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Deng H, Zhang Y, Manzoor MA, Sabir IA, Han B, Song C. Genome-scale identification, expression and evolution analysis of B-box members in Dendrobium huoshanense. Heliyon 2024; 10:e32773. [PMID: 38975129 PMCID: PMC11225821 DOI: 10.1016/j.heliyon.2024.e32773] [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: 12/10/2023] [Revised: 05/24/2024] [Accepted: 06/09/2024] [Indexed: 07/09/2024] Open
Abstract
B-box (BBX) proteins have been recognized as vital determinants in plant development, morphogenesis, and adaptive responses to a myriad of environmental stresses. These zinc-finger proteins play a pivotal role in various biological processes. Their influence spans photomorphogenesis, the regulation of flowering, and imparting resilience to a wide array of challenges, encompassing both biotic and abiotic factors. Chromosome localization, gene structure and conserved motifs, phylogenetic analysis, collinearity analysis, expression profiling, fluorescence quantitative analysis, and tobacco transient transformation methods were used for functional localization and expression pattern analysis of the DhBBX gene. A total of 23 DhBBX members were identified from Dendrobium huoshanense. Subsequent phylogenetic evaluations effectively segregated these genes into five discrete evolutionary subsets. The predictions of subcellular localizations revealed that all these proteins were localized in the nucleus. The genetic composition and patterns showed that the majority of these genes consisted of several exons, with a few variations that could be attributed to transposon insertion. A comprehensive analysis using qRT-PCR was conducted to unravel the expression patterns of these genes in D. huoshanense, with a specific concentration on their responses to various hormone treatments and cold stress. Subcellular localization reveals that DhBBX21 and DhBBX9 are located in the nucleus. Our results provide a deep comprehension of the complex regulatory mechanisms of BBXs in response to various environmental and hormonal stimuli. These discoveries encourage further detailed and focused investigations into the operational dynamics of the BBX gene family in a wider range of plant species.
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Affiliation(s)
- Hui Deng
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, 237012, China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 201109, China
| | - Irfan Ali Sabir
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bangxing Han
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, 237012, China
| | - Cheng Song
- Anhui Dabieshan Academy of Traditional Chinese Medicine, Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Luan, 237012, China
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Ahmad S, Khan K, Saleh IA, Okla MK, Alaraidh IA, AbdElgawad H, Naeem M, Ahmad N, Fahad S. TALE gene family: identification, evolutionary and expression analysis under various exogenous hormones and waterlogging stress in Cucumis sativus L. BMC PLANT BIOLOGY 2024; 24:564. [PMID: 38879470 PMCID: PMC11179211 DOI: 10.1186/s12870-024-05274-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND Three Amino acid Loop Extension (TALE) belongs to the homeobox group of genes that are important constituents of plant systems. The TALE gene family is instrumental not only in growth and development but also plays an essential role in regulating plant response to environmental adversaries. RESULTS In the present study, we isolated 21 CsTALE genes from the cucumber (Cucumis sativus L.) genome database. Bioinformatics tools were put in place to understand the structural and functional components of the CsTALE gene family. The evolutionary analysis dissected them into seven subclades (KNOX-I, KNOX-II, and BELL-I to BELL-V). The cis-acting elements in the promoter region of CsTALE genes disclosed that they are key regulators of hormonal and stress-related processes. Additionally, the STRING database advocated the concerting role of CsTALE proteins with other key transcription factors potent in plant developmental biology. The CsmiR319 and CsmiR167a-3p targeting the CsTALE15 and CsTALE16, respectively, further assert the importance of the CsTALE gene family posttranscriptional-related processes. Tissue-specific gene expression unfolded the fundamental involvement of CsTALE genes as they were expressed throughout the developmental stages. Under waterlogging stress, the CsTALE17 expressed significantly higher values in WL, WL-NAA, and WL-ETH but not in WL-MeJA-treated samples. CONCLUSIONS The present study reveals the evolution and functions of the CsTALE gene family in cucumber. Our work will provide a platform that will help future researchers address the issue of waterlogging stress in the Yangtze River Delta.
