1
|
Tu M, Li Z, Zhu Y, Wang P, Jia H, Wang G, Zhou Q, Hua Y, Yang L, Xiao J, Song G, Li Y. Potential Roles of the GRF Transcription Factors in Sorghum Internodes during Post-Reproductive Stages. PLANTS (BASEL, SWITZERLAND) 2024; 13:2352. [PMID: 39273836 DOI: 10.3390/plants13172352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024]
Abstract
Growth-regulating factor (GRF) is a plant-specific family of transcription factors crucial for meristem development and plant growth. Sorghum (Sorghum bicolor L. Moench) is a cereal species widely used for food, feed and fuel. While sorghum stems are important biomass components, the regulation of stem development and the carbohydrate composition of the stem tissues remain largely unknown. Here, we identified 11 SbGRF-encoding genes and found the SbGRF expansion driven by whole-genome duplication events. By comparative analyses of GRFs between rice and sorghum, we demonstrated the divergence of whole-genome duplication (WGD)-derived OsGRFs and SbGRFs. A comparison of SbGRFs' expression profiles supports that the WGD-duplicated OsGRFs and SbGRFs experienced distinct evolutionary trajectories, possibly leading to diverged functions. RNA-seq analysis of the internode tissues identified several SbGRFs involved in internode elongation, maturation and cell wall metabolism. We constructed co-expression networks with the RNA-seq data of sorghum internodes. Network analysis discovered that SbGRF1, 5 and 7 could be involved in the down-regulation of the biosynthesis of cell wall components, while SbGRF4, 6, 8 and 9 could be associated with the regulation of cell wall loosening, reassembly and/or starch biosynthesis. In summary, our genome-wide analysis of SbGRFs reveals the distinct evolutionary trajectories of WGD-derived SbGRF pairs. Importantly, expression analyses highlight previously unknown functions of several SbGRFs in internode elongation, maturation and the potential involvement in the metabolism of the cell wall and starch during post-anthesis stages.
Collapse
Affiliation(s)
- Min Tu
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Zhuang Li
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuanlin Zhu
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Peng Wang
- School of Mathematics and Computer Science, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hongbin Jia
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Guoli Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qin Zhou
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuqing Hua
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Lin Yang
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiangrong Xiao
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Guangsen Song
- Hubei Technical Engineering Research Center for Chemical Utilization and Engineering Development of Agricultural and Byproduct Resources, School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
2
|
Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
Collapse
Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
| |
Collapse
|
3
|
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
|
4
|
Chen X, Zhang J, Wang S, Cai H, Yang M, Dong Y. Genome-wide molecular evolution analysis of the GRF and GIF gene families in Plantae (Archaeplastida). BMC Genomics 2024; 25:74. [PMID: 38233778 PMCID: PMC10795294 DOI: 10.1186/s12864-024-10006-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Plant growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) interact with each other and collectively have important regulatory roles in plant growth, development, and stress responses. Therefore, it is of great significance to explore the systematic evolution of GRF and GIF gene families. However, our knowledge and understanding of the role of GRF and GIF genes during plant evolution has been fragmentary. RESULTS In this study, a large number of genomic and transcriptomic datasets of algae, mosses, ferns, gymnosperms and angiosperms were used to systematically analyze the evolution of GRF and GIF genes during the evolution of plants. The results showed that GRF gene first appeared in the charophyte Klebsormidium nitens, whereas the GIF genes originated relatively early, and these two gene families were mainly expanded by segmental duplication events after plant terrestrialization. During the process of evolution, the protein sequences and functions of GRF and GIF family genes are relatively conservative. As cooperative partner, GRF and GIF genes contain the similar types of cis-acting elements in their promoter regions, which enables them to have similar transcriptional response patterns, and both show higher levels of expression in reproductive organs and tissues and organs with strong capacity for cell division. Based on protein-protein interaction analysis and verification, we found that the GRF-GIF protein partnership began to be established in pteridophytes and is highly conserved across different terrestrial plants. CONCLUSIONS These results provide a foundation for further exploration of the molecular evolution and biological functions of GRF and GIF genes.
Collapse
Affiliation(s)
- Xinghao Chen
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Jun Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Hongyu Cai
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China.
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China.
| |
Collapse
|
5
|
Zhang XJ, Wu C, Liu BY, Liang HL, Wang ML, Li H. Transcriptomic and metabolomic profiling reveals the drought tolerance mechanism of Illicium difengpi (Schisandraceae). FRONTIERS IN PLANT SCIENCE 2024; 14:1284135. [PMID: 38259923 PMCID: PMC10800416 DOI: 10.3389/fpls.2023.1284135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Illicium difengpi (Schisandraceae), an endangered medicinal plant endemic to karst areas, is highly tolerant to drought and thus can be used as an ideal material for investigating adaptive mechanism to drought stress. The understanding of the drought tolerance of I. difengpi, especially at the molecular level, is lacking. In the present study, we aimed to clarify the molecular mechanism underlying drought tolerance in endemic I. difengpi plant in karst regions. The response characteristics of transcripts and changes in metabolite abundance of I. difengpi subjected to drought and rehydration were analyzed, the genes and key metabolites responsive to drought and rehydration were screened, and some important biosynthetic and secondary metabolic pathways were identified. A total of 231,784 genes and 632 metabolites were obtained from transcriptome and metabolome analyses, and most of the physiological metabolism in drought-treated I. difengpi plants recovered after rehydration. There were more upregulated genes than downregulated genes under drought and rehydration treatments, and rehydration treatment induced stable expression of 65.25% of genes, indicating that rehydration alleviated drought stress to some extent. Drought and rehydration treatment generated flavonoids, phenolic acids, flavonols, amino acids and their derivatives, as well as metabolites such as saccharides and alcohols in the leaves of I. difengpi plants, which alleviated the injury caused by excessive reactive oxygen species. The integration of transcriptome and metabolome analyses showed that, under drought stress, I. difengpi increased glutathione, flavonoids, polyamines, soluble sugars and amino acids, contributing to cell osmotic potential and antioxidant activity. The results show that the high drought tolerance and recovery after rehydration are the reasons for the normal growth of I. difengpi in karst mountain areas.
Collapse
Affiliation(s)
| | - Chao Wu
- *Correspondence: Chao Wu, ; Hui-Ling Liang,
| | | | - Hui-Ling Liang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | | | | |
Collapse
|
6
|
Lu J, Wang Z, Li J, Zhao Q, Qi F, Wang F, Xiaoyang C, Tan G, Wu H, Deyholos MK, Wang N, Liu Y, Zhang J. Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors. Int J Mol Sci 2023; 24:17107. [PMID: 38069430 PMCID: PMC10707037 DOI: 10.3390/ijms242317107] [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: 10/07/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines.
Collapse
Affiliation(s)
- Jianyu Lu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Jinxi Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Qian Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Fu Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Guofei Tan
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Hanlu Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Michael K. Deyholos
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Yingnan Liu
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin 150040, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
| |
Collapse
|
7
|
Xu W, Wang Y, Xie J, Tan S, Wang H, Zhao Y, Liu Q, El-Kassaby YA, Zhang D. Growth-regulating factor 15-mediated gene regulatory network enhances salt tolerance in poplar. PLANT PHYSIOLOGY 2023; 191:2367-2384. [PMID: 36567515 PMCID: PMC10069893 DOI: 10.1093/plphys/kiac600] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 05/16/2023]
Abstract
Soil salinity is an important determinant of crop productivity and triggers salt stress response pathways in plants. The salt stress response is controlled by transcriptional regulatory networks that maintain regulatory homeostasis through combinations of transcription factor (TF)-DNA and TF-TF interactions. We investigated the transcriptome of poplar 84 K (Populus alba × Populus glandulosa) under salt stress using samples collected at 4- or 6-h intervals within 2 days of salt stress treatment. We detected 24,973 differentially expressed genes, including 2,231 TFs that might be responsive to salt stress. To explore these interactions and targets of TFs in perennial woody plants, we combined gene regulatory networks, DNA affinity purification sequencing, yeast two-hybrid-sequencing, and multi-gene association approaches. Growth-regulating factor 15 (PagGRF15) and its target, high-affinity K+ transporter 6 (PagHAK6), were identified as an important regulatory module in the salt stress response. Overexpression of PagGRF15 and PagHAK6 in transgenic lines improved salt tolerance by enhancing Na+ transport and modulating H2O2 accumulation in poplar. Yeast two-hybrid assays identified more than 420 PagGRF15-interacting proteins, including ETHYLENE RESPONSE FACTOR TFs and a zinc finger protein (C2H2) that are produced in response to a variety of phytohormones and environmental signals and are likely involved in abiotic stress. Therefore, our findings demonstrate that PagGRF15 is a multifunctional TF involved in growth, development, and salt stress tolerance, highlighting the capability of a multifaceted approach in identifying regulatory nodes in plants.
