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Khansarinejad B, Dashti F, Buratti E, Mirzaie-Asl A, Zafari D, Romano M. Changes in the expression of COI1, TIR1, and ERF1 genes and respective MiRNAs in Fusarium basal Rot-Stressed onion. Gene 2024; 905:148212. [PMID: 38281673 DOI: 10.1016/j.gene.2024.148212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 01/30/2024]
Abstract
Fusarium oxysporum f.sp. cepae (FOC), as basal rot fungus, is the most detrimental pathogen causing a serious threat to onion productivity in the world. In this study, we first determined FOC tolerance in seven Iranian onion cultivars, two known international onions (Texas Early Grano and Sweet Yellow Spanish), and an Allium species related to the onion (Allium asarence) based on the infection severity. Then, a transcriptional screen was performed by comparing the transcript levels of some pathogen-responsive genes (ERF1, COI1, and TIR1) and their predicted miRNAs in the sensitive (Ghermeze Azarshahr Cv.) and the resistant (A. asarence) onions to determine key genes and their miRNAs involved in the defense responses of onions to FOC. From our results, a difference was found in the COI1 and ERF1 expression 48 h after inoculation with FOC as compared to the respective 24 and 72 h. It can be explained by either special mechanisms involved in raising energy consumption efficiency or the interactive effects of other genes in the jasmonic acid (JA) and ethylene (ET) signaling pathways. Moreover, expression analysis of the pathogen-responsive genes and their targeting miRNAs identified the miR-5629, which targets the COI1 gene as a likely key factor in conferring resistance in the FOC-resistant onion, i.e., A. asarence. However, exploring the function of the miRNA/target pair is highly recommended to deeply understand the effect of the miRNA/target pair-associated pathway in the control of A. asarense-FOC interaction.
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Affiliation(s)
- Bita Khansarinejad
- Department of Horticultural Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Farshad Dashti
- Department of Horticultural Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Emanuele Buratti
- Molecular Pathology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
| | - Asghar Mirzaie-Asl
- Department of Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Doustmorad Zafari
- Department of Plant Pathology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy.
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2
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Liu K, Hou Q, Yu R, Deng H, Shen L, Wang Q, Wen X. Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple. Gene 2024; 904:148164. [PMID: 38224923 DOI: 10.1016/j.gene.2024.148164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.
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Affiliation(s)
- Ke Liu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Qiandong Hou
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Luonan Shen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Institute for Forest Resources & Environment of Guizhou/ College of Forestry, Guizhou University, Guiyang 550025, China
| | - Qian Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
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3
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Wen Y, Hu P, Fang Y, Tan Y, Wang Y, Wu H, Wang J, Wu K, Chai B, Zhu L, Zhang G, Gao Z, Ren D, Zeng D, Shen L, Dong G, Zhang Q, Li Q, Xiong G, Xue D, Qian Q, Hu J. GW9 determines grain size and floral organ identity in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:915-928. [PMID: 37983630 PMCID: PMC10955487 DOI: 10.1111/pbi.14234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/22/2023]
Abstract
Grain weight is an important determinant of grain yield. However, the underlying regulatory mechanisms for grain size remain to be fully elucidated. Here, we identify a rice mutant grain weight 9 (gw9), which exhibits larger and heavier grains due to excessive cell proliferation and expansion in spikelet hull. GW9 encodes a nucleus-localized protein containing both C2H2 zinc finger (C2H2-ZnF) and VRN2-EMF2-FIS2-SUZ12 (VEFS) domains, serving as a negative regulator of grain size and weight. Interestingly, the non-frameshift mutations in C2H2-ZnF domain result in increased plant height and larger grain size, whereas frameshift mutations in both C2H2-ZnF and VEFS domains lead to dwarf and malformed spikelet. These observations indicated the dual functions of GW9 in regulating grain size and floral organ identity through the C2H2-ZnF and VEFS domains, respectively. Further investigation revealed the interaction between GW9 and the E3 ubiquitin ligase protein GW2, with GW9 being the target of ubiquitination by GW2. Genetic analyses suggest that GW9 and GW2 function in a coordinated pathway controlling grain size and weight. Our findings provide a novel insight into the functional role of GW9 in the regulation of grain size and weight, offering potential molecular strategies for improving rice yield.
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Affiliation(s)
- Yi Wen
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Peng Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Yunxia Fang
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Yiqing Tan
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yueying Wang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Hao Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Junge Wang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Bingze Chai
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Qing Li
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guosheng Xiong
- Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina
| | - Dawei Xue
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Qian Qian
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Jiang Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
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4
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Li Z, Chen H, Guan Q, Li L, Xuan YH. Gibberellic acid signaling promotes resistance to saline-alkaline stress by increasing the uptake of ammonium in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108424. [PMID: 38335888 DOI: 10.1016/j.plaphy.2024.108424] [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: 07/13/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024]
Abstract
Gibberellic acid (GA) plays important roles in diverse biological processes in plants. However, its function in rice (Oryza sativa) resistance to saline-alkaline (SAK) stress is unclear. This study showed that SAK stimuli changed GA signaling gene expression levels. Genetic analyses using the mutants of key GA signaling regulators, Slender rice 1 (SLR1) and Dwarf 1(D1), demonstrated that SLR1 negatively, while D1 positively regulated the resistance of rice to SAK stress, suggesting that the GA signaling positively regulates the resistance of rice to SAK. Further analyses revealed that SLR1 interacted with and inhibited the transcription activation activity of IDD10 and bZIP23. Furthermore, IDD10 interacted with bZIP23 to activate Ammonium transporter 1;2 (AMT1;2), and slr1, IDD10 OX and bZIP23 OX accumulated more ammonium (NH4+), while idd10 and bzip23 accumulated less NH4+ than the wild-type (WT). In addition, the bzip23 mutant was more sensitive to SAK, while bZIP23 OX was less sensitive compared with the WT, suggesting that bZIP23 positively regulates the resistance of rice to SAK. These findings demonstrate that GA signaling promoted rice's SAK resistance by regulating NH4+ uptake through the SLR1-IDD10-bZIP23 pathway.
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Affiliation(s)
- Zhuo Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Huan Chen
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University), Harbin, 150040, China
| | - Qingjie Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University), Harbin, 150040, China.
| | - Lixin Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education (Northeast Forestry University), Harbin, 150040, China.
| | - Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
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Jia HH, Xu YT, Yin ZJ, Qing M, Xie KD, Guo WW, Wu XM. Genome-wide identification of the C2H2-Zinc finger gene family and functional validation of CsZFP7 in citrus nucellar embryogenesis. PLANT REPRODUCTION 2023; 36:287-300. [PMID: 37247027 DOI: 10.1007/s00497-023-00470-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
KEY MESSAGE Genome-wide identification of C2H2-ZF gene family in the poly- and mono-embryonic citrus species and validation of the positive role of CsZFP7 in sporophytic apomixis. The C2H2 zinc finger (C2H2-ZF) gene family is involved in plant vegetative and reproductive development. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in some horticultural plants, little is known about the C2H2-ZFPs and their function in citrus. In this work, we performed a genome-wide sequence analysis and identified 97 and 101 putative C2H2-ZF gene family members in the genomes of sweet orange (C. sinensis, poly-embryonic) and pummelo (C. grandis, mono-embryonic), respectively. Phylogenetic analysis categorized citrus C2H2-ZF gene family into four clades, and their possible functions were inferred. According to the numerous regulatory elements on promoter, citrus C2H2-ZFPs can be divided into five different regulatory function types that indicate functional differentiation. RNA-seq data revealed 20 differentially expressed C2H2-ZF genes between poly-embryonic and mono-embryonic ovules at two stages of citrus nucellar embryogenesis, among them CsZFP52 specifically expressed in mono-embryonic pummelo ovules, while CsZFP7, 37, 44, 45, 67 and 68 specifically expressed in poly-embryonic sweet orange ovules. RT-qPCR further validated that CsZFP7 specifically expressed at higher levels in poly-embryonic ovules, and down-regulation of CsZFP7 in the poly-embryonic mini citrus (Fortunella hindsii) increased rate of mono-embryonic seeds compared with the wild type, indicating the regulatory potential of CsZFP7 in nucellar embryogenesis of citrus. This work provided a comprehensive analysis of C2H2-ZF gene family in citrus, including genome organization and gene structure, phylogenetic relationships, gene duplications, possible cis-elements on promoter regions and expression profiles, especially in the poly- and mono-embryogenic ovules, and suggested that CsZFP7 is involved in nucellar embryogenesis.
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Affiliation(s)
- Hui-Hui Jia
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan-Tao Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhu-Jun Yin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Qing
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kai-Dong Xie
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Wu Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Meng Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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Fang H, Shi Y, Liu S, Jin R, Sun J, Grierson D, Li S, Chen K. The transcription factor CitZAT5 modifies sugar accumulation and hexose proportion in citrus fruit. PLANT PHYSIOLOGY 2023; 192:1858-1876. [PMID: 36911987 PMCID: PMC10315291 DOI: 10.1093/plphys/kiad156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/19/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Sugars are fundamental to plant developmental processes. For fruits, the accumulation and proportion of sugars play crucial roles in the development of quality and attractiveness. In citrus (Citrus reticulata Blanco.), we found that the difference in sweetness between mature fruits of "Gongchuan" and its bud sport "Youliang" is related to hexose contents. Expression of a SuS (sucrose synthase) gene CitSUS5 and a SWEET (sugars will eventually be exported transporter) gene CitSWEET6, characterized by transcriptome analysis at different developmental stages of these 2 varieties, revealed higher expression levels in "Youliang" fruit. The roles of CitSUS5 and CitSWEET6 were investigated by enzyme activity and transient assays. CitSUS5 promoted the cleavage of sucrose to hexoses, and CitSWEET6 was identified as a fructose transporter. Further investigation identified the transcription factor CitZAT5 (ZINC FINGER OF ARABIDOPSIS THALIANA) that contributes to sucrose metabolism and fructose transportation by positively regulating CitSUS5 and CitSWEET6. The role of CitZAT5 in fruit sugar accumulation and hexose proportion was investigated by homologous transient CitZAT5 overexpression, -VIGS, and -RNAi. CitZAT5 modulates the hexose proportion in citrus by mediating CitSUS5 and CitSWEET6 expression, and the molecular mechanism explained the differences in sugar composition of "Youliang" and "Gongchuan" fruit.