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Affiliation(s)
- Sheraz Ahmad
- College of Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, PR China.
| | - Khushboo Khan
- Faculty of Crop Production Sciences, The University of Agriculture Peshawar, Peshawar, Khyber Pakhtunkhwa, 25120, Pakistan
| | | | - Mohammad K Okla
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ibrahim A Alaraidh
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Shah Fahad
- Department of Agronomy, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, 23200, Pakistan.
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Jing XQ, Shi PT, Zhang R, Zhou MR, Shalmani A, Wang GF, Liu WT, Li WQ, Chen KM. Rice kinase OsMRLK63 contributes to drought tolerance by regulating reactive oxygen species production. PLANT PHYSIOLOGY 2024; 194:2679-2696. [PMID: 38146904 DOI: 10.1093/plphys/kiad684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/16/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023]
Abstract
Drought is a major adverse environmental factor that plants face in nature but the molecular mechanism by which plants transduce stress signals and further endow themselves with tolerance remains unclear. Malectin/malectin-like domains containing receptor-like kinases (MRLKs) have been proposed to act as receptors in multiple biological signaling pathways, but limited studies show their roles in drought-stress signaling and tolerance. In this study, we demonstrate OsMRLK63 in rice (Oryza sativa L.) functions in drought tolerance by acting as the receptor of 2 rapid alkalization factors, OsRALF45 and OsRALF46. We show OsMRLK63 is a typical receptor-like kinase that positively regulates drought tolerance and reactive oxygen species (ROS) production. OsMRLK63 interacts with and phosphorylates several nicotinamide adenine dinucleotide phosphate (NADPH) oxidases with the primarily phosphorylated site at Ser26 in the N-terminal of RESPIRATORY BURST OXIDASE HOMOLOGUE A (OsRbohA). The application of the 2 small signal peptides (OsRALF45/46) on rice can greatly alleviate the dehydration of plants induced by mimic drought. This function depends on the existence of OsMRLK63 and the NADPH oxidase-dependent ROS production. The 2 RALFs interact with OsMRLK63 by binding to its extracellular domain, suggesting they may act as drought/dehydration signal sensors for the OsMRLK63-mediated process. Our study reveals a OsRALF45/46-OsMRLK63-OsRbohs module which contributes to drought-stress signaling and tolerance in rice.
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Affiliation(s)
- Xiu-Qing Jing
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, Shanxi 030619, China
| | - Peng-Tao Shi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng-Ru Zhou
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Abdullah Shalmani
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gang-Feng Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Ting Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Qiang Li
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kun-Ming Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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Phosuwan S, Nounjan N, Theerakulpisut P, Siangliw M, Charoensawan V. Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways. FRONTIERS IN PLANT SCIENCE 2024; 15:1264909. [PMID: 38463565 PMCID: PMC10920293 DOI: 10.3389/fpls.2024.1264909] [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: 07/21/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.
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Affiliation(s)
- Sunadda Phosuwan
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Noppawan Nounjan
- Biodiversity and Environmental Management Division, International College, Khon Kaen University, Khon Kaen, Thailand
| | - Piyada Theerakulpisut
- Salt-tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Zhang L, Wang Z, Ji S, Zhu G, Dong Y, Li J, Jing Y, Jin S. Ferric reduction oxidase in Lilium pumilum affects plant saline-alkaline tolerance by regulating ROS homeostasis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108305. [PMID: 38241829 DOI: 10.1016/j.plaphy.2023.108305] [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: 07/14/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 01/21/2024]
Abstract
Ferric reduction oxidase (FRO) plays important roles in biotic and abiotic stress. However, the function of ferric reduction oxidase from Lilium pumilum in response to NaHCO3 is unknown. Here we report the functional characterization of ferric reduction oxidase 7 in Lilium pumilum (LpFRO7) in stresses. Under NaHCO3 stress, the LpFRO7 overexpression lines exhibited lower accumulation of reactive oxygen species (ROS), higher activities in antioxidant enzyme (CAT, SOD and POD) and ferrite reductase, resulting in improved tolerance compared to the wild type (WT). In order to determine the functional network of LpFRO7, it was confirmed by EMSA assays, Yeast one-hybrid assays and Dual luciferase reporter assays that LpbHLH115 transcription factor can bind to the promoter of LpFRO7. Yeast two-hybrid assays, BiFC, and LCI assays were performed to prove that LpFRO7 can interact with LpTrx. Combining these findings, we concluded that LpFRO7 affects plant saline-alkaline tolerance by regulating ROS homeostasis.