Collapse
Affiliation(s)
- Weijie Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Yue Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Shuxian Tan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Haofei Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Yiyang Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Qing Liu
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT 2601, Australia
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | |
Collapse
|
8
|
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
|
9
|
Liu Y, Guo P, Wang J, Xu ZY. Growth-regulating factors: conserved and divergent roles in plant growth and development and potential value for crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1122-1145. [PMID: 36582168 DOI: 10.1111/tpj.16090] [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: 09/29/2022] [Revised: 12/13/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
High yield and stress resistance are the major prerequisites for successful crop cultivation, and can be achieved by modifying plant architecture. Evolutionarily conserved growth-regulating factors (GRFs) control the growth of different tissues and organs of plants. Here, we provide a systematic overview of the expression patterns of GRF genes and the structural features of GRF proteins in different plant species. Moreover, we illustrate the conserved and divergent roles of GRFs, microRNA396 (miR396), and GRF-interacting factors (GIFs) in leaf, root, and flower development. We also describe the molecular networks involving the miR396-GRF-GIF module, and illustrate how this module coordinates with different signaling molecules and transcriptional regulators to control development of different plant species. GRFs promote leaf growth, accelerate grain filling, and increase grain size and weight. We also provide some molecular insight into how coordination between GRFs and other signaling modules enhances crop productivity; for instance, how the GRF-DELLA interaction confers yield-enhancing dwarfism while increasing grain yield. Finally, we discuss how the GRF-GIF chimera substantially improves plant transformation efficiency by accelerating shoot formation. Overall, we systematically review the conserved and divergent roles of GRFs and the miR396-GRF-GIF module in growth regulation, and also provide insights into how GRFs can be utilized to improve the productivity and nutrient content of crop plants.
Collapse
Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
10
|
Yi W, Luan A, Liu C, Wu J, Zhang W, Zhong Z, Wang Z, Yang M, Chen C, He Y. Genome-wide identification, phylogeny, and expression analysis of GRF transcription factors in pineapple ( Ananas comosus). FRONTIERS IN PLANT SCIENCE 2023; 14:1159223. [PMID: 37123828 PMCID: PMC10140365 DOI: 10.3389/fpls.2023.1159223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Background Pineapple is the only commercially grown fruit crop in the Bromeliaceae family and has significant agricultural, industrial, economic, and ornamental value. GRF (growth-regulating factor) proteins are important transcription factors that have evolved in seed plants (embryophytes). They contain two conserved domains, QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys), and regulate multiple aspects of plant growth and stress response, including floral organ development, leaf growth, and hormone responses. The GRF family has been characterized in a number of plant species, but little is known about this family in pineapple and other bromeliads. Main discoveries We identified eight GRF transcription factor genes in pineapple, and phylogenetic analysis placed them into five subfamilies (I, III, IV, V, VI). Segmental duplication appeared to be the major contributor to expansion of the AcGRF family, and the family has undergone strong purifying selection during evolution. Relative to that of other gene families, the gene structure of the GRF family showed less conservation. Analysis of promoter cis-elements suggested that AcGRF genes are widely involved in plant growth and development. Transcriptome data and qRT-PCR results showed that, with the exception of AcGRF5, the AcGRFs were preferentially expressed in the early stage of floral organ development and AcGRF2 was strongly expressed in ovules. Gibberellin treatment significantly induced AcGRF7/8 expression, suggesting that these two genes may be involved in the molecular regulatory pathway by which gibberellin promotes pineapple fruit expansion. Conclusion AcGRF proteins appear to play a role in the regulation of floral organ development and the response to gibberellin. The information reported here provides a foundation for further study of the functions of AcGRF genes and the traits they regulate.
Collapse
Affiliation(s)
- Wen Yi
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Aiping Luan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chaoyang Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jing Wu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Zhang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ziqin Zhong
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Zhengpeng Wang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Mingzhe Yang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Chengjie Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
- *Correspondence: Yehua He, ; Chengjie Chen,
| | - Yehua He
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Areas, College of Horticulture, South China Agricultural University, Guangzhou, China
- *Correspondence: Yehua He, ; Chengjie Chen,
| |
Collapse
|
11
|
Wu Z, Chen X, Fu D, Zeng Q, Gao X, Zhang N, Wu J. Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum. BMC PLANT BIOLOGY 2022; 22:510. [PMID: 36319957 PMCID: PMC9628180 DOI: 10.1186/s12870-022-03891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRFs in sugarcane (Saccharum spp.) is still lacking. RESULTS In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance. CONCLUSION Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.
Collapse
Affiliation(s)
- Zilin Wu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Xinglong Chen
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Danwen Fu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Qiaoying Zeng
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
| | - Xiaoning Gao
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 524300, Zhanjiang, Guangdong, China
| | - Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China.
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Centre, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangzhou, Guangdong, China.
| |
Collapse
|
12
|
Lei X, Liu Z, Xie Q, Fang J, Wang C, Li J, Wang C, Gao C. Construction of two regulatory networks related to salt stress and lignocellulosic synthesis under salt stress based on a Populus davidiana × P. bolleana transcriptome analysis. PLANT MOLECULAR BIOLOGY 2022; 109:689-702. [PMID: 35486290 DOI: 10.1007/s11103-022-01267-8] [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: 10/25/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Construction of ML-hGRN for the salt pathway in Populus davidiana × P. bolleana. Construction of ML-hGRN for the lignocellulosic pathway in Populus davidiana × P. bolleana under salt stress. Many woody plants, including Populus davidiana × P. bolleana, have made great contributions to human production and life. High salt is one of the main environmental factors that restricts the growth of poplar. This study found that high salt could induce strong biochemical changes in poplar. To detect the effect of salt treatment on gene expression, 18 libraries were sequenced on the Illumina sequencing platform. The results identified a large number of early differentially expressed genes (DEGs) and a small number of late DEGs, which indicated that most of the salt response genes of poplar were early response genes. In addition, 197 TFs, including NAC, ERF, and other TFs related to salt stress, were differentially expressed during salt treatment, which indicated that these TFs may play an important role in the salt stress response of poplar. Based on the RNA-seq analysis results, multilayered hierarchical gene regulatory networks (ML-hGRNs) of salt stress- and lignocellulosic synthesis-related DEGs were constructed using the GGM algorithm. The lignocellulosic synthesis regulatory network under salt stress revealed that lignocellulosic synthesis might play an important role in the process of salt stress resistance. Furthermore, the NAC family transcription factor PdbNAC83, which was found in the upper layer in both pathways, was selected to verify the accuracy of the ML-hGRNs. DAP-seq showed that the binding site of PdbNAC83 included a "TT(G/A)C(G/T)T" motif, and ChIP-PCR further verified that PdbNAC83 can regulate the promoters of at least six predicted downstream genes (PdbNLP2-2, PdbZFP6, PdbMYB73, PdbC2H2-like, PdbMYB93-1, PdbbHLH094) by binding to the "TT(G/A)C(G/T)T" motif, which indicates that the predicted regulatory network diagram obtained in this study is relatively accurate. In conclusion, a species-specific salt response pathway might exist in poplar, and this finding lays a foundation for further study of the regulatory mechanism of the salt stress response and provides new clues for the use of genetic engineering methods to create high-quality and highly resistant forest germplasms.
Collapse
Affiliation(s)
- Xiaojin Lei
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Zhongyuan Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Qingjun Xie
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Jiaru Fang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Chunyao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Jinghang Li
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China.
| |
Collapse
|
13
|
Du W, Yang J, Li Q, Su Q, Yi D, Pang Y. Genome-Wide Identification and Characterization of Growth Regulatory Factor Family Genes in Medicago. Int J Mol Sci 2022; 23:ijms23136905. [PMID: 35805911 PMCID: PMC9266564 DOI: 10.3390/ijms23136905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 12/10/2022] Open
Abstract
Growth Regulatory Factors (GRF) are plant-specific transcription factors that play critical roles in plant growth and development as well as plant tolerance against stress. In this study, a total of 16 GRF genes were identified from the genomes of Medicago truncatula and Medicago sativa. Multiple sequence alignment analysis showed that all these members contain conserved QLQ and WRC domains. Phylogenetic analysis suggested that these GRF proteins could be classified into five clusters. The GRF genes showed similar exon–intron organizations and similar architectures in their conserved motifs. Many stress-related cis-acting elements were found in their promoter region, and most of them were related to drought and defense response. In addition, analyses on microarray and transcriptome data indicated that these GRF genes exhibited distinct expression patterns in various tissues or in response to drought and salt treatments. In particular, qPCR results showed that the expression levels of gene pairs MtGRF2–MsGRF2 and MtGRF6–MsGRF6 were significantly increased under NaCl and mannitol treatments, indicating that they are most likely involved in salt and drought stress tolerance. Collectively, our study is valuable for further investigation on the function of GRF genes in Medicago and for the exploration of GRF genes in the molecular breeding of highly resistant M. sativa.
Collapse
Affiliation(s)
- Wenxuan Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Junfeng Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Qian Li
- West Arid Region Grassland Resource and Ecology Key Laboratory, College of Grassland and Environmental Sciences, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Qian Su
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010010, China;
| | - Dengxia Yi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.Y.); (Y.P.)