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Affiliation(s)
- Heting Fang
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
| | - Yanna Shi
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
| | - Shengchao Liu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
| | - Rong Jin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Department of Horticulture and Agricultural Experiment Station, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
| | - Jun Sun
- Zhejiang Agricultural Technology Extension Center, Hangzhou 310029, China
| | - Donald Grierson
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Shaojia Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, PR China
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7
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Khan SI, Yamada R, Shiroma R, Abe T, Kozaki A. Properties of INDETERMINATE DOMAIN Proteins from Physcomitrium patens: DNA-Binding, Interaction with GRAS Proteins, and Transcriptional Activity. Genes (Basel) 2023; 14:1249. [PMID: 37372429 DOI: 10.3390/genes14061249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins are plant-specific transcription factors that interact with GRAS proteins, such as DELLA and SHORT ROOT (SHR), to regulate target genes. The combination of IDD and DELLA proteins regulates genes involved in gibberellic acid (GA) synthesis and GA signaling, whereas the combination of IDD with the complex of SHR and SCARECROW, another GRAS protein, regulates genes involved in root tissue formation. Previous bioinformatic research identified seven IDDs, two DELLA, and two SHR genes in Physcomitrium patens, a model organism for non-vascular plants (bryophytes), which lack a GA signaling pathway and roots. In this study, DNA-binding properties and protein-protein interaction of IDDs from P. patens (PpIDD) were analyzed. Our results showed that the DNA-binding properties of PpIDDs were largely conserved between moss and seed plants. Four PpIDDs showed interaction with Arabidopsis DELLA (AtDELLA) proteins but not with PpDELLAs, and one PpIDD showed interaction with PpSHR but not with AtSHR. Moreover, AtIDD10 (JACKDAW) interacted with PpSHR but not with PpDELLAs. Our results indicate that DELLA proteins have modified their structure to interact with IDD proteins during evolution from moss lineage to seed plants, whereas the interaction of IDD and SHR was already present in moss lineage.
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Affiliation(s)
- Saiful Islam Khan
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ren Yamada
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ryoichi Shiroma
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tatsuki Abe
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Akiko Kozaki
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
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8
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Liu Z, Sun Z, Ke H, Chen B, Gu Q, Zhang M, Wu N, Chen L, Li Y, Meng C, Wang G, Wu L, Zhang G, Ma Z, Zhang Y, Wang X. Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton. Int J Mol Sci 2023; 24:ijms24098293. [PMID: 37175999 PMCID: PMC10179096 DOI: 10.3390/ijms24098293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC3F5 population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement.
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Affiliation(s)
- Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Nan Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liting Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yanbin Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
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9
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Xu Y, Hu R, Li S. Regulation of seed coat mucilage production and modification in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 328:111591. [PMID: 36623642 DOI: 10.1016/j.plantsci.2023.111591] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The Arabidopsis seed coat mucilage is a polysaccharide-rich matrix synthesized by the seed coat epidermal cells. It is a specialized cell wall mainly composed of three types of polysaccharides (i. e. pectin, hemicellulose, and cellulose), and represents as an ideal model system for plant cell wall research. A large number of genes responsible for the synthesis and modification of cell wall polysaccharides have been identified using this model system. Moreover, a subset of regulators controlling mucilage production and modification have been characterized, and the underlying transcriptional regulatory mechanisms have been elucidated. This substantially contributes to the understanding of the molecular mechanisms underlying mucilage synthesis and modification. In this review, we concisely summarize the various genes and regulators involved in seed coat cell differentiation, mucilage biosynthesis and modification, and secondary cell wall formation. In particular, we put emphasis on the latest knowledge gained regarding the transcriptional regulation of mucilage production, which is composed of a hierarchal cascade with three-layer transcriptional regulators. Collectively, we propose an updated schematic framework of the genetic regulatory network controlling mucilage production and modification in the Arabidopsis mucilage secretory cells.
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Affiliation(s)
- Yan Xu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China
| | - Ruibo Hu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China.
| | - Shengjun Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China.
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10
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Guo X, Zhou M, Chen J, Shao M, Zou L, Ying Y, Liu S. Genome-Wide Identification of the Highly Conserved INDETERMINATE DOMAIN ( IDD) Zinc Finger Gene Family in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2022; 23:ijms232213952. [PMID: 36430436 PMCID: PMC9695771 DOI: 10.3390/ijms232213952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins, a family of transcription factors unique to plants, function in multiple developmental processes. Although the IDD gene family has been identified in many plants, little is known about it in moso bamboo. In this present study, we identified 32 PheIDD family genes in moso bamboo and randomly sequenced the full-length open reading frames (ORFs) of ten PheIDDs. All PheIDDs shared a highly conserved IDD domain that contained two canonical C2H2-ZFs, two C2HC-ZFs, and a nuclear localization signal. Collinearity analysis showed that segmental duplication events played an important role in expansion of the PheIDD gene family. Synteny analysis indicated that 30 PheIDD genes were orthologous to those of rice (Oryza sativa). Thirty PheIDDs were expressed at low levels, and most PheIDDs exhibited characteristic organ-specific expression patterns. Despite their diverse expression patterns in response to exogenous plant hormones, 8 and 22 PheIDDs responded rapidly to IAA and 6-BA treatments, respectively. The expression levels of 23 PheIDDs were closely related to the outgrowth of aboveground branches and 20 PheIDDs were closely related to the awakening of underground dormant buds. In addition, we found that the PheIDD21 gene generated two products by alternative splicing. Both isoforms interacted with PheDELLA and PheSCL3. Furthermore, both isoforms could bind to the cis-elements of three genes (PH02Gene17121, PH02Gene35441, PH02Gene11386). Taken together, our work provides valuable information for studying the molecular breeding mechanism of lateral organ development in moso bamboo.
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Liu J, Shu D, Tan Z, Ma M, Guo N, Gao S, Duan G, Kuai B, Hu Y, Li S, Cui D. The Arabidopsis IDD14 transcription factor interacts with bZIP-type ABFs/AREBs and cooperatively regulates ABA-mediated drought tolerance. THE NEW PHYTOLOGIST 2022; 236:929-942. [PMID: 35842794 DOI: 10.1111/nph.18381] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The INDETERMINATE DOMAIN (IDD) transcription factors mediate various aspects of plant growth and development. We previously reported that an Arabidopsis IDD subfamily regulates spatial auxin accumulation, and thus organ morphogenesis and gravitropic responses. However, its functions in stress responses are not well defined. Here, we use a combination of physiological, biochemical, molecular, and genetic approaches to provide evidence that the IDD14 cooperates with basic leucine zipper-type binding factors/ABA-responsive element (ABRE)-binding proteins (ABRE-binding factors (ABFs)/AREBs) in ABA-mediated drought tolerance. idd14-1D, a gain-of-function mutant of IDD14, exhibits decreased leaf water loss and improved drought tolerance, whereas inactivation of IDD14 in idd14-1 results in increased transpiration and reduced drought tolerance. Altered IDD14 expression affects ABA sensitivity and ABA-mediated stomatal closure. IDD14 can physically interact with ABF1-4 and subsequently promote their transcriptional activities. Moreover, ectopic expression and mutation of ABFs could, respectively, suppress and enhance plant sensitivity to drought stress in the idd14-1 mutant. Our results demonstrate that IDD14 forms a functional complex with ABFs and positively regulates drought-stress responses, thus revealing a previously unidentified role of IDD14 in ABA signaling and drought responses.
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Affiliation(s)
- Jing Liu
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Defeng Shu
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Zilong Tan
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Mei Ma
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Ning Guo
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
- School of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Shan Gao
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Benke Kuai
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shipeng Li
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Dayong Cui
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
- School of Life Sciences, Shandong Normal University, Jinan, 250014, China
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12
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Ramtekey V, Cherukuri S, Kumar S, V. SK, Sheoran S, K. UB, K. BN, Kumar S, Singh AN, Singh HV. Seed Longevity in Legumes: Deeper Insights Into Mechanisms and Molecular Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:918206. [PMID: 35968115 PMCID: PMC9364935 DOI: 10.3389/fpls.2022.918206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Sustainable agricultural production largely depends upon the viability and longevity of high-quality seeds during storage. Legumes are considered as rich source of dietary protein that helps to ensure nutritional security, but associated with poor seed longevity that hinders their performance and productivity in farmer's fields. Seed longevity is the key determinant to assure proper seed plant value and crop yield. Thus, maintenance of seed longevity during storage is of prime concern and a pre-requisite for enhancing crop productivity of legumes. Seed longevity is significantly correlated with other seed quality parameters such as germination, vigor, viability and seed coat permeability that affect crop growth and development, consequently distressing crop yield. Therefore, information on genetic basis and regulatory networks associated with seed longevity, as well as molecular dissection of traits linked to longevity could help in developing crop varieties with good storability. Keeping this in view, the present review focuses towards highlighting the molecular basis of seed longevity, with special emphasis on candidate genes and proteins associated with seed longevity and their interplay with other quality parameters. Further, an attempt was made to provide information on 3D structures of various genetic loci (genes/proteins) associated to seed longevity that could facilitate in understanding the interactions taking place within the seed at molecular level. This review compiles and provides information on genetic and genomic approaches for the identification of molecular pathways and key players involved in the maintenance of seed longevity in legumes, in a holistic manner. Finally, a hypothetical fast-forward breeding pipeline has been provided, that could assist the breeders to successfully develop varieties with improved seed longevity in legumes.