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Affiliation(s)
- Ling Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
| | - Zongying Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
| | - Shangwei Ji
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
| | - Guoqing Zhu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
| | - Yi Dong
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China; Aulin College, Northeast Forestry University, Harbin, Heilongjiang, China.
| | - Ji Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
| | - Yibo Jing
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China; Aulin College, Northeast Forestry University, Harbin, Heilongjiang, China.
| | - Shumei Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
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6
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Guan J, Zhang Z, Shi G. Genome-Wide Identification of the Ferric Chelate Reductase ( FRO) Gene Family in Peanut and Its Diploid Progenitors: Structure, Evolution, and Expression Profiles. PLANTS (BASEL, SWITZERLAND) 2024; 13:418. [PMID: 38337951 PMCID: PMC10857631 DOI: 10.3390/plants13030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
The ferric chelate reductase (FRO) family plays a vital role in metal ion homeostasis in a variety of locations in the plants. However, little is known about this family in peanut (Arachis hypogaea). This study aimed to identify FRO genes from the genomes of peanut and the two diploid progenitors (A. duranensis and A. ipaensis) and to analyze their gene/protein structures and evolution. In addition, transcriptional responses of AhFRO genes to Fe deficiency and/or Cu exposure were investigated in two peanut cultivars with different Fe deficiency tolerance (Silihong and Fenghua 1). A total of nine, four, and three FRO genes were identified in peanut, A. duranensis, and A. ipaensis, respectively, which were divided into three groups. Most AhFRO genes underwent WGD/segmental duplication, leading to the expansion of the AhFRO gene family. In general, clustered members share similar gene/protein structures. However, significant divergences occurred in AhFRO2 genes. Three out of five AhFRO2 genes were lowly expressed in all tissues under normal conditions, which may be beneficial for avoiding gene loss. Transcription analysis revealed that AhFRO2 and AhFRO7 genes might be involved in the reduction of Fe/Cu in plasma membranes and plastids, respectively. AhFRO8 genes appear to confer Fe reduction in the mitochondria. Moreover, Fe deficiency induced an increase of Cu accumulation in peanut plants in which AhFRO2.2/2.4/2.5 and FRO7.1/7.2 might be involved. Our findings provided new clues for further understanding the roles of AhFRO genes in the Fe/Cu interaction in peanut.