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.Y.); (Y.P.)
| |
Collapse
|
14
|
Meng L, Li X, Hou Y, Li Y, Hu Y. Functional conservation and divergence in plant-specific GRF gene family revealed by sequences and expression analysis. Open Life Sci 2022; 17:155-171. [PMID: 35350448 PMCID: PMC8919827 DOI: 10.1515/biol-2022-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 12/03/2021] [Accepted: 01/03/2022] [Indexed: 11/24/2022] Open
Abstract
Unique to plants, growth regulatory factors (GRFs) play important roles in plant growth and reproduction. This study investigated the evolutionary and functional characteristics associated with plant growth. Using genome-wide analysis of 15 plant species, 173 members of the GRF family were identified and phylogenetically categorized into six groups. All members contained WRC and QLQ conserved domains, and the family’s expansion largely depended on segmental duplication. The promoter region of the GRF gene family mainly contained four types of cis-acting elements (light-responsive elements, development-related elements, hormone-responsive elements, and environmental stress-related elements) that are mainly related to gene expression levels. Functional divergence analysis revealed that changes in amino acid site evolution rate played a major role in the differentiation of the GRF gene family, with ten significant sites identified. Six significant sites were identified for positive selection. Moreover, the four groups of coevolutionary sites identified may play a key role in regulating the transcriptional activation of the GRF protein. Expression profiles revealed that GRF genes were generally highly expressed in young plant tissues and had tissue or organ expression specificity, demonstrating their functional conservation with distinct divergence. The results of these sequence and expression analyses are expected to provide molecular evolutionary and functional references for the plant GRF gene family.
Collapse
Affiliation(s)
- Lingyan Meng
- College of Life Sciences, Capital Normal University , Beijing 100048 , China
| | - Xiaomeng Li
- College of Life Sciences, Capital Normal University , Beijing 100048 , China
| | - Yue Hou
- College of Life Sciences, Capital Normal University , Beijing 100048 , China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University , Beijing 100048 , China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University , Beijing 100048 , China
| |
Collapse
|
15
|
Jasmonic Acid-Dependent MYC Transcription Factors Bind to a Tandem G-Box Motif in the YUCCA8 and YUCCA9 Promoters to Regulate Biotic Stress Responses. Int J Mol Sci 2021; 22:ijms22189768. [PMID: 34575927 PMCID: PMC8468920 DOI: 10.3390/ijms22189768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
The indole-3-pyruvic acid pathway is the main route for auxin biosynthesis in higher plants. Tryptophan aminotransferases (TAA1/TAR) and members of the YUCCA family of flavin-containing monooxygenases catalyze the conversion of l-tryptophan via indole-3-pyruvic acid to indole-3-acetic acid (IAA). It has been described that jasmonic acid (JA) locally produced in response to mechanical wounding triggers the de novo formation of IAA through the induction of two YUCCA genes, YUC8 and YUC9. Here, we report the direct involvement of a small number of basic helix-loop-helix transcription factors of the MYC family in this process. We show that the JA-mediated regulation of the expression of the YUC8 and YUC9 genes depends on the abundance of MYC2, MYC3, and MYC4. In support of this observation, seedlings of myc knockout mutants displayed a strongly reduced response to JA-mediated IAA formation. Furthermore, transactivation assays provided experimental evidence for the binding of MYC transcription factors to a particular tandem G-box motif abundant in the promoter regions of YUC8 and YUC9, but not in the promoters of the other YUCCA isogenes. Moreover, we demonstrate that plants that constitutively overexpress YUC8 and YUC9 show less damage after spider mite infestation, thereby underlining the role of auxin in plant responses to biotic stress signals.
Collapse
|
16
|
Wang KL, Zhang Y, Zhang HM, Lin XC, Xia R, Song L, Wu AM. MicroRNAs play important roles in regulating the rapid growth of the Phyllostachys edulis culm internode. THE NEW PHYTOLOGIST 2021; 231:2215-2230. [PMID: 34101835 DOI: 10.1111/nph.17542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Moso bamboo (Phyllostachys edulis) is a fast-growing species with uneven growth and lignification from lower to upper segments within one internode. MicroRNAs (miRNAs) play a vital role in post-transcriptional regulation in plants. However, how miRNAs regulate fast growth in bamboo internodes is poorly understood. In this study, one moso bamboo internode was divided during early rapid growth into four segments called F4 (bottom) to F1 (upper) and these were then analysed for transcriptomes, miRNAs and degradomes. The F4 segment had a higher number of actively dividing cells as well as a higher content of auxin (IAA), cytokinin (CK) and gibberellin (GA) compared with the F1 segment. RNA-seq analysis showed DNA replication and cell division-associated genes highly expressed in F4 rather than in F1. In total, 63 miRNAs (DEMs) were identified as differentially expressed between F4 and F1. The degradome and the transcriptome indicated that many downstream transcription factors and hormonal responses genes were modulated by DEMs. Several miR-target interactions were further validated by tobacco co-infiltration. Our findings give new insights into miRNA-mediated regulatory pathways in bamboo, and will contribute to a comprehensive understanding of the molecular mechanisms governing rapid growth.
Collapse
Affiliation(s)
- Kai-Li Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanyuan Zhang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, 510642, China
| | - Heng-Mu Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xin-Chun Lin
- The State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, China
| | - Rui Xia
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Lili Song
- The State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, China
| | - Ai-Min Wu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, 510642, China
| |
Collapse
|
17
|
Khanna K, Ohri P, Bhardwaj R. Genetic toolbox and regulatory circuits of plant-nematode associations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:137-146. [PMID: 34038810 DOI: 10.1016/j.plaphy.2021.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Plant-nematode associations are the most imperative area of study that forms the basis to understand their regulatory networks and coordinated functional aspects. Nematodes are highly parasitic organisms known so far, to cause relentless damage towards agricultural crops on a global scale. They pierce the roots of host plants and form neo-plastic feeding structures to extract out resources for their functional development. Moreover, they undergo re-differentiation within plant cells to form giant multi-nucleate feeding structures or syncytium. All these processes are facilitated by numerous transcriptomic, proteomic, metabolomic and epigenetic modifications, that regulate different biological attractions among plants and nematodes. Nevertheless, these mechanisms are quite remarkable and have been explored in the present review. Here, we have shed light on genomic as well as genetic approaches to acquire an effective understanding regarding plant-nematode associations. Transcriptomics have revealed an extensive network to unravel feeding mechanism of nematodes through gene-expression programming of target genes. Also, the regulatory circuits of epigenetic alterations through DNA-methylation, non-coding RNAs and histone modifications very well explain epigenetic profiling within plants. Since decades, research have observed many intricacies to elucidate the dynamic nature of epigenetic modulations in plant-nematode attractions. By this review, we have highlighted the functional aspects of small RNAs in inducing plant-nematode parasitism along with the putative role of miRNAs. These RNAs act as chief genetic elements to mediate the expressional changes in plants through post-transcriptional silencing of various effector proteins as well as transcriptional factors. A pragmatic role of miRNAs in modulating gene expression in nematode infection and feeding site development have also been reviewed. Hence, they have been considered master regulators for functional reprogramming the expression during establishment of feeding sites. We have also encapsulated the advancement of genome-broadened DNA-methylation and untangled the nematode mediated dynamic alterations within plant methylome along with assessing transcriptional activities of various genes and transposons. In particular, we have highlighted the role of effector proteins in stimulating epigenetic changes. Finally, we have emerged towards a molecular-based core understanding about plant-nematode associations.
Collapse
Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| |
Collapse
|
18
|
Park S, Wijeratne AJ, Moon Y, Waterland NL. Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing. PLoS One 2021; 16:e0250284. [PMID: 33901201 PMCID: PMC8075263 DOI: 10.1371/journal.pone.0250284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Water deficit limits plant growth and development, resulting in quality loss of horticultural crops. However, there is limited information on gene regulation and signaling pathways related to water deficit stress response at multiple time points. The objective of this research was to investigate global gene expression patterns under water deficit stress to provide an insight into how petunia (Petunia ×hybrida 'Mitchell Diploid') responded in the process of stress. Nine-week-old petunias were irrigated daily or placed under water stress by withholding water. Stressed plants reduced stomatal conductance after five days of water deficit, indicating they perceived stress and initiated stress response mechanisms. To analyze transcriptomic changes at the early stage of water deficit, leaf tissue samples were collected 1, 3, and 5 days after water was withheld for RNA sequencing. Under water deficit stress, 154, 3611, and 980 genes were upregulated and 41, 2806, and 253 genes were downregulated on day 1, 3, and 5, respectively. Gene Ontology analysis revealed that redox homeostasis processes through sulfur and glutathione metabolism pathways, and hormone signal transduction, especially abscisic acid and ethylene, were enriched under water deficit stress. Thirty-four transcription factor families were identified, including members of AP2/ERF, NAC, MYB-related, C2H2, and bZIP families, and TFs in AP2/ERF family was the most abundant in petunia. Interestingly, only one member of GRFs was upregulated on day 1, while most of TFs were differentially expressed on day 3 and/or 5. The transcriptome data from this research will provide valuable molecular resources for understanding the early stages of water stress-responsive networks as well as engineering petunia with enhanced water stress tolerance.
Collapse
Affiliation(s)
- Suejin Park
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Youyoun Moon
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Nicole L. Waterland
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| |
Collapse
|
19
|
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
|
20
|
Huang W, He Y, Yang L, Lu C, Zhu Y, Sun C, Ma D, Yin J. Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum. PeerJ 2021; 9:e10701. [PMID: 33552727 PMCID: PMC7821759 DOI: 10.7717/peerj.10701] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
The Growth-Regulating Factor (GRF) family encodes a type of plant-specific transcription factor (TF). GRF members play vital roles in plant development and stress response. Although GRF family genes have been investigated in a variety of plants, they remain largely unstudied in bread wheat (Triticum aestivum L.). The present study was conducted to comprehensively identify and characterize the T. aestivum GRF (TaGRF) gene family members. We identified 30 TaGRF genes, which were divided into four groups based on phylogenetic relationship. TaGRF members within the same subgroup shared similar motif composition and gene structure. Synteny analysis suggested that duplication was the dominant reason for family member expansion. Expression pattern profiling showed that most TaGRF genes were highly expressed in growing tissues, including shoot tip meristems, stigmas and ovaries, suggesting their key roles in wheat growth and development. Further qRT-PCR analysis revealed that all 14 tested TaGRFs were significantly differentially expressed in responding to drought or salt stresses, implying their additional involvement in stress tolerance of wheat. Our research lays a foundation for functional determination of TaGRFs, and will help to promote further scrutiny of their regulatory network in wheat development and stress response.