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Affiliation(s)
| | | | - Sunil Kumar
- Indian Agricultural Statistics Research Institute-IASRI, New Delhi, India
| | | | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, India
| | - Udaya Bhaskar K.
- ICAR-Indian Institute of Seed Science, Regional Station, Bengaluru, India
| | - Bhojaraja Naik K.
- ICAR-Indian Institute of Seed Science, Regional Station, Bengaluru, India
| | - Sanjay Kumar
- ICAR-Indian Institute of Seed Science, Mau, India
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Hussain A, Liu J, Mohan B, Burhan A, Nasim Z, Bano R, Ameen A, Zaynab M, Mukhtar MS, Pajerowska-Mukhtar KM. A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. Sci Rep 2022; 12:12328. [PMID: 35853967 PMCID: PMC9296551 DOI: 10.1038/s41598-022-16602-8] [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: 01/29/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
Zinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs in Gossypium sp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species.
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Affiliation(s)
- Athar Hussain
- Genomics Lab, School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Jinbao Liu
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Binoop Mohan
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Akif Burhan
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Zunaira Nasim
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Raveena Bano
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Ayesha Ameen
- Office of Research Innovation and Commercialization, University of Management and Technology, Lahore, 54770, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA.
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Cota-Ruiz K, Oh S, Montgomery BL. Phytochrome-Dependent Regulation of ZFP6 and ZFPH Impacts Photomorphogenesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:846262. [PMID: 35720591 PMCID: PMC9198550 DOI: 10.3389/fpls.2022.846262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Phytochromes (phy) are key regulators of photomorphogenesis in plants. Among the different phys characterized in higher plants (i.e., phyA to phyE), phyA and phyB primarily regulate phenotypic responses in plants under far-red (FR) and red (R) conditions, respectively. Recent findings suggest that some zinc finger proteins (ZFPs) are involved in plant light-modulated morphogenesis. However, the interaction(s) between phyA, phyB and ZFP homologs potentially involved in photomorphogenesis, as well as their phenotypic and molecular effects in Arabidopsis seedlings exposed to R and FR light remain to be elucidated fully. Prior analyses with phytochrome chromophore deficient lines indicated that ZFP6 expression is misregulated compared to levels in Col-0 wild type (WT). Here, we used plants with phytochrome chromophore or apoprotein (specifically phyA and phyB) deficiencies, lines with mutations in ZFP6 and ZFP6 HOMOLOG (ZFPH) genes, and plants overexpressing ZFP6 to examine regulatory interactions between phytochromes, ZFP6, and ZFPH. Our results indicate that phytochromes are required for downregulation of ZFP6 and ZFPH and suggest a role for light-regulated control of ZFP levels in phytochrome-dependent photomorphogenesis. Conversely, PHYB is downregulated in zfp6 mutants under R light. Analyses of a zfp6zfph double mutant confirmed disruption in photomorphogenic phenotypes, including the regulation of hypocotyl elongation in seedlings grown under FR light. In addition, PIF3 and PIF4 levels are transcriptionally regulated by ZFP6 and ZFPH in a gibberellic acid-dependent manner. ZFP6 overexpression resulted in opposite phenotypic responses to those observed in the zfp6 and zfph mutants grown in FR and R light, as well as a reduction in the rosette size of mature ZFP6 OX plants relative to WT under white light. Based on these observations, we provide insight into how phy and ZFPs interact to regulate specific aspects of light-dependent processes in Arabidopsis.
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Affiliation(s)
- Keni Cota-Ruiz
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Sookyung Oh
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Beronda L. Montgomery
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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15
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Ji X, Gao Q, Chen F, Bai M, Zhuang Z, Peng Y. Mutant lpa1 Analysis of ZmLPA1 Gene Regulates Maize Leaf-Angle Development through the Auxin Pathway. Int J Mol Sci 2022; 23:ijms23094886. [PMID: 35563277 PMCID: PMC9102400 DOI: 10.3390/ijms23094886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Maize plant type is one of the main factors determining maize yield, and leaf angle is an important aspect of plant type. The rice Loose Plant Architecture1 (LPA1) gene and Arabidopsis AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene are related to their leaf angle. However, the homologous ZmLPA1 in maize has not been studied. In this study, the changing of leaf angle, as well as gene expression in leaves in maize mutant lpa1 and wild-type ‘B73’ under different IAA concentrations were investigated. The regulation effect of IAA on the leaf angle of lpa1 was significantly stronger than that of the wild type. Transcriptome analysis showed that different exogenous IAA treatments had a common enrichment pathway—the indole alkaloid biosynthesis pathway—and among the differentially expressed genes, four genes—AUX1, AUX/IAA, ARF and SAUR—were significantly upregulated. This study revealed the regulation mechanism of ZmLPA1 gene on maize leaf angle and provided a promising gene resource for maize breeding.
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Affiliation(s)
- Xiangzhuo Ji
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Qiaohong Gao
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
| | - Fenqi Chen
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Mingxing Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Zelong Zhuang
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.J.); (Q.G.); (F.C.); (M.B.); (Z.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-138-9323-8528
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Li F, Chen X, Yang B, Guang Y, Wu D, Shi Z, Li Y. Transcriptome Analysis Revealed the Molecular Response Mechanism of High-Resistant and Low-Resistant Alfalfa Varieties to Verticillium Wilt. FRONTIERS IN PLANT SCIENCE 2022; 13:931001. [PMID: 35783960 PMCID: PMC9243768 DOI: 10.3389/fpls.2022.931001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/30/2022] [Indexed: 05/17/2023]
Abstract
Following infestation by Verticillium wilt, alfalfa (Medicago sativa L.) often shows symptoms such as disease spots, leaf loss, stem, and leaf yellowing, resulting in the decline of alfalfa yield and quality and causing significant losses to the alfalfa industry. The popularization and planting of disease-resistant varieties is the most effective method to prevent and control Verticillium wilt of alfalfa. Therefore, it is particularly important to reveal the resistance mechanism of Verticillium wilt resistant varieties of alfalfa. In this study, the physiological and biochemical indexes were measured on days 7, 14, 21, and 28 after inoculation with Verticillium alfalfae for investigating the response mechanisms of two alfalfa varieties, high-resistant WL343HQ, and low-resistant Dryland. Transcriptome sequencing of alfalfa samples infected with V. alfalfae and uninfected alfalfa samples was performed to analyze the potential functions and signaling pathways of differentially expressed genes (DEGs) by GO classification and KEGG enrichment analysis. Meanwhile, weighted gene co-correlation network analysis (WGCNA) algorithm was used to construct a co-expression network of DEGs. Inoculation with V. alfalfae significantly affected net photosynthetic rate, stomatal conductance, chlorophyll content, MDA content, JA and SA concentrations, and NO and H2O2 contents in both WL343HQ and Dryland inoculated with V. alfalfae. Most of the transcription factors in plants were classified in the WRKY, NAC, and bHLH families. WGCNA analysis showed that the number of transcription factors related to plant growth and disease resistance was higher in the corresponding modules of WL343HQ disease groups on days 7 and 28 (WVa) and (WVd) than in the corresponding modules of Dryland disease groups on days 7 and 21 (HVa) and (HVc). These findings provide data for further gene function validation and also provide a reference for in-depth studies on interactions between plants and pathogens.
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Duan G, Ma X, Shi Z, Yang Y, Chen H, Huang Q, Yang J. MoSDT1 triggers defense response through modulating phosphorylated proteins in rice. PLANT MOLECULAR BIOLOGY 2022; 108:15-30. [PMID: 34622380 DOI: 10.1007/s11103-021-01201-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
MoSDT1, a rice blast fungus transcription factor, is as an inducer to activate defense response through mainly mediating phosphorylated proteins in rice. Pathogen effector proteins play a dual role in infecting the host or triggering a defense response. Our previous research found a Magnaporthe oryzae effector, MoSDT1, which could activate the rice defense response when it was overexpressed in rice. However, we still know little about the mechanisms on how MoSDT1 in vivo or in vitro influences the resistance ability of rice. Our results showed that decreased ROS and increased lignin contents appeared along with significant upregulation of defense-related genes, raffinose synthesis gene, and phenylalanine ammonialyase gene. Moreover, we revealed that the contents of lignin were increased, which was in accordance with the upregulation of its precursor phenylalanine gene despite the fact that the glutamate-/thiamine-responsive genes were inhibited in MoSDT1 transgenic rice, and these indicated that MoSDT1 triggered the defense system of rice in vivo. Interestingly, in vitro studies, we further found that MoSDT1 induced the defense system by ROS synthesis, callose deposition, PR gene expression and SA/JA synthesis/signal genes using the purified prokaryotic expression system in rice plants. In addition, this defense response was confirmed to be activated by the zinc finger domain of MoSDT1 via prokaryotic expression of MoSDT1 truncated mutants in rice plants. To elucidate the regulative effects of MoSDT1 on protein phosphorylation in rice, phosphoproteome analysis was performed in both MoSDT1-transgenic and wild type rice. We found that MoSDT1 specifically up-regulated the expression levels of a few phosphorylated proteins, which were involved in multiple functions, such as biotic/abiotic stress and growth. In addition, the motifs in these specific proteins ranked the top among the top-five conserved motifs in the MoSDT1-transgenic rice. MoSDT1 played a crucial role in enhancing rice resistance by modulating several genes and signaling pathways.