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Affiliation(s)
| | | | - Gangrong Shi
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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7
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Joshi G, Soe YP, Palanog A, Hore TK, Nha CT, Calayugan MI, Inabangan-Asilo MA, Amparado A, Pandey ID, Cruz PCS, Hernandez JE, Swamy BPM. Meta-QTL s and haplotypes for efficient zinc biofortification of rice. THE PLANT GENOME 2023; 16:e20315. [PMID: 36896580 DOI: 10.1002/tpg2.20315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Biofortification of rice with improved grain zinc (Zn) content is the most sustainable and cost-effective approach to address Zn malnutrition in Asia. Genomics-assisted breeding using precise and consistent Zn quantitative trait loci (QTLs), genes, and haplotypes can fast-track the development of Zn biofortified rice varieties. We conducted the meta-analysis of 155 Zn QTLs reported from 26 different studies. Results revealed 57 meta-QTLs with a significant reduction of 63.2% and 80% in the number and confidence interval of the Zn QTLs, respectively. Meta-quantitative trait loci (MQTLs) regions were found to be enriched with diverse metal homeostasis genes; at least 11 MQTLs were colocated with 20 known major genes involved in the production of root exudates, metal uptake, transport, partitioning, and loading into grains in rice. These genes were differentially expressed in vegetative and reproductive tissues, and a complex web of interactions were observed among them. We identified superior haplotypes and their combinations for nine candidate genes (CGs), and the frequency and allelic effects of superior haplotypes varied in different subgroups. The precise MQTLs with high phenotypic variance, CGs, and superior haplotypes identified in our study are useful for an efficient Zn biofortification of rice and to ensure Zn as an essential component of all the future rice varieties through mainstreaming of Zn breeding.
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Affiliation(s)
- Gaurav Joshi
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | | | - Tapas Kumer Hore
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Chau Thanh Nha
- Philippines Rice Research Institute, Muñoz, Nueva Ecija, Philippines
| | | | - Mary Ann Inabangan-Asilo
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Amery Amparado
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
| | - Indra Deo Pandey
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | | | - B P Mallikarjuna Swamy
- Rice Genetic Design and Validation Unit, International Rice Research Institute, Los Baños, Philippines
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Zhang H, Hu L, Du X, Shah AA, Ahmad B, Yang L, Mu Z. Response and Tolerance of Macleaya cordata to Excess Zinc Based on Transcriptome and Proteome Patterns. PLANTS (BASEL, SWITZERLAND) 2023; 12:2275. [PMID: 37375899 DOI: 10.3390/plants12122275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Macleaya cordata is a dominant plant of mine tailings and a zinc (Zn) accumulator with high Zn tolerance. In this study, M. cordata seedlings cultured in Hoagland solution were treated with 200 μmol·L-1 of Zn for 1 day or 7 days, and then, their leaves were taken for a comparative analysis of the transcriptomes and proteomes between the leaves of the control and Zn treatments. Differentially expressed genes included those that were iron (Fe)-deficiency-induced, such as vacuolar iron transporter VIT, ABC transporter ABCI17 and ferric reduction oxidase FRO. Those genes were significantly upregulated by Zn and could be responsible for Zn transport in the leaves of M. cordata. Differentially expressed proteins, such as chlorophyll a/b-binding proteins, ATP-dependent protease, and vacuolar-type ATPase located on the tonoplast, were significantly upregulated by Zn and, thus, could be important in chlorophyll biosynthesis and cytoplasm pH stabilization. Moreover, the changes in Zn accumulation, the production of hydrogen peroxide, and the numbers of mesophyll cells in the leaves of M. cordata were consistent with the expression of the genes and proteins. Thus, the proteins involved in the homeostasis of Zn and Fe are hypothesized to be the keys to the tolerance and accumulation of Zn in M. cordata. Such mechanisms in M. cordata can suggest novel approaches to genetically engineering and biofortifying crops.