Collapse
Affiliation(s)
- Wendi Huang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yiqin He
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Lei Yang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Chen Lu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yongxing Zhu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Cai Sun
- Plant Protection and Fruiter Technical Extension Station, Wanzhou District, Chongqing, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China.,Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Junliang Yin
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China.,Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| |
Collapse
|
21
|
Kumar V, Donev EN, Barbut FR, Kushwah S, Mannapperuma C, Urbancsok J, Mellerowicz EJ. Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development. FRONTIERS IN PLANT SCIENCE 2020; 11:588846. [PMID: 33414796 PMCID: PMC7783096 DOI: 10.3389/fpls.2020.588846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/18/2020] [Indexed: 05/21/2023]
Abstract
Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.
Collapse
Affiliation(s)
- Vikash Kumar
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Evgeniy N. Donev
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Félix R. Barbut
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sunita Kushwah
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Chanaka Mannapperuma
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - János Urbancsok
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ewa J. Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| |
Collapse
|
22
|
Abstract
Epigenetic mechanisms play fundamental roles in regulating numerous biological processes in various developmental and environmental contexts. Three highly interconnected epigenetic control mechanisms, including small noncoding RNAs, DNA methylation, and histone modifications, contribute to the establishment of plant epigenetic profiles. During the past decade, a growing body of experimental work has revealed the intricate, diverse, and dynamic roles that epigenetic modifications play in plant-nematode interactions. In this review, I summarize recent progress regarding the functions of small RNAs in mediating plant responses to infection by cyst and root-knot nematodes, with a focus on the functions of microRNAs. I also recapitulate recent advances in genome-wide DNA methylation analysis and discuss how cyst nematodes induce extensive and dynamic changes in the plant methylome that impact the transcriptional activity of genes and transposable elements. Finally, the potential role of nematode effector proteins in triggering such epigenome changes is discussed.
Collapse
Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA;
| |
Collapse
|
23
|
Rossmann S, Richter R, Sun H, Schneeberger K, Töpfer R, Zyprian E, Theres K. Mutations in the miR396 binding site of the growth-regulating factor gene VvGRF4 modulate inflorescence architecture in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1234-1248. [PMID: 31663642 DOI: 10.1111/tpj.14588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 09/27/2019] [Accepted: 10/11/2019] [Indexed: 05/09/2023]
Abstract
Bunch rot caused by Botrytis cinerea infections is a notorious problem in grapevine cultivation. To produce high quality fruits, grapevine plants are treated with fungicides, which is cost intensive and harmful to the environment. Conversely, loose cluster bunches show a considerably enhanced physical resilience to bunch diseases. With the aim to identify genetic determinants that modulate the development of bunch architecture, we have compared loose and compact 'Pinot noir' clones. Loose cluster architecture was found to be correlated with increased berry size, elongated rachis and elongated pedicels. Using transcriptome analysis in combination with whole genome sequencing, we have identified a growth-regulating factor gene, VvGRF4, upregulated and harbours heterozygous mutations in the loose cluster clones. At late stages of inflorescence development, the mRNA pools of loose cluster clones contain predominantly mRNAs derived from the mutated alleles, which are resistant to miR396 degradation. Expression of the VvGRF4 gene and its mutated variants in Arabidopsis demonstrates that it promotes pedicel elongation. Taken together, VvGRF4 modulates bunch architecture in grapevine 'Pinot noir' clones. This trait can be introduced into other cultivars using marker-assisted breeding or CRISPR-Cas9 technology. Related growth-regulating factors or other genes of the same pathway may have similar functions.
Collapse
Affiliation(s)
- Susanne Rossmann
- Max Planck Institute for Plant Breeding Research, 50931, Cologne, Germany
| | - Robert Richter
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius-Kuehn Institute, 76833, Siebeldingen, Germany
| | - Hequan Sun
- Max Planck Institute for Plant Breeding Research, 50931, Cologne, Germany
| | | | - Reinhard Töpfer
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius-Kuehn Institute, 76833, Siebeldingen, Germany
| | - Eva Zyprian
- Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, Julius-Kuehn Institute, 76833, Siebeldingen, Germany
| | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, 50931, Cologne, Germany
| |
Collapse
|
24
|
Piya S, Liu J, Burch-Smith T, Baum TJ, Hewezi T. A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1402-1417. [PMID: 31701146 PMCID: PMC7031083 DOI: 10.1093/jxb/erz502] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/05/2019] [Indexed: 05/21/2023]
Abstract
Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth-defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth-defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.
Collapse
Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Jinyi Liu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Present address: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Correspondence:
| |
Collapse
|
25
|
An J, Niu H, Ni Y, Jiang Y, Zheng Y, He R, Li J, Jiao Z, Zhang J, Li H, Li Q, Niu J. The miRNA-mRNA Networks Involving Abnormal Energy and Hormone Metabolisms Restrict Tillering in a Wheat Mutant dmc. Int J Mol Sci 2019; 20:E4586. [PMID: 31533225 PMCID: PMC6770018 DOI: 10.3390/ijms20184586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/14/2019] [Accepted: 09/15/2019] [Indexed: 02/07/2023] Open
Abstract
Tillers not only determine plant architecture but also influence crop yield. To explore the miRNA regulatory network restraining tiller development in a dwarf-monoculm wheat mutant (dmc) derived from Guomai 301 (wild type, WT), we employed miRNome and transcriptome integrative analysis, real-time qRT-PCR, histochemistry, and determinations of the key metabolites and photosynthesis parameters. A total of 91 differentially expressed miRNAs (DEMs) were identified between dmc and WT. Among them, 40 key DEMs targeted 45 differentially expressed genes (DEGs) including the key DEGs encode growth-regulating factors (GRF), auxin response factors (ARF), and other proteins involved in the metabolisms of hormones and carbohydrates, etc. Compared with WT, both the chlorophyll contents and the photosynthesis rate were lower in dmc. The contents of glucose, sucrose, fructose, and maltose were lower in dmc. The contents of auxin (IAA) and zeatin (ZA) were significantly lower, but gibberellin (GA) was significantly higher in the tiller tissues of dmc. This research demonstrated that the DEMs regulating hormone and carbohydrate metabolisms were important causes for dmc to not tiller. A primary miRNA-mRNA regulatory model for dmc tillering was established. The lower photosynthesis rate, insufficient energy, and abnormal hormone metabolisms restrict tillering in dmc.
Collapse
Affiliation(s)
- Junhang An
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Hao Niu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, China.
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Yongxing Zheng
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Ruishi He
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Junchang Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Jing Zhang
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Huijuan Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| |
Collapse
|
26
|
Abstract
GROWTH-REGULATING FACTORs (GRFs) are sequence-specific DNA-binding transcription factors that regulate various aspects of plant growth and development. GRF proteins interact with a transcription cofactor, GRF-INTERACTING FACTOR (GIF), to form a functional transcriptional complex. For its activities, the GRF-GIF duo requires the SWITCH2/SUCROSE NONFERMENTING2 chromatin remodeling complex. One of the most conspicuous roles of the duo is conferring the meristematic potential on the proliferative and formative cells during organogenesis. GRF expression is post-transcriptionally down-regulated by microRNA396 (miR396), thus constructing the GRF-GIF-miR396 module and fine-tuning the duo’s action. Since the last comprehensive review articles were published over three years ago, many studies have added further insight into its action and elucidated new biological roles. The current review highlights recent advances in our understanding of how the GRF-GIF-miR396 module regulates plant growth and development. In addition, I revise the previous view on the evolutionary origin of the GRF gene family.
Collapse
Affiliation(s)
- Jeong Hoe Kim
- Department of Biology, School of Biological Sciences, Kyungpook National University, Daegu 41566, Korea
| |
Collapse
|
27
|
Arora H, Padmaja KL, Paritosh K, Mukhi N, Tewari AK, Mukhopadhyay A, Gupta V, Pradhan AK, Pental D. BjuWRR1, a CC-NB-LRR gene identified in Brassica juncea, confers resistance to white rust caused by Albugo candida. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2223-2236. [PMID: 31049632 DOI: 10.1007/s00122-019-03350-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/20/2019] [Indexed: 05/28/2023]
Abstract
BjuWRR1, a CNL-type R gene, was identified from an east European gene pool line of Brassica juncea and validated for conferring resistance to white rust by genetic transformation. White rust caused by the oomycete pathogen Albugo candida is a significant disease of crucifer crops including Brassica juncea (mustard), a major oilseed crop of the Indian subcontinent. Earlier, a resistance-conferring locus named AcB1-A5.1 was mapped in an east European gene pool line of B. juncea-Donskaja-IV. This line was tested along with some other lines of B. juncea (AABB), B. rapa (AA) and B. nigra (BB) for resistance to six isolates of A. candida collected from different mustard growing regions of India. Donskaja-IV was found to be completely resistant to all the tested isolates. Sequencing of a BAC spanning the locus AcB1-A5.1 showed the presence of a single CC-NB-LRR protein encoding R gene. The genomic sequence of the putative R gene with its native promoter and terminator was used for the genetic transformation of a susceptible Indian gene pool line Varuna and was found to confer complete resistance to all the isolates. This is the first white rust resistance-conferring gene described from Brassica species and has been named BjuWRR1. Allelic variants of the gene in B. juncea germplasm and orthologues in the Brassicaceae genomes were studied to understand the evolutionary dynamics of the BjuWRR1 gene.