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Affiliation(s)
- Guihua Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Xiaoqing Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Zhufeng Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Yaqiong Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Qiong Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China.
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China.
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China.
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China.
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Li J, Zhang L, Yuan Y, Wang Q, Elbaiomy RG, Zhou W, Wu H, Soaud SA, Abbas M, Chen B, Zhao D, El-Sappah AH. In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth. Front Genet 2021; 12:770427. [PMID: 34804129 PMCID: PMC8602080 DOI: 10.3389/fgene.2021.770427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.
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Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Litian Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining, China
| | - Yibing Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | | | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Hui Wu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Deming Zhao
- Yibin Academy of Agricultural Sciences, Yibin, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Wang Z, Wong DCJ, Wang Y, Xu G, Ren C, Liu Y, Kuang Y, Fan P, Li S, Xin H, Liang Z. GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response. PLANT PHYSIOLOGY 2021; 186:1660-1678. [PMID: 33752238 PMCID: PMC8260143 DOI: 10.1093/plphys/kiab142] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/01/2021] [Indexed: 05/19/2023]
Abstract
Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.
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Affiliation(s)
- Zemin Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Darren Chern Jan Wong
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guangzhao Xu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Chong Ren
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
| | - Yanfei Liu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
- China Wine Industry Technology Institute, Yinchuan 750021, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese academy of Sciences, Wuhan 430074, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, China
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20
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Canales J, Verdejo J, Carrasco-Puga G, Castillo FM, Arenas-M A, Calderini DF. Transcriptome Analysis of Seed Weight Plasticity in Brassica napus. Int J Mol Sci 2021; 22:4449. [PMID: 33923211 PMCID: PMC8123204 DOI: 10.3390/ijms22094449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source-sink (S-S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S-S ratio. We found that a reduction in the S-S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW-SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield.
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Affiliation(s)
- Javier Canales
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile; (F.M.C.); (A.A.-M.)
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), 8331150 Santiago, Chile
| | - José Verdejo
- Graduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
| | - Gabriela Carrasco-Puga
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
| | - Francisca M. Castillo
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile; (F.M.C.); (A.A.-M.)
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), 8331150 Santiago, Chile
| | - Anita Arenas-M
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile; (F.M.C.); (A.A.-M.)
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), 8331150 Santiago, Chile
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, Chile;
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21
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Sharma R, Mahanty B, Mishra R, Joshi RK. Genome wide identification and expression analysis of pepper C 2H 2 zinc finger transcription factors in response to anthracnose pathogen Colletotrichum truncatum. 3 Biotech 2021; 11:118. [PMID: 33747699 PMCID: PMC7933328 DOI: 10.1007/s13205-020-02601-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022] Open
Abstract
Although, the C2H2 zinc finger (ZF) family of plant transcription factors have been implicated in multiple biological processes, they are yet to be characterized in the economically important chilli pepper (Capsicum annuum). In this study, a total of 79 C2H2 ZF genes were identified in the pepper genome. Phylogenetic analysis categorized the pepper C2H2 ZF (CaZF) members into five subfamilies each with unique conserved domains and functions. Genomic organization revealed that CaZF genes have variable number of introns consistent with the characteristics defined by the evolutionary analysis. Segmental duplication-based purifying selection contributed to the expansion of CaZF genes in pepper. Additionally, 11 CaZF genes were identified as targets for 38 miRNAs indicating their role in post-transcriptional silencing-mediated genetic regulation. Gene expression analysis revealed that 18 CaZF genes were differentially expressed post-infection with the anthrocnose pathogen Colletotrichum truncatum, uncovering their potential function in pepper response to biotic stresses. Moreover, CaZFs were significantly induced post-treatment with methyl jasmonate and ethylene indicating their role in defense signaling. Notably, the MeJA responsive cis-elements were detected in the promoter regions of majority of CaZF genes, suggesting that CaZFs may be implicated in defense-responsive signal cross talking. Additionally, 18 CaZF genes were differentially expressed under drought and heat treatment, indicating their involvement in plant response to abiotic stresses. Overall, a comprehensive analysis of CaZF gene family in pepper provided significant insights into the understanding of C2H2 ZF-mediated stress regulation network, which would benefit the genetic improvement of pepper and other allied plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02601-x.
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Affiliation(s)
- Richa Sharma
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
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22
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Lu Y, Zeng J, Liu Q. The Rice miR396-GRF-GIF-SWI/SNF Module: A Player in GA Signaling. FRONTIERS IN PLANT SCIENCE 2021; 12:786641. [PMID: 35087553 PMCID: PMC8786800 DOI: 10.3389/fpls.2021.786641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Rice Growth-Regulating Factors (GRFs) were originally identified to be gibberellin (GA)-induced, but the nature of GA induction has remained unknown because most reports thereafter focused on revealing their roles in growth-promoting activities. GRFs have the WRC (Trp, Arg, Cys) domain to target DNA and contain the QLQ (Gln, Leu, Gln) domain to interact with GRF-Interacting Factor (GIF), which recruits ATP-dependent DNA translocase Switch/Sucrose Non-fermenting (SWI/SNF) for chromatin remodeling. Both GRFs and GIFs exhibit transcriptional activities but GIFs lack a DNA-binding domain. So, GRFs act like a navigator in the GRF-GIF-SWI/SNF complex, determining when and where the complex should work on. The levels of most rice GRFs can be sensitively regulated by miR396, which responds to many developmental and environmental factors. Recent clues from several studies highlight the original question of how GRFs participate in GA signaling. DELLA (contain DELLA motif) protein plays dual roles in controlling the level of GRFs by regulating the level of miR396 and interacting with GRFs. Here we address the question of why this complex plays an essential role in controlling plant growth focusing on the action of GA signaling pivot, DELLA.
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Affiliation(s)
- Yuzhu Lu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- *Correspondence: Yuzhu Lu
| | - Jia Zeng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Qiaoquan Liu
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23
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Wang ST, Guo XF, Yao TS, Xuan YH. Indeterminate domain 3 negatively regulates plant erectness and the resistance of rice to sheath blight by controlling PIN-FORMED gene expressions. PLANT SIGNALING & BEHAVIOR 2020; 15:1809847. [PMID: 32842845 PMCID: PMC7588189 DOI: 10.1080/15592324.2020.1809847] [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: 07/23/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 05/31/2023]
Abstract
Plant architecture and disease resistance are the key factors that control the production of yield. However, the mechanism behind these factors is largely unknown. In this study, we identified that indeterminate domain 3 (IDD3) was obviously induced by inoculation of Rhizoctonia solani AG1-IA. Plants that overexpressed IDD3 (IDD3 OX) were more susceptible, while idd3 mutants showed a similar response to sheath blight disease compared with wild-type plants. Interestingly, IDD3 OX plants developed a wider tiller angle and exhibited altered shoot gravitropism, while idd3 knock-out mutants showed no visible morphological differences compared with the wild-type plants. IDD3 is ubiquitously expressed in different tissues and stages, and the IDD3 transcript was induced by exogenously applied auxin. Expression of the PIN-FORMED (PIN) and Aux/IAA genes was altered in IDD3 OX compared with wild-type plants. Furthermore, IDD3 OX plants are sensitive to auxin and the polar auxin transporter inhibitor N-1-naphthylphalamic acid (NPA). Further yeast-one hybrid, chromatin immunoprecipitation (ChIP) and transient assays revealed that IDD3 directly represses PIN1b via promoter binding. Inoculation with R. solani indicated that PIN1b RNAi plants are more susceptible to sheath blight disease (ShB) compared with the wild-type. Taken together, our analyses suggest that IDD3 controls plant architecture and the resistance of rice to ShB via the regulation of PIN auxin transporter genes.
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Affiliation(s)
- Si Ting Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xiao Fan Guo
- School of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Ting Shan Yao
- Citrus Research Institute, Southwest University, Chongqing, China
| | - Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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24
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Liao X, Wang L, Zhu S, Zheng F, Yang C. Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato (Solanum lycopersicum). J Appl Genet 2020; 62:1-15. [PMID: 33034011 DOI: 10.1007/s13353-020-00587-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/20/2020] [Accepted: 09/09/2020] [Indexed: 01/22/2023]
Abstract
C2H2 zinc finger proteins (ZFPs) play essential roles in leaf morphogenesis and floral development, as well as heat stress response and trichome formation, which activate or inhibit gene transcription mainly through interactions with nucleic acids, such as single-strand DNA, RNA binding or RNA/DNA bidirectional binding, and protein interaction. Single C2H2 ZFPs is the subfamily of ZFPs, but little of single C2H2 ZFP family is known in tomato. In this study, we identified 30 single ZFP genes in tomato using bioinformatics-based methods. Gene structures, phylogeny, conserved motifs, cis-element of promoter, chromosomal localization, gene duplication, and expression patterns of these single C2H2 ZFP genes were analyzed. Sequence analysis showed that most single C2H2 ZFP genes possessed only one exon, except for SlC1-liZFP1 and SlC1-liZFP2. These single C2H2 ZFP genes were asymmetrically distributed on 10 chromosomes, excluding 2 and 12 chromosomes. In addition, 24 of these genes were predicated to have experienced segmental duplication. Cis-element prediction indicated that many important elements were located in the putative promoter regions, like light and gibberellic acid (GA)-responsive elements. The expression profiles of these genes in different tissues and various hormones and stress treatment were further analyzed. Many genes were lowly expressed in all tissues, whereas some were specifically expressed in certain tissues, like SlC1-liZFP2 in young leaves, and SlC1-liZFP15 in fruits. Furthermore, these genes could also be induced by several hormones and stresses, including IAA, ETH, GA, cold, and drought. This study sets a good foundation for further characterizing the biological roles of single C2H2 ZFP genes in tomato.