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Affiliation(s)
- Hongxiao Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Linfeng Hu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinlong Du
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Assar Ali Shah
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Baseer Ahmad
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Yang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zhiying Mu
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
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Ren C, Luo G, Li X, Yao A, Liu W, Zhang L, Wang Y, Li W, Han D. MxFRO4 confers iron and salt tolerance through up-regulating antioxidant capacity associated with the ROS scavenging. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:154001. [PMID: 37187152 DOI: 10.1016/j.jplph.2023.154001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/19/2023] [Accepted: 05/01/2023] [Indexed: 05/17/2023]
Abstract
Iron is involved in various metabolic pathways of plants. Stress from iron deficiency and toxicity in the soil adversely affects plant growth. Therefore, studying the mechanism of iron absorption and transport by plants is of important for resistance to iron stress and to increase crop yield. In this study, Malus xiaojinensis (a Fe-efficient Malus plant) was used as research material. A ferric reduction oxidase (FRO) family gene member was cloned and named MxFRO4. The MxFRO4 encoded a protein of 697 amino acid residues with a predicted molecular weight of 78.54 kDa and a theoretical isoelectric point of 4.90. A subcellular localization assay showed that the MxFRO4 protein was localized on the cell membrane. The expression of MxFRO4 was enriched in immature leaves and roots of M. xiaojinensis, and was strongly affected by low-iron, high-iron, and salt treatments. After introduction of MxFRO4 into Arabidopsis thaliana, the iron and salt stress tolerance of transgenic A. thaliana was greatly improved. Under exposure to low-iron and high-iron stresses, the primary root length, seedling fresh weight, contents of proline, chlorophyll, and iron, and iron(III) chelation activity of the transgenic lines were significantly increased compared with the wild type. The contents of chlorophyll and proline, and the activities of the antioxidant enzymes superoxide dismutase, peroxidase, and catalase were significantly higher in transgenic A. thaliana overexpressing MxFRO4 under salt stress compared with the wild type, whereas the malondialdehyde content was decreased. These results suggest that MxFRO4 contributes to alleviating the effects of low-iron, high-iron, and salinity stresses in transgenic A. thaliana.
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Affiliation(s)
- Chuankun Ren
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Guijie Luo
- Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, 223800, PR China
| | - Xingguo Li
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Anqi Yao
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Wanda Liu
- Horticulture Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, 150040, PR China
| | - Lihua Zhang
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yu Wang
- Horticulture Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, 150040, PR China
| | - Wenhui Li
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, 150030, PR China.
| | - Deguo Han
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, 150030, PR China.
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10
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Feng Z, Ji S, Cui D. Integration of the Metabolomic and Transcriptome Analysis Reveals the Remarkable Compounds of G. bicolor Young and Mature Leaves under Different Iron Nutrient Conditions. Int J Mol Sci 2022; 23:ijms23031160. [PMID: 35163082 PMCID: PMC8835294 DOI: 10.3390/ijms23031160] [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: 12/18/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Gynura bicolor (Roxb. ex Willd.) DC. (G. bicolor) is a functional vegetable rich in iron (Fe) and widely grown in Asia (e.g., Japan and China). Because most Fe in the soil exists in the form of insoluble oxides or hydroxides, it is difficult for plants to obtain Fe from the soil. A comparative metabolomic and transcriptome study was carried out to investigate the effect of Fe deficiency on metabolite synthesis and gene expression in young and mature leaves of G. bicolor. Fe deficiency caused chlorosis and decreased the chlorophyll content in young leaves. The metabolomic results for young leaves showed that l-glutamate and 4-hydroxybutanoic acid lactone significantly increased and decreased, respectively. The transcriptome results showed that the expression levels of genes involved in ferric reduction oxidase 7 and 14-kDa proline-rich protein DC2.15-like were significantly upregulated and downregulated, respectively. However, Fe deficiency had little effect on mature leaves.
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Affiliation(s)
- Zhe Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; (Z.F.); (S.J.)
- Key Laboratory of on Site Processing Equipment for Agricultural Products, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Shuyu Ji
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; (Z.F.); (S.J.)
- Key Laboratory of on Site Processing Equipment for Agricultural Products, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Di Cui
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; (Z.F.); (S.J.)