Collapse
Affiliation(s)
- Heena Arora
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - K Lakshmi Padmaja
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Nitika Mukhi
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - A K Tewari
- Department of Plant Pathology, Govind Ballabh Pant University of Agriculture and Technology, Udham Singh Nagar, Pantnagar, Uttarakhand, 263145, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Akshay K Pradhan
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
| |
Collapse
|
28
|
Conserved miR396b-GRF Regulation Is Involved in Abiotic Stress Responses in Pitaya ( Hylocereus polyrhizus). Int J Mol Sci 2019; 20:ijms20102501. [PMID: 31117184 PMCID: PMC6566180 DOI: 10.3390/ijms20102501] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/05/2019] [Accepted: 05/16/2019] [Indexed: 12/26/2022] Open
Abstract
MicroRNA396 (miR396) is a conserved microRNA family that targets growth-regulating factors (GRFs), which play significant roles in plant growth and stress responses. Available evidence justifies the idea that miR396-targeted GRFs have important functions in many plant species; however, no genome-wide analysis of the pitaya (Hylocereus polyrhizus) miR396 gene has yet been reported. Further, its biological functions remain elusive. To uncover the regulatory roles of miR396 and its targets, the hairpin sequence of pitaya miR396b and the open reading frame (ORF) of its target, HpGRF6, were isolated from pitaya. Phylogenetic analysis showed that the precursor miR396b (MIR396b) gene of plants might be clustered into three major groups, and, generally, a more recent evolutionary relationship in the intra-family has been demonstrated. The sequence analysis indicated that the binding site of hpo-miR396b in HpGRF6 is located at the conserved motif which codes the conserved "RSRKPVE" amino acid in the Trp-Arg-Cys (WRC) region. In addition, degradome sequencing analysis confirmed that four GRFs (GRF1, c56908.graph_c0; GRF4, c52862.graph_c0; GRF6, c39378.graph_c0 and GRF9, c54658.graph_c0) are hpo-miR396b targets that are regulated by specific cleavage at the binding site between the 10th and 11th nucleotides from the 5' terminus of hpo-miR396b. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that hpo-miR396b is down-regulated when confronted with drought stress (15% polyethylene glycol, PEG), and its expression fluctuates under other abiotic stresses, i.e., low temperature (4 ± 1 °C), high temperature (42 ± 1 °C), NaCl (100 mM), and abscisic acid (ABA; 0.38 mM). Conversely, the expression of HpGRF6 showed the opposite trend to exposure to these abiotic stresses. Taken together, hpo-miR396b plays a regulatory role in the control of HpGRF6, which might influence the abiotic stress response of pitaya. This is the first documentation of this role in pitaya and improves the understanding of the molecular mechanisms underlying the tolerance to drought stress in this fruit.
Collapse
|
29
|
Noon JB, Hewezi T, Baum TJ. Homeostasis in the soybean miRNA396-GRF network is essential for productive soybean cyst nematode infections. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1653-1668. [PMID: 30715445 PMCID: PMC6411377 DOI: 10.1093/jxb/erz022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/15/2019] [Indexed: 05/20/2023]
Abstract
Heterodera glycines, the soybean cyst nematode, penetrates soybean roots and migrates to the vascular cylinder where it forms a feeding site called the syncytium. MiRNA396 (miR396) targets growth-regulating factor (GRF) genes, and the miR396-GRF1/3 module is a master regulator of syncytium development in model cyst nematode H. schachtii infection of Arabidopsis. Here, we investigated whether this regulatory system operates similarly in soybean roots and is likewise important for H. glycines infection. We found that a network involving nine MIR396 and 23 GRF genes is important for normal development of soybean roots and that GRF function is specified in the root apical meristem by miR396. All MIR396 genes are down-regulated in the syncytium during its formation phase while, specifically, 11 different GRF genes are up-regulated. The switch to the syncytium maintenance phase coincides with up-regulation of MIR396 and down-regulation of the 11 GRF genes specifically via post-transcriptional regulation by miR396. Furthermore, interference with the miR396-GRF6/8-13/15-17/19 regulatory network, through either overexpression or knockdown experiments, does not affect the number of H. glycines juveniles that enter the vascular cylinder to initiate syncytia, but specifically inhibits efficient H. glycines development to adult females. Therefore, homeostasis in the miR396-GRF6/8-13/15-17/19 regulatory network is essential for productive H. glycines infections.
Collapse
Affiliation(s)
- Jason B Noon
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| |
Collapse
|
30
|
Li W, Jia Y, Liu F, Wang F, Fan F, Wang J, Zhu J, Xu Y, Zhong W, Yang J. Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice. Int J Mol Sci 2019; 20:E222. [PMID: 30626113 PMCID: PMC6337123 DOI: 10.3390/ijms20010222] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/26/2018] [Accepted: 12/31/2018] [Indexed: 12/20/2022] Open
Abstract
Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.
Collapse
Affiliation(s)
- Wenqi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Yulin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jinyan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Weigong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| |
Collapse
|
31
|
Li WQ, Jia YL, Liu FQ, Wang FQ, Fan FJ, Wang J, Zhu JY, Xu Y, Zhong WG, Yang J. Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice. RSC Adv 2018; 8:34408-34417. [PMID: 35548658 PMCID: PMC9087051 DOI: 10.1039/c8ra04993a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/09/2018] [Indexed: 11/26/2022] Open
Abstract
Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae, a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of the 4709 lncRNAs identified, 2518 and 2191 were up- and down-regulated in response to D. zeae infection, respectively. Expression changes of 17 selected lncRNAs and their predicted targets with a potential role in defense response were investigated by qPCR. The expression levels of five lncRNAs were up-regulated while their cognate candidate target genes were down-regulated upon D. zeae infection. In addition, several lncRNAs were predicted to be target mimics of osa-miR396 and osa-miR156. These results suggest that lncRNAs might play a role in response to D. zeae infection by regulating the transcript levels of their targets and miRNAs in rice.
Collapse
Affiliation(s)
- Wen Qi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Yu Lin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center Stuttgart 72160 USA
| | - Feng Quan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Fang Quan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Fang Jun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jin Yan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Wei Gong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| |
Collapse
|
32
|
Omidbakhshfard MA, Fujikura U, Olas JJ, Xue GP, Balazadeh S, Mueller-Roeber B. GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia. PLoS Genet 2018; 14:e1007484. [PMID: 29985961 PMCID: PMC6053248 DOI: 10.1371/journal.pgen.1007484] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 07/19/2018] [Accepted: 06/13/2018] [Indexed: 12/21/2022] Open
Abstract
Leaf growth is a complex process that involves the action of diverse transcription factors (TFs) and their downstream gene regulatory networks. In this study, we focus on the functional characterization of the Arabidopsis thaliana TF GROWTH-REGULATING FACTOR9 (GRF9) and demonstrate that it exerts its negative effect on leaf growth by activating expression of the bZIP TF OBP3-RESPONSIVE GENE 3 (ORG3). While grf9 knockout mutants produce bigger incipient leaf primordia at the shoot apex, rosette leaves and petals than the wild type, the sizes of those organs are reduced in plants overexpressing GRF9 (GRF9ox). Cell measurements demonstrate that changes in leaf size result from alterations in cell numbers rather than cell sizes. Kinematic analysis and 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay revealed that GRF9 restricts cell proliferation in the early developing leaf. Performing in vitro binding site selection, we identified the 6-base motif 5'-CTGACA-3' as the core binding site of GRF9. By global transcriptome profiling, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) we identified ORG3 as a direct downstream, and positively regulated target of GRF9. Genetic analysis of grf9 org3 and GRF9ox org3 double mutants reveals that both transcription factors act in a regulatory cascade to control the final leaf dimensions by restricting cell number in the developing leaf.