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Affiliation(s)
- Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Wang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shunhua Zhu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Zhang T, Tan M, Geng L, Li J, Xiang Y, Zhang B, Zhao Y. New insight into comprehensive analysis of INDETERMINATE DOMAIN (IDD) gene family in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:547-556. [PMID: 32912488 DOI: 10.1016/j.plaphy.2020.06.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
The INDETERMINATE DOMAIN (IDD) transcription factor (TF), as a family of plant-specific zinc-finger proteins, regulates a variety of development processes and abiotic stresses in plants. IDD genes have been identified and characterized in other plants, however, the rice IDD family genes have not been investigated at genome-wide. In this study, 15 OsIDD genes were identified in rice genome and phylogenetically classified into two groups. Conserved motifs and potential interaction protein analysis about OsIDD proteins were carried out. Exon-intron structures, cis-acting elements and expression profiles of OsIDD genes were also examined. Exon-intron structures analysis revealed that overall structures of OsIDD genes were relatively conserved although they contained different numbers of introns. Cis-acting elements analysis suggested that most OsIDD gene transcripts could be induced by various abiotic stresses and phytohormones. The expression patterns of OsIDD genes were detected by qRT-PCR under cold and drought conditions, and by exogenous auxin (2,4-D), gibberellin (GA3), and abscisic acid (ABA) treatments, respectively. The results showed that the OsIDDs might play essential roles under abiotic stresses and hormone responses. Distinct expression profiles in tissues/organs suggested that OsIDDs might be involved in different development processes in rice. More interestingly, the prediction of protein-protein interactions (PPIs) revealed OsIDDs could cooperate with some histone modifiers. Yeast two-hybrid assays were performed and confirmed it. Collectively, these results provide a foundation for further elucidation on the molecular mechanisms of OsIDD genes and advance our understanding of their biological function in rice.
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Affiliation(s)
- Ting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Mingfang Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jiajia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Bang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China.
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26
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Prochetto S, Reinheimer R. Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms. ANNALS OF BOTANY 2020; 126:85-101. [PMID: 32206771 PMCID: PMC7304464 DOI: 10.1093/aob/mcaa052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
INTRODUCTION The Indeterminate Domain (IDD) proteins are a plant-specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, but the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail. METHODS In this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes. KEY RESULTS We identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, but all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns. CONCLUSIONS IDDs were present in the last common ancestor of Streptophyta. On land, IDDs duplicated extensively, leading to ten lineages. Later, IDDs were recruited by angiosperms where they diversified greatly in number, C-terminal and expression patterns. Interestingly, such diversification occurred during the evolution of novel traits of the plant body. This study provides a solid framework of the orthology relationships of green land plant IDD transcription factors, thus increasing the accuracy of orthologue identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.
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Affiliation(s)
- Santiago Prochetto
- Fellow of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), FBCB, Santa Fe, Argentina
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
| | - Renata Reinheimer
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), FBCB, Santa Fe, Argentinaand
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
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27
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Gene Regulation via the Combination of Transcription Factors in the INDETERMINATE DOMAIN and GRAS Families. Genes (Basel) 2020; 11:genes11060613. [PMID: 32498388 PMCID: PMC7349898 DOI: 10.3390/genes11060613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/29/2022] Open
Abstract
INDETERMINATE DOMAIN (IDD) family proteins are plant-specific transcription factors. Some Arabidopsis IDD (AtIDD) proteins regulate the expression of SCARECROW (SCR) by interacting with GRAS family transcription factors SHORT-ROOT (SHR) and SCR, which are involved in root tissue formation. Some AtIDD proteins regulate genes involved in the synthesis (GA3ox1) or signaling (SCL3) of gibberellic acid (GA) by interacting with DELLA proteins, a subfamily of the GRAS family. We analyzed the DNA binding properties and protein–protein interactions of select AtIDD proteins. We also investigated the transcriptional activity of the combination of AtIDD and GRAS proteins (AtIDD proteins combined with SHR and SCR or with REPRESSOR of ga1-3 (RGA)) on the promoters of SCR,SCL3, and GA3ox1 by conducting a transient assay using Arabidopsis culture cells. Our results showed that the SCR promoter could be activated by the IDD and RGA complexes and that the SCL3 and GA3ox1 promoters could be activated by the IDD, SHR, and SCR complexes, indicating the possibility that these complexes regulate and consequently coordinate the expression of genes involved in GA synthesis (GA3ox1), GA signaling (SCL3), and root formation (SCR).
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Li SF, Allen PJ, Napoli RS, Browne RG, Pham H, Parish RW. MYB-bHLH-TTG1 Regulates Arabidopsis Seed Coat Biosynthesis Pathways Directly and Indirectly via Multiple Tiers of Transcription Factors. PLANT & CELL PHYSIOLOGY 2020; 61:1005-1018. [PMID: 32154880 DOI: 10.1093/pcp/pcaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
MYB-bHLH-WDR (MBW) transcription factor (TF) complexes regulate Arabidopsis seed coat development including mucilage and tannin biosynthesis. The R2R3 MYBs MYB5, MYB23 and TRANSPARENT TESTA2 (TT2) participate in the MBW complexes with the WD-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1). These complexes regulate GLABRA2 (GL2) and TTG2 expression in developing seeds. Microarray transcriptome analysis of ttg1-1- and wild-type (Ler) developing seeds identified 246 TTG1-regulated genes, which include all known metabolic genes of the tannin biosynthetic pathway. The first detailed TTG1-dependent metabolic pathways could be proposed for the biosynthesis of mucilage, jasmonic acid (JA) and cuticle including wax ester in developing seeds. We also assigned many known and previously uncharacterized genes to the activation/inactivation of hormones, plant immunity and nutrient transport. The promoters of six cuticle pathway genes were active in developing seeds. Expression of 11 genes was determined in the developing seeds of the combinatorial mutants of MYB5, MYB23 and TT2, and in the combinatorial mutants of GL2, HOMEODOMAIN GLABROUS2 (HDG2) and TTG2. These six TFs positively co-regulated the expression of four repressor genes while three of the six TFs repressed the wax biosynthesis genes examined, suggesting that the three TFs upregulate the expression of these repressor genes, which, in turn, repress the wax biosynthesis genes. Chromatin immunoprecipitation analysis identified 21 genes directly regulated by MYB5 including GL2, HDG2, TTG2, four repressor genes and various metabolic genes. We propose a multi-tiered regulatory mechanism by which MBWs regulate tannin, mucilage, JA and cuticle biosynthetic pathways.
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Affiliation(s)
- Song Feng Li
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Patrick J Allen
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Ross S Napoli
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Richard G Browne
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Hanh Pham
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Roger W Parish
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
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Wang L, Yang Y, Zhang S, Che Z, Yuan W, Yu D. GWAS reveals two novel loci for photosynthesis-related traits in soybean. Mol Genet Genomics 2020; 295:705-716. [PMID: 32166500 DOI: 10.1007/s00438-020-01661-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/27/2020] [Indexed: 10/24/2022]
Abstract
Photosynthesis plays an extremely important role throughout the life cycle of plants. Improving the photosynthetic rate is a major target for increasing crop productivity. This study was conducted to identify single nucleotide polymorphisms (SNPs) associated with the net photosynthetic rate (Pn), stomatal conductance (Cond), intercellular carbon dioxide concentration (Ci) and transpiration rate (Trmmol) through genome-wide association study (GWAS) and to inspect the relationships among these traits in soybean (Glycine max (L.) Merr.). A population of 219 soybean accessions was used in this research. A total of 12 quantitative trait loci (QTLs) associated with Pn, Cond, Ci and Trmmol were detected and distributed on chromosomes 1, 2, 6, 7, 9, 11, 12, 13, 15, 16, 18, and 19, and some of these QTL overlapped with previously reported QTLs. Furthermore, four candidate genes were identified, and there were significantly different expression levels between the high-light-efficiency accessions and low-light-efficiency accessions. These putative genes may participate in the regulation of photosynthesis through different metabolic pathways. Therefore, the associated novel QTLs and candidate genes detected in this study will provide a theoretical basis for genetic studies of photosynthesis and provide new avenues for crop improvement.
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Affiliation(s)
- Li Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuming Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuyu Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhijun Che
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Wenjie Yuan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
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Lu Y, Feng Z, Meng Y, Bian L, Xie H, Mysore KS, Liang J. SLENDER RICE1 and Oryza sativa INDETERMINATE DOMAIN2 Regulating OsmiR396 Are Involved in Stem Elongation. PLANT PHYSIOLOGY 2020; 182:2213-2227. [PMID: 31953375 PMCID: PMC7140908 DOI: 10.1104/pp.19.01008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/27/2019] [Indexed: 05/04/2023]
Abstract
GAs play key roles in controlling cell proliferation through the GIBBERELLIN INSENSITIVE DWARF1/DELLA-mediated pathway. However, how DELLA proteins affect downstream pathways is not well understood. Therefore, discovering the signaling events downstream of DELLAs is key to better understanding the roles of GAs in plant development. Here, we discovered that miR396 is regulated by SLENDER RICE1 (SLR1) in controlling cell proliferation. The positive response of rice (Oryza sativa) GROWTH-REGULATING FACTORs (OsGRFs) to GAs was found to be caused by a negative response of miR396 to GAs. miR396 acts downstream of SLR1 and upstream of GA-induced cell-cycle genes. Rice INDETERMINATE DOMAIN2 (OsIDD2) directly binds the promoter of OsmiR396a and can interact with SLR1 in vivo and in vitro. Rice lines overexpressing miR396a (miR396OE) or OsIDD2 (OsIDD2OE) displayed dwarfism resulting from higher abundance of miR396 RNA. However, the stem elongation of OsIDD2OE plants could be significantly stimulated by applying exogenous GA3, while that of miR396OE plants could not. Rice with OsIDD2 knocked down by RNA interference showed a slr1-like phenotype, in which the expression of miR396 was inhibited while its targets were enhanced. The protein levels of OsIDD2 were unaffected by GA in wild-type and OsIDD2OE plants, implying that OsIDD2 promotes the expression of miR396 and likely requires the coactivator of SLR1. Taken together, these results provided a close link between SLR1/OsIDD2 and GRFs via a negative regulator, miR396, and thus highlighted a molecular mechanism of GA-mediated cell proliferation in rice.
