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Ercoli MF, Ramos PZ, Jain R, Pilotte J, Dong OX, Thompson T, Wells CI, Elkins JM, Edwards AM, Couñago RM, Drewry DH, Ronald PC. An open source plant kinase chemogenomics set. PLANT DIRECT 2022; 6:e460. [PMID: 36447653 PMCID: PMC9694430 DOI: 10.1002/pld3.460] [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: 06/17/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.
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Affiliation(s)
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - Rashmi Jain
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Joseph Pilotte
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Ty Thompson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Carrow I. Wells
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Jonathan M. Elkins
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
- Centre for Medicines DiscoveryUniversity of OxfordOxfordUK
| | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - David H. Drewry
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
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Yoo YH, Jiang X, Jung KH. An Abiotic Stress Responsive U-Box E3 Ubiquitin Ligase Is Involved in OsGI-Mediating Diurnal Rhythm Regulating Mechanism. PLANTS 2020; 9:plants9091071. [PMID: 32825403 PMCID: PMC7569774 DOI: 10.3390/plants9091071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022]
Abstract
The plant U-box (PUB) protein is the E3 ligase that plays roles in the degradation or post-translational modification of target proteins. In rice, 77 U-box proteins were identified and divided into eight classes according to the domain configuration. We performed a phylogenomic analysis by integrating microarray expression data under abiotic stress to the phylogenetic tree context. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) expression analyses identified that eight, twelve, and eight PUB family genes are associated with responses to drought, salinity, and cold stress, respectively. In total, 16 genes showed increased expression in response to three abiotic stresses. Among them, the expression of OsPUB2 in class II and OsPUB33, OsPUB39, and OsPUB41 in class III increased in all three abiotic stresses, indicating their involvement in multiple abiotic stress regulation. In addition, we identified the circadian rhythmic expression for three out of 16 genes responding to abiotic stress through meta-microarray expression data analysis. Among them, OsPUB4 is predicted to be involved in the rice GIGANTEA (OsGI)-mediating diurnal rhythm regulating mechanism. In the last, we constructed predicted protein-protein interaction networks associated with OsPUB4 and OsGI. Our analysis provides essential information to improve environmental stress tolerance mediated by the PUB family members in rice.
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Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members. 3 Biotech 2020; 10:139. [PMID: 32158635 DOI: 10.1007/s13205-020-2120-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/05/2020] [Indexed: 10/24/2022] Open
Abstract
APETALA2/Ethylene-Responsive transcription factors (AP2/ERF), with their multifunctional roles in plant development, hormone signaling and stress tolerance, are important candidates for engineering crop plants. Here, we report identification and analysis of gene structure, phylogenetic distribution, expression, chromosomal localization and cis-acting promoter analysis of AP2/ERF genes in the C4 crop plant sorghum. We identified 158 ERF genes in sorghum with 52 of them encoding dehydration-responsive binding elements (DREB) while 106 code for ERF subfamily proteins. Phylogenetic analysis organized sorghum ERF proteins into 11 distinct groups exhibiting clade-specific expansion. About 68% ERF genes have paralogs indicating gene duplications as major cause of expansion of ERF family in sorghum. Analysis of spatiotemporal expression patterns using publicly available data revealed their tissue/genotype-preferential accumulation. In addition, 40 ERF genes exhibited differential accumulation in response to heat and/or drought stress. About 25% of the segmental gene pairs and eleven tandem duplicated genes exhibited high correlation (> 0.7) in their expression patterns indicating genetic redundancy. Comparative phylogenomic analysis of sorghum ERFs with 74 genetically characterized ERF genes from other plant species provided significant clues to sorghum ERF functions. Overall data generated here provides an overview of evolutionary relationship among ERF gene family members in sorghum and with respect to previously characterized ERF genes from other plant species. This information will be instrumental in initiating functional genomic studies of ERF candidates in sorghum.