Collapse
Affiliation(s)
| | - Ushio Fujikura
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam‐Golm, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam‐Golm, Germany
| | | | - Salma Balazadeh
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam‐Golm, Germany
- Max‐Planck Institute of Molecular Plant Physiology, Potsdam‐Golm, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam‐Golm, Germany
- Max‐Planck Institute of Molecular Plant Physiology, Potsdam‐Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Department Plant Development, Plovdiv, Bulgaria
- * E-mail:
| |
Collapse
|
33
|
Xie S, Jiang H, Ding T, Xu Q, Chai W, Cheng B. Bacillus amyloliquefaciens FZB42 represses plant miR846 to induce systemic resistance via a jasmonic acid-dependent signalling pathway. MOLECULAR PLANT PATHOLOGY 2018; 19:1612-1623. [PMID: 29090851 PMCID: PMC6638179 DOI: 10.1111/mpp.12634] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/28/2017] [Accepted: 10/25/2017] [Indexed: 05/21/2023]
Abstract
Bacillus amyloliquefaciens FZB42 is a type of plant growth-promoting rhizobacterium (PGPR) which activates induced systemic resistance (ISR) in Arabidopsis. Blocking of the synthesis of cyclic lipopeptides and 2,3-butanediol by FZB42, which have been demonstrated to be involved in the priming of ISR, results in the abolishment of the plant defence responses. To further clarify the ISR activated by PGPRs at the microRNA (miRNA) level, small RNA (sRNA) libraries from Arabidopsis leaves after root irrigation with FZB42, FZB42ΔsfpΔalsS and control were constructed and sequenced. After fold change selection, promoter analysis and target prediction, miR846-5p and miR846-3p from the same precursor were selected as candidate ISR-associated miRNAs. miR846 belongs to the non-conserved miRNAs, specifically exists in Arabidopsis and its function in the plant defence response remains unclear. The disease severity of transgenic Arabidopsis overexpressing miR846 (OEmiR846) or knockdown miR846 (STTM846) against Pseudomonas syringae DC3000 suggests that the miR846 expression level in Arabidopsis is negatively correlated with disease resistance. Moreover, miR846 in Arabidopsis Col-0 is repressed after methyl jasmonate treatment. In addition, jasmonic acid (JA) signalling-related genes are up-regulated in STTM846, and the stomatal apertures of STTM846 are also less than those in Arabidopsis Col-0 after methyl jasmonate treatment. Furthermore, the disease resistance of STTM846 transgenic Arabidopsis against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is blocked by the addition of the JA biosynthetic inhibitor diethyldiethiocarbamic acid (DIECA). Taken together, our results suggest that B. amyloliquefaciens FZB42 inoculation suppresses miR846 expression to induce Arabidopsis systemic resistance via a JA-dependent signalling pathway.
Collapse
Affiliation(s)
- Shanshan Xie
- Key Laboratory of Crop Biology of Anhui ProvinceAgricultural UniversityHefeiAnhui 230036China
| | - Haiyang Jiang
- Key Laboratory of Crop Biology of Anhui ProvinceAgricultural UniversityHefeiAnhui 230036China
| | - Ting Ding
- Key Laboratory of Crop Biology of Anhui ProvinceAgricultural UniversityHefeiAnhui 230036China
| | - Qianqian Xu
- Key Laboratory of Crop Biology of Anhui ProvinceAgricultural UniversityHefeiAnhui 230036China
| | - Wenbo Chai
- Key Laboratory of Crop Biology of Anhui ProvinceAgricultural UniversityHefeiAnhui 230036China
| | - Beijiu Cheng
- Key Laboratory of Crop Biology of Anhui ProvinceAgricultural UniversityHefeiAnhui 230036China
| |
Collapse
|
34
|
Chandran V, Wang H, Gao F, Cao XL, Chen YP, Li GB, Zhu Y, Yang XM, Zhang LL, Zhao ZX, Zhao JH, Wang YG, Li S, Fan J, Li Y, Zhao JQ, Li SQ, Wang WM. miR396- OsGRFs Module Balances Growth and Rice Blast Disease-Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:1999. [PMID: 30693011 PMCID: PMC6339958 DOI: 10.3389/fpls.2018.01999] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/24/2018] [Indexed: 05/18/2023]
Abstract
Fitness cost is a common phenomenon in rice blast disease-resistance breeding. MiR396 is a highly conserved microRNA (miRNA) family targeting Growth Regulating Factor (OsGRF) genes. Mutation at the target site of miR396 in certain OsGRF gene or blocking miR396 expression leads to increased grain yield. Here we demonstrated that fitness cost can be trade-off in miR396-OsGRFs module via balancing growth and immunity against the blast fungus. The accumulation of miR396 isoforms was significantly increased in a susceptible accession, but fluctuated in a resistant accession upon infection of Magnaporthe oryzae. The transgenic lines over-expressing different miR396 isoforms were highly susceptible to M. oryzae. In contrast, overexpressing target mimicry of miR396 to block its function led to enhanced resistance to M. oryzae in addition to improved yield traits. Moreover, transgenic plants overexpressing OsGRF6, OsGRF7, OsGRF8, and OsGRF9 exhibited enhanced resistance to M. oryzae, but showed different alteration of growth. While overexpression of OsGRF7 led to defects in growth, overexpression of OsGRF6, OsGRF8, and OsGRF9 resulted in better or no significant change of yield traits. Collectively, our results indicate that miR396 negatively regulates rice blast disease- resistance via suppressing multiple OsGRFs, which in turn differentially control growth and yield. Therefore, miR396-OsGRFs could be a potential module to demolish fitness cost in rice blast disease-resistance breeding.
Collapse
Affiliation(s)
| | - He Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Feng Gao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao-Long Cao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yun-Ping Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guo-Bang Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xue-Mei Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ling-Li Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Xue Zhao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing-Hao Zhao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ying-Ge Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shuangcheng Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Fan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ji-Qun Zhao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shao-Qing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Shao-Qing Li, Wen-Ming Wang,
| | - Wen-Ming Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Shao-Qing Li, Wen-Ming Wang,
| |
Collapse
|
35
|
Chen L, Meng J, Zhai J, Xu P, Luan Y. MicroRNA396a-5p and -3p induce tomato disease susceptibility by suppressing target genes and upregulating salicylic acid. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:177-187. [PMID: 29223339 DOI: 10.1016/j.plantsci.2017.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/02/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
Plants have evolved a variety of mechanisms to perceive and resist the assault of pathogens. The biotrophs, necrotrophs and hemibiotrophs are types of plant pathogens that activate diverse salicylic acid (SA) and jasmonic acid (JA) signaling pathways. In this study we showed that the expressions of miR396a-5p and -3p in Solanum lycopersicum (S. lycopersicum) were both down-regulated after infection by hemibiotroph Phytophthora infestans (P. infestans) and necrotroph Botrytis cinerea (B. cinerea) infection. Overexpression of miR396a-5p and -3p in transgenic tomato enhanced the susceptibility of S. lycopersicum to P. infestans and B. cinerea infection and the tendency to produce reactive oxygen species (ROS) under pathogen-related biotic stress. Additionally, miR396a regulated growth-regulating factor1 (GRF1), salicylic acid carboxyl methyltransferase (SAMT), glycosyl hydrolases (GH) and nucleotide-binding site-leucine-rich repeat (NBS-LRR) and down-regulated their levels. This ultimately led to inhibition of the expression of pathogenesis-related 1 (PR1), TGA transcription factors1 and 2 (TGA1 and TGA2) and JA-dependent proteinase inhibitors I and II (PI I and II), but enhanced the endogenous SA content and nonexpressor of pathogenesis-related genes 1 (NPR1) expression. Taken together, our results showed that negative regulation of target genes and their downstream genes expressions by miR396a-5p and -3p are critical for tomato abiotic stresses via affecting SA or JA signaling pathways.
Collapse
Affiliation(s)
- Lei Chen
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Junmiao Zhai
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Pinsan Xu
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian 116024, China.
| |
Collapse
|
36
|
Piya S, Kihm C, Rice JH, Baum TJ, Hewezi T. Cooperative Regulatory Functions of miR858 and MYB83 during Cyst Nematode Parasitism. PLANT PHYSIOLOGY 2017; 174:1897-1912. [PMID: 28512179 PMCID: PMC5490899 DOI: 10.1104/pp.17.00273] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/13/2017] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) recently have been established as key regulators of transcriptome reprogramming that define cell function and identity. Nevertheless, the molecular functions of the greatest number of miRNA genes remain to be determined. Here, we report cooperative regulatory functions of miR858 and its MYB83 transcription factor target gene in transcriptome reprogramming during Heterodera cyst nematode parasitism of Arabidopsis (Arabidopsis thaliana). Gene expression analyses and promoter-GUS fusion assays documented a role of miR858 in posttranscriptional regulation of MYB83 in the Heterodera schachtii-induced feeding sites, the syncytia. Constitutive overexpression of miR858 interfered with H. schachtii parasitism of Arabidopsis, leading to reduced susceptibility, while reduced miR858 abundance enhanced plant susceptibility. Similarly, MYB83 expression increases were conducive to nematode infection because overexpression of a noncleavable coding sequence of MYB83 significantly increased plant susceptibility, whereas a myb83 mutation rendered the plants less susceptible. In addition, RNA-seq analysis revealed that genes involved in hormone signaling pathways, defense response, glucosinolate biosynthesis, cell wall modification, sugar transport, and transcriptional control are the key etiological factors by which MYB83 facilitates nematode parasitism of Arabidopsis. Furthermore, we discovered that miR858-mediated silencing of MYB83 is tightly regulated through a feedback loop that might contribute to fine-tuning the expression of more than a thousand of MYB83-regulated genes in the H. schachtii-induced syncytium. Together, our results suggest a role of the miR858-MYB83 regulatory system in finely balancing gene expression patterns during H. schachtii parasitism of Arabidopsis to ensure optimal cellular function.
Collapse
Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Christina Kihm
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
| |
Collapse
|
37
|
Shin SJ, Lee JH, Kwon HB. Genome-wide identification and characterization of drought responsive MicroRNAs in Solanum tuberosum L. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0586-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
38
|
Khatun K, Robin AHK, Park JI, Nath UK, Kim CK, Lim KB, Nou IS, Chung MY. Molecular Characterization and Expression Profiling of Tomato GRF Transcription Factor Family Genes in Response to Abiotic Stresses and Phytohormones. Int J Mol Sci 2017; 18:ijms18051056. [PMID: 28505092 PMCID: PMC5454968 DOI: 10.3390/ijms18051056] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 12/22/2022] Open
Abstract
Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (Solanum lycopersicum) have not been extensively explored. In this study, we characterized the 13 SlGRF genes. In silico analysis of protein motif organization, intron–exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the SlGRF genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that SlGRFs are important during growth and development of these tissues. Some of the SlGRF genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different SlGRFs under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of SlGRF genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.
