
Affiliation(s)
- Xiaoqian Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lichun Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuzhang Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Markus Schmid
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Yanwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Correspondence: ; Tel.: +86-010-62338105
| |
Collapse
|
47
|
Samperna S, Boari A, Vurro M, Salzano AM, Reveglia P, Evidente A, Gismondi A, Canini A, Scaloni A, Marra M. Arabidopsis Defense against the Pathogenic Fungus Drechslera gigantea Is Dependent on the Integrity of the Unfolded Protein Response. Biomolecules 2021; 11:biom11020240. [PMID: 33567651 PMCID: PMC7915340 DOI: 10.3390/biom11020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/25/2022] Open
Abstract
Drechslera gigantea Heald & Wolf is a worldwide-spread necrotrophic fungus closely related to the Bipolaris genus, well-known because many member species provoke severe diseases in cereal crops and studied because they produce sesterpenoid phytoxins named ophiobolins which possess interesting biological properties. The unfolded protein response (UPR) is a conserved mechanism protecting eukaryotic cells from the accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER). In plants, consolidated evidence supports the role of UPR in the tolerance to abiotic stress, whereas much less information is available concerning the induction of ER stress by pathogen infection and consequent UPR elicitation as part of the defense response. In this study, the infection process of D. gigantea in Arabidopsis thaliana wild type and UPR-defective bzip28 bzip60 double mutant plants was comparatively investigated, with the aim to address the role of UPR in the expression of resistance to the fungal pathogen. The results of confocal microscopy, as well as of qRT-PCR transcript level analysis of UPR genes, proteomics, microRNAs expression profile and HPLC-based hormone analyses demonstrated that ophiobolin produced by the fungus during infection compromised ER integrity and that impairment of the IRE1/bZIP60 pathway of UPR hampered the full expression of resistance, thereby enhancing plant susceptibility to the pathogen.
Collapse
Affiliation(s)
- Simone Samperna
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (S.S.); (A.G.); (A.C.)
| | - Angela Boari
- Institute of Sciences of Food Production, National Research Institute, 70126 Bari, Italy; (A.B.); (M.V.)
| | - Maurizio Vurro
- Institute of Sciences of Food Production, National Research Institute, 70126 Bari, Italy; (A.B.); (M.V.)
| | - Anna Maria Salzano
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; (A.M.S.); (A.S.)
| | - Pierluigi Reveglia
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Naples, Italy; (P.R.); (A.E.)
| | - Antonio Evidente
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Naples, Italy; (P.R.); (A.E.)
| | - Angelo Gismondi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (S.S.); (A.G.); (A.C.)
| | - Antonella Canini
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (S.S.); (A.G.); (A.C.)
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; (A.M.S.); (A.S.)
| | - Mauro Marra
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (S.S.); (A.G.); (A.C.)
- Correspondence:
| |
Collapse
|
48
|
Fracasso A, Vallino M, Staropoli A, Vinale F, Amaducci S, Carra A. Increased water use efficiency in miR396-downregulated tomato plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110729. [PMID: 33487336 DOI: 10.1016/j.plantsci.2020.110729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
MicroRNAs regulate plant development and responses to biotic and abiotic stresses but their impact on water use efficiency (WUE) is poorly known. Increasing WUE is a major task in crop improvement programs aimed to meet the challenges posed by the reduction in water availability associated with the ongoing climatic change. We have examined the physiological and molecular response to water stress of tomato (Solanum lycopersicum L.) plants downregulated for miR396 by target mimicry. In water stress conditions, miR396-downregulated plants displayed reduced transpiration and a less then proportional decrease in the photosynthetic rate that resulted in higher WUE. The increase in WUE was associated with faster foliar accumulation of abscisic acid (ABA), with the induction of several drought-protective genes and with the activation of the jasmonic acid (JA) and γ-aminobutyric acid (GABA) pathways. We propose a model in which the downregulation of miR396 leads to the activation of a complex molecular response to water stress. This response acts synergistically with a set of leaf morphological modifications to increase stomatal closure and preserve the efficiency of the photosynthetic activity, ultimately resulting in higher WUE.
Collapse
Affiliation(s)
- Alessandra Fracasso
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Torino, Italy
| | - Alessia Staropoli
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 80055 Portici, Italy
| | - Francesco Vinale
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 80055 Portici, Italy; Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, 80137, Italy
| | - Stefano Amaducci
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Andrea Carra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Torino, Italy.
| |
Collapse
|
49
|
Waheed S, Anwar M, Saleem MA, Wu J, Tayyab M, Hu Z. The Critical Role of Small RNAs in Regulating Plant Innate Immunity. Biomolecules 2021; 11:biom11020184. [PMID: 33572741 PMCID: PMC7912340 DOI: 10.3390/biom11020184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Plants, due to their sessile nature, have an innate immune system that helps them to defend against different pathogen infections. The defense response of plants is composed of a highly regulated and complex molecular network, involving the extensive reprogramming of gene expression during the presence of pathogenic molecular signatures. Plants attain proper defense against pathogens through the transcriptional regulation of genes encoding defense regulatory proteins and hormone signaling pathways. Small RNAs are emerging as versatile regulators of plant development and act in different tiers of plant immunity, including pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). The versatile regulatory functions of small RNAs in plant growth and development and response to biotic and abiotic stresses have been widely studied in recent years. However, available information regarding the contribution of small RNAs in plant immunity against pathogens is more limited. This review article will focus on the role of small RNAs in innate immunity in plants.
Collapse
Affiliation(s)
- Saquib Waheed
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Correspondence: (M.A.); (Z.H.)
| | - Muhammad Asif Saleem
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Jinsong Wu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
| | - Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China;
- Correspondence: (M.A.); (Z.H.)
| |
Collapse
|
50
|
Elucidating micro RNAs role in different plant-pathogen interactions. Mol Biol Rep 2020; 47:8219-8227. [PMID: 32909216 DOI: 10.1007/s11033-020-05810-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/30/2020] [Accepted: 09/03/2020] [Indexed: 01/23/2023]
Abstract
Bacteria, fungi, virus and nematode constitute the primary class of pathogens causing plant diseases. Plant-pathogen interactions are crucial for the identification of the host and pathogen and further establishments of a network of interaction that can cross regulate the gene expressions in both sides. After infection, the correct identification of pathogen through various molecular interactions elicit a defense response against the pathogen by alteration of gene expression by the host. Co-evolution of pathogen gives them the ability to counter the virulence response of the host and pathogen can also modulate the host gene expression pattern to make it more susceptible to the infection. Small non-coding RNA molecules (siRNAs and miRNAs) efficiently modulate gene expression at the transcriptional and post-transcriptional level and play a vital role in host defense. The pathogen can also use this double-sided sward in their defense by deregulating the plant immunity via transcriptional control of plant genes utilizing RNA interference or suppressing the host RNA interference response with the help of various RNA silencing suppressor proteins. This mini-review focused on the miRNAs involvement in host defense and how different families of these non-coding regulatory RNAs regulate the defense response against the pathogen.
Collapse
|