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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Pei W, Jain A, Ai H, Liu X, Feng B, Wang X, Sun Y, Xu G, Sun S. OsSIZ2 regulates nitrogen homeostasis and some of the reproductive traits in rice. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:51-60. [PMID: 30530203 DOI: 10.1016/j.jplph.2018.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
Small ubiquitin-related modifier (SUMO) is a post-translational modification of proteins that has important roles in plant growth and development as well as nutrition study. OsSIZ1, a SUMO E3 ligase in rice (Oryza sativa), exerts regulatory influence on nitrogen (N) homeostasis. Here, we investigated the biological function of OsSIZ2, a paralog of OsSIZ1, in the responses to nitrogen, anther dehiscence, and seed length using a reverse genetics approach. The expression of OsSIZ2 was increased during N deficiency. Under -N condition, total N concentration in the root of OsSIZ2-Ri plants and ossiz2 was significantly increased compared with wild type. Further, 15N-labelled uptake assay revealed the role of OsSIZ2 in acquisition and mobilization of N. Moreover, qRT-PCR analyses revealed that several genes involved in the maintenance of N homeostasis were altered in OsSIZ2 mutants. In addition, ossiz2 indicated obvious defects in anther dehiscence, pollen fertility, and seed set percentage. Interestingly, however, the seed length was longer in the mutant compared with wild type. Overall, these results suggest pivotal roles of OsSIZ2 in regulating homeostasis of N and different agronomic traits including anther and seed development.
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Affiliation(s)
- Wenxia Pei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Kant Kalwar NH-11C, Jaipur, India
| | - Hao Ai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Xiuli Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Bing Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Xiaowen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, China.
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Chandran AKN, Bhatnagar N, Yoo YH, Moon S, Park SA, Hong WJ, Kim BG, An G, Jung KH. Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles. PLANT MOLECULAR BIOLOGY 2018; 96:17-34. [PMID: 29086189 DOI: 10.1007/s11103-017-0675-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Nikita Bhatnagar
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sun-Ah Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
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Pei W, Jain A, Sun Y, Zhang Z, Ai H, Liu X, Wang H, Feng B, Sun R, Zhou H, Xu G, Sun S. OsSIZ2 exerts regulatory influences on the developmental responses and phosphate homeostasis in rice. Sci Rep 2017; 7:12280. [PMID: 28947784 PMCID: PMC5612973 DOI: 10.1038/s41598-017-10274-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023] Open
Abstract
OsSIZ1, a small ubiquitin-related modifier (SUMO) E3 ligase, exerts regulatory influences on the developmental responses and phosphate (Pi) homeostasis in rice (Oryza sativa). Whether paralogs OsSIZ1 and OsSIZ2 are functionally redundant or the latter regulates these traits independent of the former is not known. To determine this, in this study, OsSIZ2 was functionally characterized by employing reverse genetic approaches. Although the relative expression of OsSIZ2 was spatiotemporally regulated, it showed constitutive expression in root and leaf blade irrespective of Pi regime. Analysis of T-DNA insertion knockout (ossiz2) and RNAi-mediated knockdown (Ri1-3) mutants revealed positive influences on growth and developmental responses including yield-related traits. On the contrary, these mutants exhibited negative effects on the concentrations of Pi and total P in different tissues. The relative expression levels of some of the genes that are involved in Pi sensing and signaling cascades were differentially modulated in the mutants. Further, attenuation in the expression levels of OsSIZ2 in the roots of ossiz1 and relatively similar trend of the effects of the mutation in OsSIZ1 and OsSIZ2 on growth and development and total P concentration in different tissues suggested a prevalence of partial functional redundancy between these paralogs.
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Affiliation(s)
- Wenxia Pei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ajay Jain
- Amity Centre of Nano Biotechnology and Plant Nutrition, Kant Kalwar, NH-11C, Jaipur, 303002, India
| | - Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhantian Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Hao Ai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiuli Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Huadun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China.,Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bing Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Rui Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Hongmin Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China.
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