Collapse
Affiliation(s)
- Khadiza Khatun
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Chang Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701, Korea.
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701, Korea.
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Mi-Young Chung
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| |
Collapse
|
39
|
Li S, Castillo-González C, Yu B, Zhang X. The functions of plant small RNAs in development and in stress responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:654-670. [PMID: 27943457 DOI: 10.1111/tpj.13444] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 05/22/2023]
Abstract
Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta-siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta-siRNAs in plant physiology and development.
Collapse
Affiliation(s)
- Shengjun Li
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0660, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics & Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|
40
|
Soto-Suárez M, Baldrich P, Weigel D, Rubio-Somoza I, San Segundo B. The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens. Sci Rep 2017; 7:44898. [PMID: 28332603 PMCID: PMC5362962 DOI: 10.1038/srep44898] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in regulating gene expression during plant development. Although a substantial fraction of plant miRNAs has proven responsive to pathogen infection, their role in disease resistance remains largely unknown, especially during fungal infections. In this study, we screened Arabidopsis thaliana lines in which miRNA activity has been reduced using artificial miRNA target mimics (MIM lines) for their response to fungal pathogens. Reduced activity of miR396 (MIM396 plants) was found to confer broad resistance to necrotrophic and hemibiotrophic fungal pathogens. MiR396 levels gradually decreased during fungal infection, thus, enabling its GRF (GROWTH-REGULATING FACTOR) transcription factor target genes to trigger host reprogramming. Pathogen resistance in MIM396 plants is based on a superactivation of defense responses consistent with a priming event during pathogen infection. Notably, low levels of miR396 are not translated in developmental defects in absence of pathogen challenge. Our findings support a role of miR396 in regulating plant immunity, and broaden our knowledge about the molecular players and processes that sustain defense priming. That miR396 modulates innate immunity without growth costs also suggests fine-tuning of miR396 levels as an effective biotechnological means for protection against pathogen infection.
Collapse
Affiliation(s)
- Mauricio Soto-Suárez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB. Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB. Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ignacio Rubio-Somoza
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB. Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB. Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| |
Collapse
|
41
|
Hewezi T, Piya S, Qi M, Balasubramaniam M, Rice JH, Baum TJ. Arabidopsis miR827 mediates post-transcriptional gene silencing of its ubiquitin E3 ligase target gene in the syncytium of the cyst nematode Heterodera schachtii to enhance susceptibility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:179-192. [PMID: 27304416 DOI: 10.1111/tpj.13238] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/08/2016] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a major class of small non-coding RNAs with emerging functions in biotic and abiotic interactions. Here, we report on a new functional role of Arabidopsis miR827 and its NITROGEN LIMITATION ADAPTATION (NLA) target gene in mediating plant susceptibility to the beet cyst nematode Heterodera schachtii. Cyst nematodes are sedentary endoparasites that induce the formation of multinucleated feeding structures termed syncytia in the roots of host plants. Using promoter:GUS fusion assays we established that miR827 was activated in the initial feeding cells and this activation was maintained in the syncytium during all sedentary stages of nematode development. Meanwhile, the NLA target gene, which encodes an ubiquitin E3 ligase enzyme, was post-transcriptionally silenced in the syncytium to permanently suppress its activity during all nematode parasitic stages. Overexpression of miR827 in Arabidopsis resulted in hyper-susceptibility to H. schachtii. In contrast, inactivation of miR827 activity through target mimicry or by overexpression a miR827-resistant cDNA of NLA produced the opposite phenotype of reduced plant susceptibility to H. schachtii. Gene expression analysis of several pathogenesis-related genes together with Agrobacterium-mediated transient expression in Nicotiana benthamiana provided strong evidence that miR827-mediated downregulation of NLA to suppress basal defense pathways. In addition, using yeast two-hybrid screens we identified several candidates of NLA-interacting proteins that are involved in a wide range of biological processes and molecular functions, including three pathogenesis-related proteins. Taken together, we conclude that nematode-activated miR827 in the syncytium is necessary to suppress immune responses in order to establish infection and cause disease.
Collapse
Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | | | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
42
|
MicroRNA393 is involved in nitrogen-promoted rice tillering through regulation of auxin signal transduction in axillary buds. Sci Rep 2016; 6:32158. [PMID: 27574184 PMCID: PMC5004122 DOI: 10.1038/srep32158] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Rice tillering has an important influence on grain yield, and is promoted by nitrogen (N) fertilizer. Several genes controlling rice tillering, which are regulated by poor N supply, have been identified. However, the molecular mechanism associated with the regulation of tillering based on N supply is poorly understood. Here, we report that rice microRNA393 (OsmiR393) is involved in N-mediated tillering by decreasing auxin signal sensitivity in axillary buds. Expression analysis showed that N fertilizer causes up-regulation of OsmiR393, but down-regulation of two target genes (OsAFB2 and OsTB1). In situ expression analysis showed that OsmiR393 is highly expressed in the lateral axillary meristem. OsmiR393 overexpression mimicked N-mediated tillering in wild type Zhonghua 11 (ZH11). Mutation of OsMIR393 in ZH11 repressed N-promoted tillering, which simulated the effects of limited N, and this could not be restored by supplying N fertilizer. Western blot analysis showed that OsIAA6 was accumulated in both OsmiR393-overexpressing lines and N-treated wild type rice, but was reduced in the OsMIR393 mutant. Therefore, we deduced that N-induced OsmiR393 accumulation reduces the expression of OsTIR1 and OsAFB2, which alleviates sensitivity to auxin in the axillary buds and stabilizes OsIAA6, thereby promoting rice tillering.
Collapse
|
43
|
Liu SC, Jin JQ, Ma JQ, Yao MZ, Ma CL, Li CF, Ding ZT, Chen L. Transcriptomic Analysis of Tea Plant Responding to Drought Stress and Recovery. PLoS One 2016; 11:e0147306. [PMID: 26788738 PMCID: PMC4720391 DOI: 10.1371/journal.pone.0147306] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/01/2016] [Indexed: 11/18/2022] Open
Abstract
Tea plant (Camellia sinensis) is an economically important beverage crop. Drought stress (DS) seriously limits the growth and development of tea plant, thus affecting crop yield and quality. To elucidate the molecular mechanisms of tea plant responding to DS, we performed transcriptomic analysis of tea plant during the three stages [control (CK) and during DS, and recovery (RC) after DS] using RNA sequencing (RNA-Seq). Totally 378.08 million high-quality trimmed reads were obtained and assembled into 59,674 unigenes, which were extensively annotated. There were 5,955 differentially expressed genes (DEGs) among the three stages. Among them, 3,948 and 1,673 DEGs were up-regulated under DS and RC, respectively. RNA-Seq data were further confirmed by qRT-PCR analysis. Genes involved in abscisic acid (ABA), ethylene, and jasmonic acid biosynthesis and signaling were generally up-regulated under DS and down-regulated during RC. Tea plant potentially used an exchange pathway for biosynthesis of indole-3-acetic acid (IAA) and salicylic acid under DS. IAA signaling was possibly decreased under DS but increased after RC. Genes encoding enzymes involved in cytokinin synthesis were up-regulated under DS, but down-regulated during RC. It seemed probable that cytokinin signaling was slightly enhanced under DS. In total, 762 and 950 protein kinases belonging to 26 families were differentially expressed during DS and RC, respectively. Overall, 547 and 604 transcription factor (TF) genes belonging to 58 families were induced in the DS vs. CK and RC vs. DS libraries, respectively. Most members of the 12 TF families were up-regulated under DS. Under DS, genes related to starch synthesis were down-regulated, while those related to starch decomposition were up-regulated. Mannitol, trehalose and sucrose synthesis-related genes were up-regulated under DS. Proline was probably mainly biosynthesized from glutamate under DS and RC. The mechanism by which ABA regulated stomatal movement under DS and RC was partly clarified. These results document the global and novel responses of tea plant during DS and RC. These data will serve as a valuable resource for drought-tolerance research and will be useful for breeding drought-resistant tea cultivars.