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Affiliation(s)
- Yuzhu Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, Jiangsu 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Zhen Feng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Yunlong Meng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Liying Bian
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Hong Xie
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | | | - Jiansheng Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
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Sun Q, Li DD, Chu J, Yuan DP, Li S, Zhong LJ, Han X, Xuan YH. Indeterminate Domain Proteins Regulate Rice Defense to Sheath Blight Disease. RICE (NEW YORK, N.Y.) 2020; 13:15. [PMID: 32140886 PMCID: PMC7058748 DOI: 10.1186/s12284-020-0371-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/28/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Loose Plant Architecture 1 (LPA1), an indeterminate domain (IDD) protein, exhibits almost no expression in the leaves, but the overexpression of LPA1 significantly increases the resistance of rice to sheath blight disease (ShB) via the activation of PIN-FORMED 1a (PIN1a). RESULTS In this study, we determined that Rhizoctonia solani infection significantly induced LPA1 expression in the leaves, and lpa1 was more susceptible to R. solani compared with the wild-type and revertant plants. In addition, infection with R. solani altered the expression of IDD3, IDD5, IDD10, and IDD13, and yeast two-hybrid, split-GFP, and coimmunoprecipitation assays showed that LPA1 interacts with IDD3 and IDD13. IDD13 RNAi plants were more susceptible, while IDD13 overexpressors were less susceptible to ShB compared with the wild-type. In parallel, idd3 exhibited no significant differences, while IDD3 overexpressors were more susceptible compared to the wild-type response to ShB. Additional chromatin-immunoprecipitation and electrophoretic mobility shift assay experiments indicated that IDD13 and IDD3 bound to the PIN1a promoter, and the transient assay indicated that IDD13 and IDD3 positively and negatively regulate PIN1a expression, respectively. Moreover, IDD13, IDD3, and LPA1 form a transcription factor complex that regulates PIN1a. A genetic study showed that the LPA1 repressor lines were similar to lpa1/IDD13 RNAi and were more susceptible than the lpa1 and IDD13 RNAi plants in response to ShB. The overexpression of IDD13 increased resistance to ShB in the lpa1 background. CONCLUSIONS Taken together, our analyses established that IDD3, IDD13, and LPA1 form a transcription factor complex to regulate the defense of rice against ShB possibly via the regulation of PIN1a.
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Affiliation(s)
- Qian Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Dan Dan Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jin Chu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - De Peng Yuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuang Li
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- College of Life Science, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Li Juan Zhong
- Microbial Research Institute, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
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Han G, Lu C, Guo J, Qiao Z, Sui N, Qiu N, Wang B. C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:115. [PMID: 32153617 PMCID: PMC7044346 DOI: 10.3389/fpls.2020.00115] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/24/2020] [Indexed: 05/04/2023]
Abstract
Abiotic stresses such as drought and salinity are major environmental factors that limit crop yields. Unraveling the molecular mechanisms underlying abiotic stress resistance is crucial for improving crop performance and increasing productivity under adverse environmental conditions. Zinc finger proteins, comprising one of the largest transcription factor families, are known for their finger-like structure and their ability to bind Zn2+. Zinc finger proteins are categorized into nine subfamilies based on their conserved Cys and His motifs, including the Cys2/His2-type (C2H2), C3H, C3HC4, C2HC5, C4HC3, C2HC, C4, C6, and C8 subfamilies. Over the past two decades, much progress has been made in understanding the roles of C2H2 zinc finger proteins in plant growth, development, and stress signal transduction. In this review, we focus on recent progress in elucidating the structures, functions, and classifications of plant C2H2 zinc finger proteins and their roles in abiotic stress responses.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chaoxia Lu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ziqi Qiao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Nianwei Qiu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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Liew LC, Narsai R, Wang Y, Berkowitz O, Whelan J, Lewsey MG. Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:700-715. [PMID: 31628689 DOI: 10.1111/tpj.14574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
The distinct functions of individual cell types require cells to express specific sets of genes. The germinating seed is an excellent model to study genome regulation between cell types since the majority of the transcriptome is differentially expressed in a short period, beginning from a uniform, metabolically inactive state. In this study, we applied laser-capture microdissection RNA-sequencing to small numbers of cells from the plumule, radicle tip and scutellum of germinating barley seeds every 8 h, over a 48 h time course. Tissue-specific gene expression was notably common; 25% (910) of differentially expressed transcripts in plumule, 34% (1876) in radicle tip and 41% (2562) in scutellum were exclusive to that organ. We also determined that tissue-specific storage of transcripts occurs during seed development and maturation. Co-expression of genes had strong spatiotemporal structure, with most co-expression occurring within one organ and at a subset of specific time points during germination. Overlapping and distinct enrichment of functional categories were observed in the tissue-specific profiles. We identified candidate transcription factors amongst these that may be regulators of spatiotemporal gene expression programs. Our findings contribute to the broader goal of generating an integrative model that describes the structure and function of individual cells within seeds during germination.
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Affiliation(s)
- Lim Chee Liew
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Yan Wang
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
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Lantican DV, Strickler SR, Canama AO, Gardoce RR, Mueller LA, Galvez HF. De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 (BETHESDA, MD.) 2019; 9:2377-2393. [PMID: 31167834 PMCID: PMC6686914 DOI: 10.1534/g3.119.400215] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/23/2022]
Abstract
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
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Affiliation(s)
- Darlon V Lantican
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | | | - Alma O Canama
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | - Roanne R Gardoce
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Hayde F Galvez
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
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Völz R, Rayapuram N, Hirt H. Phosphorylation regulates the activity of INDETERMINATE-DOMAIN (IDD/BIRD) proteins in response to diverse environmental conditions. PLANT SIGNALING & BEHAVIOR 2019; 14:e1642037. [PMID: 31314681 PMCID: PMC6768238 DOI: 10.1080/15592324.2019.1642037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/01/2019] [Accepted: 06/27/2019] [Indexed: 05/29/2023]
Abstract
INDETERMINATE-DOMAIN proteins (IDDs) belong to a diverse plant-specific family of transcriptional regulators that coordinate distinct functions during plant growth and development. The functions of several of these IDD members are transcriptionally regulated, but so far nothing is known about the regulation at the post-translational level in spite of the fact that post-translational modifications of these proteins have been reported in several large-scale proteomics studies. Recently, we showed that IDD4 is a repressor of basal immunity and its characteristic traits are predominantly determined by the phosphorylation at two distinct phosphorylation sites. This finding prompted us to comprehensively review phosphorylation of the various IDD members from the plethora of phosphoproteomics studies demonstrating the post-translational modification of IDDs at highly conserved sites under various experimental conditions. We reckon that the phosphorylation of IDDs is an underrated mechanistic aspect in their regulation and we postulate their importance in IDD/BIRD functioning.
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Affiliation(s)
- Ronny Völz
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources and Plant Immunity Research Center, Seoul National University, Seoul, Korea
| | - Naganand Rayapuram
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
- University of Vienna, Vienna, Austria
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Vï Lz R, Kim SK, Mi J, Mariappan KG, Siodmak A, Al-Babili S, Hirt H. A Chimeric IDD4 Repressor Constitutively Induces Immunity in Arabidopsis via the Modulation of Salicylic Acid and Jasmonic Acid Homeostasis. PLANT & CELL PHYSIOLOGY 2019; 60:1536-1555. [PMID: 30989238 DOI: 10.1093/pcp/pcz057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
INDETERMINATE DOMAIN (IDD)/BIRD proteins belong to a highly conserved plant-specific group of transcription factors with dedicated functions in plant physiology and development. Here, we took advantage of the chimeric repressor gene-silencing technology (CRES-T, SRDX) to widen our view on the role of IDD4/IMPERIAL EAGLE and IDD family members in plant immunity. The hypomorphic idd4SRDX lines are compromised in growth and show a robust autoimmune phenotype. Hormonal measurements revealed the concomitant accumulation of salicylic acid and jasmonic acid suggesting that IDDs are involved in regulating the metabolism of these biotic stress hormones. The analysis of immunity-pathways showed enhanced activation of immune MAP kinase-signaling pathways, the accumulation of hydrogen peroxide and spontaneous programmed cell death. The transcriptome of nonelicited idd4SRDX lines can be aligned to approximately 40% of differentially expressed genes (DEGs) in flg22-treated wild-type plants. The pattern of DEGs implies IDDs as pivotal repressors of flg22-dependent gene induction. Infection experiments showed the increased resistance of idd4SRDX lines to Pseudomonas syringae and Botrytis cinerea implying a function of IDDs in defense adaptation to hemibiotrophs and necrotrophs. Genome-wide IDD4 DNA-binding studies (DAP-SEQ) combined with DEG analysis of idd4SRDX lines identified IDD4-regulated functional gene clusters that contribute to plant growth and development. In summary, we discovered that the expression of idd4SRDX activates a wide range of defense-related traits opening up the possibility to apply idd4SRDX as a powerful tool to stimulate innate immunity in engineered crops.