Collapse
Affiliation(s)
- Sheng-Chuan Liu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
- Guizhou Tea Research Institute, Guiyang, Guizhou, China
| | - Ji-Qiang Jin
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Ming-Zhe Yao
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Chun-Lei Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Chun-Fang Li
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Zhao-Tang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| |
Collapse
|
44
|
Chen L, Luan Y, Zhai J. Sp-miR396a-5p acts as a stress-responsive genes regulator by conferring tolerance to abiotic stresses and susceptibility to Phytophthora nicotianae infection in transgenic tobacco. PLANT CELL REPORTS 2015; 34:2013-25. [PMID: 26242449 DOI: 10.1007/s00299-015-1847-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/27/2015] [Accepted: 07/15/2015] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Overexpression of Sp-miR396a-5p in tobacco increased tolerance to salt, drought, cold stress and susceptibility to Phytophthora nicotianae infection. MicroRNA396 (miR396) is one of the conserved microRNA families in plants, and it targeted growth-regulating factors (GRFs) family. The GRF transcription factors are associated with growth and stress responses. However, the molecular mechanisms of miR396 responding to environmental stresses are elusive. The purpose of this study was to explore the function of tomato miR396a-5p (Sp-miR396a-5p) in Solanaceae responses to abiotic and biotic stresses. We showed that Sp-miR396a-5p transcript levels were up-regulated under salt and drought stresses and down-regulated after Phytophthora infestans (P. infestans) infection. Consistently, overexpression of Sp-miR396a-5p in tobacco enhanced its tolerance to salt, drought and cold stresses. Additionally, the expression of Sp-miR396a-5p was found to be down-regulated under pathogen-related biotic stress. Tobacco plants overexpressing Sp-miR396a-5p showed increased susceptibility to Phytophthora nicotianae (P. nicotianae) infection. Physiological analysis indicated that Sp-miR396a-5p overexpression enhanced osmoregulation and decreased production of reactive oxygen species (ROS). Furthermore, four Sp-miR396a-5p target genes, NtGRF1, NtGRF3, NtGRF7 and NtGRF8, were down-regulated in these plants. Our results suggested that Sp-miR396a-5p plays critical roles in both abiotic stresses through targeting NtGRF7-regulated expression of osmotic stress-responsive genes and pathogen infection via the regulatory networks of NtGRF1 and NtGRF3.
Collapse
Affiliation(s)
- Lei Chen
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, People's Republic of China
| | - Yushi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, People's Republic of China.
| | - Junmiao Zhai
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, People's Republic of China
| |
Collapse
|
45
|
Kim JH, Tsukaya H. Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6093-107. [PMID: 26160584 DOI: 10.1093/jxb/erv349] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Transcription factors are key regulators of gene expression and play pivotal roles in all aspects of living organisms. Therefore, identification and functional characterization of transcription factors is a prerequisite step toward understanding life. This article reviews molecular and biological functions of the two transcription regulator families, GROWTH-REGULATING FACTOR (GRF) and GRF-INTERACTING FACTOR (GIF), which have only recently been recognized. A myriad of experimental evidence clearly illustrates that GRF and GIF are bona fide partner proteins and form a plant-specific transcriptional complex. One of the most conspicuous outcomes from this research field is that the GRF-GIF duo endows the primordial cells of vegetative and reproductive organs with a meristematic specification state, guaranteeing the supply of cells for organogenesis and successful reproduction. It has recently been shown that GIF1 proteins, also known as ANGUSTIFOLIA3, recruit chromatin remodelling complexes to target genes, and that AtGRF expression is directly activated by the floral identity factors, APETALA1 and SEPALLATA3, providing an important insight into understanding of the action of GRF-GIF. Moreover, GRF genes are extensively subjected to post-transcriptional control by microRNA396, revealing the presence of a complex regulatory circuit in regulation of plant growth and development by the GRF-GIF duo.
Collapse
Affiliation(s)
- Jeong Hoe Kim
- Department of Biology, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Korea
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| |
Collapse
|
46
|
Omidbakhshfard MA, Proost S, Fujikura U, Mueller-Roeber B. Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology. MOLECULAR PLANT 2015; 8:998-1010. [PMID: 25620770 DOI: 10.1016/j.molp.2015.01.013] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/21/2014] [Accepted: 01/13/2015] [Indexed: 05/18/2023]
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.
Collapse
Affiliation(s)
- Mohammad Amin Omidbakhshfard
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Sebastian Proost
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ushio Fujikura
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany; Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| |
Collapse
|
47
|
Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
Collapse
Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| |
Collapse
|
48
|
Djami-Tchatchou AT, Dubery IA. Lipopolysaccharide perception leads to dynamic alterations in the microtranscriptome of Arabidopsis thaliana cells and leaf tissues. BMC PLANT BIOLOGY 2015; 15:79. [PMID: 25848807 PMCID: PMC4354979 DOI: 10.1186/s12870-015-0465-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/20/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are non-coding RNA molecules which have recently emerged as important gene regulators in plants and their gene expression analysis is becoming increasingly important. miRNAs regulate gene expression at the post-transcriptional level by translational repression or target degradation of specific mRNAs and gene silencing. In order to profile the microtranscriptome of Arabidopsis thaliana leaf and callus tissues in response to bacterial lipopolysaccharide (LPS), small RNA libraries were constructed at 0 and 3 h post induction with LPS and sequenced by Illumina sequencing technology. RESULTS Differential regulation of subset of miRNAs in response to LPS treament was observed. Small RNA reads were mapped to the miRNA database and 358 miRNAs belonging to 49 miRNA families in the callus tissues and 272 miRNAs belonging to 40 miRNA families in the leaf tissues were identified. Moreover, target genes for all the identified miRNAs families in the leaf tissues and 44 of the 49 miRNAs families in the callus tissues were predicted. The sequencing analysis showed that in both callus and leaf tissues, various stress regulated-miRNAs were differentially expressed and real time PCR validated the expression profile of miR156, miR158, miR159, miR169, miR393, miR398, miR399 and miR408 along with their target genes. CONCLUSION A. thaliana callus and leaf callus tissues respond to LPS as a microbe-associated molecular pattern molecule through dynamic changes to the microtranscriptome associated with differential transcriptional regulation in support of immunity and basal resistance.
Collapse
Affiliation(s)
- Arnaud T Djami-Tchatchou
- Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, 2006 South Africa
| | - Ian A Dubery
- Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, 2006 South Africa
| |
Collapse
|
49
|
Vercruyssen L, Tognetti VB, Gonzalez N, Van Dingenen J, De Milde L, Bielach A, De Rycke R, Van Breusegem F, Inzé D. GROWTH REGULATING FACTOR5 stimulates Arabidopsis chloroplast division, photosynthesis, and leaf longevity. PLANT PHYSIOLOGY 2015; 167:817-32. [PMID: 25604530 PMCID: PMC4348790 DOI: 10.1104/pp.114.256180] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/16/2015] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) leaf development relies on subsequent phases of cell proliferation and cell expansion. During the proliferation phase, chloroplasts need to divide extensively, and during the transition from cell proliferation to expansion, they differentiate into photosynthetically active chloroplasts, providing the plant with energy. The transcription factor GROWTH REGULATING FACTOR5 (GRF5) promotes the duration of the cell proliferation period during leaf development. Here, it is shown that GRF5 also stimulates chloroplast division, resulting in a higher chloroplast number per cell with a concomitant increase in chlorophyll levels in 35S:GRF5 leaves, which can sustain higher rates of photosynthesis. Moreover, 35S:GRF5 plants show delayed leaf senescence and are more tolerant for growth on nitrogen-depleted medium. Cytokinins also stimulate leaf growth in part by extending the cell proliferation phase, simultaneously delaying the onset of the cell expansion phase. In addition, cytokinins are known to be involved in chloroplast development, nitrogen signaling, and senescence. Evidence is provided that GRF5 and cytokinins synergistically enhance cell division and chlorophyll retention after dark-induced senescence, which suggests that they also cooperate to stimulate chloroplast division and nitrogen assimilation. Taken together with the increased leaf size, ectopic expression of GRF5 has great potential to improve plant productivity.
Collapse
Affiliation(s)
- Liesbeth Vercruyssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Vanesa B Tognetti
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Judith Van Dingenen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Agnieszka Bielach
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Riet De Rycke
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| |
Collapse
|
50
|
Kshirsagar M, Schleker S, Carbonell J, Klein-Seetharaman J. Techniques for transferring host-pathogen protein interactions knowledge to new tasks. Front Microbiol 2015; 6:36. [PMID: 25699028 PMCID: PMC4313693 DOI: 10.3389/fmicb.2015.00036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/12/2015] [Indexed: 11/17/2022] Open
Abstract
We consider the problem of building a model to predict protein-protein interactions (PPIs) between the bacterial species Salmonella Typhimurium and the plant host Arabidopsis thaliana which is a host-pathogen pair for which no known PPIs are available. To achieve this, we present approaches, which use homology and statistical learning methods called “transfer learning.” In the transfer learning setting, the task of predicting PPIs between Arabidopsis and its pathogen S. Typhimurium is called the “target task.” The presented approaches utilize labeled data i.e., known PPIs of other host-pathogen pairs (we call these PPIs the “source tasks”). The homology based approaches use heuristics based on biological intuition to predict PPIs. The transfer learning methods use the similarity of the PPIs from the source tasks to the target task to build a model. For a quantitative evaluation we consider Salmonella-mouse PPI prediction and some other host-pathogen tasks where known PPIs exist. We use metrics such as precision and recall and our results show that our methods perform well on the target task in various transfer settings. We present a brief qualitative analysis of the Arabidopsis-Salmonella predicted interactions. We filter the predictions from all approaches using Gene Ontology term enrichment and only those interactions involving Salmonella effectors. Thereby we observe that Arabidopsis proteins involved e.g., in transcriptional regulation, hormone mediated signaling and defense response may be affected by Salmonella.
Collapse
Affiliation(s)
- Meghana Kshirsagar
- School of Computer Science, Language Technologies Institute, Carnegie Mellon University Pittsburgh, PA, USA
| | - Sylvia Schleker
- Metabolic and Vascular Health, Warwick Medical School, University of Warwick Coventry, UK ; Molecular Phytomedicine, Institute of Crop Science and Resource Conservation, University of Bonn Bonn, Germany
| | - Jaime Carbonell
- School of Computer Science, Language Technologies Institute, Carnegie Mellon University Pittsburgh, PA, USA
| | | |
Collapse
|