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Affiliation(s)
- Ronny Vï Lz
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources and Plant Immunity Research Center, Seoul National University, Seoul, Korea
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jianing Mi
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anna Siodmak
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Al-Babili
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Universit� Paris-Sud, Universit� Evry, Universit� Paris-Saclay, B�timent 630, Orsay, France
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
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Pradit N, Rodriguez-Saona C, Kawash J, Polashock J. Phytoplasma Infection Influences Gene Expression in American Cranberry. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang T, Yang B, Guan Q, Chen X, Zhong Z, Huang W, Zhu W, Tian J. Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors. BMC PLANT BIOLOGY 2019; 19:198. [PMID: 31088368 PMCID: PMC6518806 DOI: 10.1186/s12870-019-1803-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/26/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Lonicera japonica Thunb. flower has been used for the treatment of various diseases for a long time and attracted many studies on its potential effects. Transcription factors (TFs) regulate extensive biological processes during plant development. As the restricted reports of L. japonica on TFs, our work was carried out to better understand the TFs' regulatory roles under different developmental stages in L. japonica. RESULTS In this study, 1316 TFs belonging to 52 families were identified from the transcriptomic data, and corresponding expression profiles during the L. japonica flower development were comprehensively analyzed. 917 (69.68%) TFs were differentially expressed. TFs in bHLH, ERF, MYB, bZIP, and NAC families exhibited obviously altered expression during flower growth. Based on the analysis of differentially expressed TFs (DETFs), TFs in MYB, WRKY, NAC and LSD families that involved in phenylpropanoids biosynthesis, senescence processes and antioxidant activity were detected. The expression of MYB114 exhibited a positive correlation with the contents of luteoloside; Positive correlation was observed among the expression of MYC12, chalcone synthase (CHS) and flavonol synthase (FLS), while negative correlation was observed between the expression of MYB44 and the synthases; The expression of LSD1 was highly correlated with the expression of SOD and the total antioxidant capacity, while the expression of LOL1 and LOL2 exhibited a negative correlation with them; Many TFs in NAC and WRKY families may be potentially involved in the senescence process regulated by hormones and reactive oxygen species (ROS). The expression of NAC19, NAC29, and NAC53 exhibited a positive correlation with the contents of ABA and H2O2, while the expression of WRKY53, WRKY54, and WRKY70 exhibited a negative correlation with the contents of JA, SA and ABA. CONCLUSIONS Our study provided a comprehensive characterization of the expression profiles of TFs during the developmental stages of L. japonica. In addition, we detected the key TFs that may play significant roles in controlling active components biosynthesis, antioxidant activity and flower senescence in L. japonica, thereby providing valuable insights into the molecular networks underlying L. japonica flower development.
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Affiliation(s)
- Tantan Wang
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Bingxian Yang
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, 310018 People’s Republic of China
| | - Qijie Guan
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Xi Chen
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Zhuoheng Zhong
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Wei Huang
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Wei Zhu
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Jingkui Tian
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027 People’s Republic of China
- Zhejiang-Malaysia Joint Research Center for Traditional Medicine, Zhejiang University, Hangzhou, 310027 People’s Republic of China
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Kumar M, Le DT, Hwang S, Seo PJ, Kim HU. Role of the INDETERMINATE DOMAIN Genes in Plants. Int J Mol Sci 2019; 20:ijms20092286. [PMID: 31075826 PMCID: PMC6539433 DOI: 10.3390/ijms20092286] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Dung Thi Le
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
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Su X, Meng T, Zhao Y, Li G, Cheng X, Abdullah M, Sun X, Cai Y, Lin Y. Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear ( Pyrus bretschneideri). PeerJ 2019; 7:e6628. [PMID: 30941270 PMCID: PMC6440465 DOI: 10.7717/peerj.6628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 12/12/2022] Open
Abstract
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Tiankai Meng
- School of Life Sciences and Technology, TongJi University, Shanghai, China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Xu Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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41
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Staszak AM, Rewers M, Sliwinska E, Klupczynska EA, Pawlowski TA. DNA synthesis pattern, proteome, and ABA and GA signalling in developing seeds of Norway maple (Acer platanoides). FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:152-164. [PMID: 32172757 DOI: 10.1071/fp18074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/13/2018] [Indexed: 06/10/2023]
Abstract
Mature seeds of Norway maple exhibit desiccation tolerance and deep physiological dormancy. Flow cytometry, proteomics, and immunodetection have been combined to investigate seed development of this species. DNA content analysis revealed that cell cycle/endoreduplication activity differs between seed organs and developmental stages. In the embryo axis, the proportion of the nuclei with the highest DNA content (4C) increases at the beginning of maturation (17 weeks after flowering; WAF), and then is stable until the end of maturation, to increase again after drying. In cotyledons, during maturation endopolyploid nuclei (8C) occur and the intensity of endoreduplication increases up to 21 WAF, and then is stable until development is completed. In dry mature seeds, the proportion of 4C nuclei is high, and reaches 36% in the embryo axis and 52% in cotyledons. Proteomic studies revealed that energy and carbon metabolism, fatty acid biosynthesis, storage and antioxidant proteins are associated with seed development. Study of the ABI5 protein, a transcription factor involved in ABA signalling, and the RGL2 protein, a repressor of the GA signalling indicates that the highest accumulation of these proteins occurs in fully-matured and dried seeds. It is suggested that this increase in accumulation can be associated with completion of maturation, mainly with desiccation and dormancy acquisition.
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Affiliation(s)
- Aleksandra M Staszak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Monika Rewers
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Avenue. 7, 85-789 Bydgoszcz, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Avenue. 7, 85-789 Bydgoszcz, Poland
| | - Ewelina A Klupczynska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Tomasz A Pawlowski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
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42
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Golz JF, Allen PJ, Li SF, Parish RW, Jayawardana NU, Bacic A, Doblin MS. Layers of regulation - Insights into the role of transcription factors controlling mucilage production in the Arabidopsis seed coat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:179-192. [PMID: 29807590 DOI: 10.1016/j.plantsci.2018.04.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 05/12/2023]
Abstract
A polysaccharide-rich mucilage is released from the seed coat epidermis of numerous plant species and has been intensively studied in the model plant Arabidopsis. This has led to the identification of a large number of genes involved in the synthesis, secretion and modification of cell wall polysaccharides such as pectin, hemicellulose and cellulose being identified. These genes include a small network of transcription factors (TFs) and transcriptional co-regulators, that not only regulate mucilage production, but epidermal cell differentiation and in some cases flavonoid biosynthesis in the internal endothelial layer of the seed coat. Here we focus on the function of these regulators and propose a simplified model where they are assigned to a hierarchical gene network with three regulatory levels (tiers) as a means of assisting in the interpretation of the complexity. We discuss limitations of current methodologies and highlight some of the problems associated with defining the function of TFs, particularly those that perform different functions in adjacent layers of the seed coat. We suggest approaches that should provide a more accurate picture of the function of transcription factors involved with mucilage production and release.
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Affiliation(s)
- John F Golz
- School of BioSciences, University of Melbourne, Royal Parade, Parkville, VIC 3010, Australia.
| | - Patrick J Allen
- Department of Animal, Plant and Soil Sciences, AgriBio Centre, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Song F Li
- Department of Animal, Plant and Soil Sciences, AgriBio Centre, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Roger W Parish
- Department of Animal, Plant and Soil Sciences, AgriBio Centre, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Nadeeka U Jayawardana
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Monika S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
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43
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Coelho CP, Huang P, Lee DY, Brutnell TP. Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants. TRENDS IN PLANT SCIENCE 2018; 23:66-78. [PMID: 29056440 DOI: 10.1016/j.tplants.2017.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 05/27/2023]
Abstract
The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C4 kranz anatomy, with implications for the engineering of C4 traits into C3 crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C4 photosynthesis and other developmental processes.
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Affiliation(s)
- Carla P Coelho
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA. http://twitter.com/coelhopcarla%20
| | - Pu Huang
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Dong-Yeon Lee
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Thomas P Brutnell
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA; Laboratory website: https://www.brutnelllab.org/.
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44
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45
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Wang DZ, Jin YN, Ding XH, Wang WJ, Zhai SS, Bai LP, Guo ZF. Gene Regulation and Signal Transduction in the ICE-CBF-COR Signaling Pathway during Cold Stress in Plants. BIOCHEMISTRY (MOSCOW) 2017; 82:1103-1117. [PMID: 29037131 DOI: 10.1134/s0006297917100030] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Low temperature is an abiotic stress that adversely affects the growth and production of plants. Resistance and adaptation of plants to cold stress is dependent upon the activation of molecular networks and pathways involved in signal transduction and the regulation of cold-stress related genes. Because it has numerous and complex genes, regulation factors, and pathways, research on the ICE-CBF-COR signaling pathway is the most studied and detailed, which is thought to be rather important for cold resistance of plants. In this review, we focus on the function of each member, interrelation among members, and the influence of manipulators and repressors in the ICE-CBF-COR pathway. In addition, regulation and signal transduction concerning plant hormones, circadian clock, and light are discussed. The studies presented provide a detailed picture of the ICE-CBF-COR pathway.
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Affiliation(s)
- Da-Zhi Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.
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46
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Van De Velde K, Ruelens P, Geuten K, Rohde A, Van Der Straeten D. Exploiting DELLA Signaling in Cereals. TRENDS IN PLANT SCIENCE 2017; 22:880-893. [PMID: 28843766 DOI: 10.1016/j.tplants.2017.07.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/13/2017] [Accepted: 07/29/2017] [Indexed: 05/04/2023]
Abstract
The spectacular yield increases in rice and wheat during the green revolution were partly realized by reduced gibberellin (GA) synthesis or sensitivity, both causing the accumulation of DELLA proteins. Although insights into the regulation of plant growth and development by DELLA proteins advanced rapidly in arabidopsis (Arabidopsis thaliana), DELLA-mediated regulation of downstream responses in cereals has received little attention to date. Furthermore, translating this research from arabidopsis to cereals is challenging given their different growth patterns and our phylogenetic analysis which reveals that DELLA-related DGLLA proteins exist in cereals but not in arabidopsis. Therefore, understanding the molecular basis of DELLA function in cereals holds great potential to improve yield. In this review, we propose to extend the focus of DELLA functional research to cereals, and highlight the appropriate tools that are now available to achieve this.
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Affiliation(s)
- Karel Van De Velde
- R&D Innovation Center, Bayer CropScience, Technologiepark 38, Ghent, Belgium; Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, Belgium
| | - Philip Ruelens
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, Belgium
| | - Koen Geuten
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, Belgium
| | - Antje Rohde
- R&D Innovation Center, Bayer CropScience, Technologiepark 38, Ghent, Belgium; Equal contributions
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, Belgium; Equal contributions; ORCID ID 0000-0002-7755-1420.
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47
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Pereira Lima JJ, Buitink J, Lalanne D, Rossi RF, Pelletier S, da Silva EAA, Leprince O. Molecular characterization of the acquisition of longevity during seed maturation in soybean. PLoS One 2017; 12:e0180282. [PMID: 28700604 PMCID: PMC5507495 DOI: 10.1371/journal.pone.0180282] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/13/2017] [Indexed: 11/18/2022] Open
Abstract
Seed longevity, defined as the ability to remain alive during storage, is an important agronomic factor. Poor longevity negatively impacts seedling establishment and consequently crop yield. This is particularly problematic for soybean as seeds have a short lifespan. While the economic importance of soybean has fueled a large number of transcriptome studies during embryogenesis and seed filling, the mechanisms regulating seed longevity during late maturation remain poorly understood. Here, a detailed physiological and molecular characterization of late seed maturation was performed in soybean to obtain a comprehensive overview of the regulatory genes that are potentially involved in longevity. Longevity appeared at physiological maturity at the end of seed filling before maturation drying and progressively doubled until the seeds reached the dry state. The increase in longevity was associated with the expression of genes encoding protective chaperones such as heat shock proteins and the repression of nuclear and chloroplast genes involved in a range of chloroplast activities, including photosynthesis. An increase in the raffinose family oligosaccharides (RFO)/sucrose ratio together with changes in RFO metabolism genes was also associated with longevity. A gene co-expression network analysis revealed 27 transcription factors whose expression profiles were highly correlated with longevity. Eight of them were previously identified in the longevity network of Medicago truncatula, including homologues of ERF110, HSF6AB, NFXL1 and members of the DREB2 family. The network also contained several transcription factors associated with auxin and developmental cell fate during flowering, organ growth and differentiation. A transcriptional transition occurred concomitant with seed chlorophyll loss and detachment from the mother plant, suggesting the activation of a post-abscission program. This transition was enriched with AP2/EREBP and WRKY transcription factors and genes associated with growth, germination and post-transcriptional processes, suggesting that this program prepares the seed for the dry quiescent state and germination.
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Affiliation(s)
- Juliana Joice Pereira Lima
- Faculdade de Ciências Agronômicas, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, São Paulo State, Brazil
- Institut de Recherche en Horticulture et Semences, INRA, Agrocampus Ouest, Université d’Angers, SFR QUASAV, Beaucouzé, France
| | - Julia Buitink
- Institut de Recherche en Horticulture et Semences, INRA, Agrocampus Ouest, Université d’Angers, SFR QUASAV, Beaucouzé, France
| | - David Lalanne
- Institut de Recherche en Horticulture et Semences, INRA, Agrocampus Ouest, Université d’Angers, SFR QUASAV, Beaucouzé, France
| | - Rubiana Falopa Rossi
- Faculdade de Ciências Agronômicas, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, São Paulo State, Brazil
- Institut de Recherche en Horticulture et Semences, INRA, Agrocampus Ouest, Université d’Angers, SFR QUASAV, Beaucouzé, France
| | - Sandra Pelletier
- Institut de Recherche en Horticulture et Semences, INRA, Agrocampus Ouest, Université d’Angers, SFR QUASAV, Beaucouzé, France
| | | | - Olivier Leprince
- Institut de Recherche en Horticulture et Semences, INRA, Agrocampus Ouest, Université d’Angers, SFR QUASAV, Beaucouzé, France
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Abstract
The biological activity and geographical distribution of honey bees is strongly temperature-dependent, due to their ectothermic physiology. In China, the endemic Apis cerana cerana exhibits stronger cold hardiness than Western honey bees, making the former species important pollinators of winter-flowering plants. Although studies have examined behavioral and physiological mechanisms underlying cold resistance in bees, data are scarce regarding the exact molecular mechanisms. Here, we investigated gene expression in A. c. cerana under two temperature treatments, using transcriptomic analysis to identify differentially expressed genes (DEGs) and relevant biological processes, respectively. Across the temperature treatments, 501 DEGs were identified. A gene ontology analysis showed that DEGs were enriched in pathways related to sugar and amino acid biosynthesis and metabolism, as well as calcium ion channel activity. Additionally, heat shock proteins, zinc finger proteins, and serine/threonine-protein kinases were differentially expressed between the two treatments. The results of this study provide a general digital expression profile of thermoregulation genes responding to cold hardiness in A. c. cerana. Our data should prove valuable for future research on cold tolerance mechanisms in insects, and may be beneficial in breeding efforts to improve bee hardiness.
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49
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Li Y, Dai C, Hu C, Liu Z, Kang C. Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:164-176. [PMID: 27997733 DOI: 10.1111/tpj.13462] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/23/2016] [Accepted: 12/14/2016] [Indexed: 05/21/2023]
Abstract
Alternative splicing (AS) is a key post-transcriptional regulatory mechanism, yet little information is known about its roles in fruit crops. Here, AS was globally analyzed in the wild strawberry Fragaria vesca genome with RNA-seq data derived from different stages of fruit development. The AS landscape was characterized and compared between the single-molecule, real-time (SMRT) and Illumina RNA-seq platform. While SMRT has a lower sequencing depth, it identifies more genes undergoing AS (57.67% of detected multiexon genes) when it is compared with Illumina (33.48%), illustrating the efficacy of SMRT in AS identification. We investigated different modes of AS in the context of fruit development; the percentage of intron retention (IR) is markedly reduced whereas that of alternative acceptor sites (AA) is significantly increased post-fertilization when compared with pre-fertilization. When all the identified transcripts were combined, a total of 66.43% detected multiexon genes in strawberry undergo AS, some of which lead to a gain or loss of conserved domains in the gene products. The work demonstrates that SMRT sequencing is highly powerful in AS discovery and provides a rich data resource for later functional studies of different isoforms. Further, shifting AS modes may contribute to rapid changes of gene expression during fruit set.
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Affiliation(s)
- Yongping Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chungen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongchi Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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50
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Deng L, Li L, Zhang S, Shen J, Li S, Hu S, Peng Q, Xiao J, Wu C. Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice. PLoS Genet 2017; 13:e1006642. [PMID: 28234896 PMCID: PMC5345856 DOI: 10.1371/journal.pgen.1006642] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/10/2017] [Accepted: 02/17/2017] [Indexed: 11/19/2022] Open
Abstract
The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants. Previously, we cloned Rice Indeterminate 1 (RID1), which acts as the master switch for the transition from the vegetative to reproductive phase in rice. Although the photoperiod pathway of RID1 inducing expression of the florigen genes Hd3a and RFT1 via Ehd1 has been established, the alternative pathways for the essential flowering transition need to be further examined. Here, we identified a Suppressor of rid1 (SID1), which rescues the never-flowering phenotype of rid1. SID1 encodes an INDETERMINATE DOMAIN (IDD) transcription factor. Mutation in SID1 showed the delayed flowering phenotype. Gain-of-function of SID1, OsIDD1, or OsIDD6 could restore the rid1 to flowering. Further analyses showed SID1 and RID1 directly target the promoter regions of Hd3a and RFT1, two florigen genes in rice. Taken together, our results reveal an autonomous flowering pathway might be mediated by RID1, thereby controlling the phase transition from vegetative to reproductive development in rice. Transition from vegetative to reproductive phase is a critical developmental switch in the life cycle of higher plants. In rice, our previous work suggested Rice Indeterminate 1 (RID1) acts as the master switch for the transition to flowering. Mutation in RID1 results in a never-flowering phenotype. In order to uncover the molecular network regulated by RID1, a Suppressor of rid1 (SID1) was identified in this study. Both SID1 and RID1 encode a plant-specific INDETERMINATE DOMAIN (IDD) transcription factor. Overexpression of SID1, OsIDD1, or OsIDD6 could rescue the never-flowering phenotype of rid1. Molecular data indicate both SID1 and RID1 physically bind the promoters of the florigen genes Hd3a and RFT1 in rice. Thus, we propose that the transition to flowering could be regulated by RID1 through the autonomous pathway, in addition to the photoperiod pathway.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Lingmei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jianqiang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shaobo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Sifan Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Qiang Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- * E-mail:
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