- Key Laboratory of on Site Processing Equipment for Agricultural Products, 866 Yuhangtang Road, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-159-256-006-17
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Jing XQ, Li WQ, Zhou MR, Shi PT, Zhang R, Shalmani A, Muhammad I, Wang GF, Liu WT, Chen KM. Rice Carbohydrate-Binding Malectin-Like Protein, OsCBM1, Contributes to Drought-Stress Tolerance by Participating in NADPH Oxidase-Mediated ROS Production. RICE (NEW YORK, N.Y.) 2021; 14:100. [PMID: 34874506 PMCID: PMC8651890 DOI: 10.1186/s12284-021-00541-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
Carbohydrate-binding malectin/malectin-like domain-containing proteins (CBMs) are a recently identified protein subfamily of lectins that participates various functional bioprocesses in the animal, bacterial, and plant kingdoms. However, little is known the roles of CBMs in rice development and stress response. In this study, OsCBM1, which encodes a protein containing only one malectin-like domain, was cloned and characterized. OsCBM1 is localized in both the endoplasmic reticulum and plasma membrane. Its transcripts are dominantly expressed in leaves and could be significantly stimulated by a number of phytohormone applications and abiotic stress treatments. Overexpression of OsCBM1 increased drought tolerance and reactive oxygen species production in rice, whereas the knockdown of the gene decreased them. OsCBM1 physically interacts with OsRbohA, a NADPH oxidase, and the expression of OsCBM1 in osrbohA, an OsRbohA-knockout mutant, is significantly downregulated under both normal growth and drought stress conditions. Meanwhile, OsCBM1 can also physically interacts with OsRacGEF1, a specific guanine nucleotide exchange factor for the Rop/Rac GTPase OsRac1, and transient coexpression of OsCBM1 with OaRacGEF1 significantly enhanced ROS production. Further transcriptome analysis showed that multiple signaling regulatory mechanisms are involved in the OsCBM1-mediated processes. All these results suggest that OsCBM1 participates in NADPH oxidase-mediated ROS production by interacting with OsRbohA and OsRacGEF1, contributing to drought stress tolerance of rice. Multiple signaling pathways are likely involved in the OsCBM1-mediated stress tolerance in rice.
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Affiliation(s)
- Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
- Department of Biology, Taiyuan Normal University, Taiyuan, 030619 Shanxi China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng-Ru Zhou
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Peng-Tao Shi
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ran Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Gang-Feng Wang
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
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Wu D, He G, Tian W, Saleem M, Li D, Huang Y, Meng L, He Y, Liu Y, He T. OPT gene family analysis of potato (Solanum tuberosum) responding to heavy metal stress: Comparative omics and co-expression networks revealed the underlying core templates and specific response patterns. Int J Biol Macromol 2021; 188:892-903. [PMID: 34352321 DOI: 10.1016/j.ijbiomac.2021.07.183] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/02/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Oligopeptides transporter (OPT) can maintain intracellular metal homeostat, however, their evolutionary characteristics, as well as their expression patterns in heavy metal exposure, remain unclear. Compared with previous OPT family identification, we identified 94 OPT genes (including 21 in potato) in potato and 4 other plants by HMMER program based on OPT domain (PF03169) for the first time. Secondly, conserved and special OPTs were found through comprehensive analysis. Thirdly, spatio-temporal tissue specific expression patterns and co-expression frameworks of potato OPT genes under different heavy metal stress were constructed. These data can provide excellent gene resources for food security and soil remediation.
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Affiliation(s)
- Danxia Wu
- College of Agricultural, Guizhou University, Guiyang 550025, China.
| | - Guandi He
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering and College of Life Sciences Guizhou University, Guiyang 550025, China
| | - Weijun Tian
- College of Agricultural, Guizhou University, Guiyang 550025, China
| | - Muhammad Saleem
- Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical College, Lahore, Pakistan
| | - Dandan Li
- College of Agricultural, Guizhou University, Guiyang 550025, China
| | - Yun Huang
- College of Agricultural, Guizhou University, Guiyang 550025, China
| | - Lulu Meng
- College of Agricultural, Guizhou University, Guiyang 550025, China
| | - Yeqing He
- College of Agricultural, Guizhou University, Guiyang 550025, China
| | - Yao Liu
- College of Agricultural, Guizhou University, Guiyang 550025, China
| | - Tengbing He
- College of Agricultural, Guizhou University, Guiyang 550025, China; Institute of New Rural Development of Guizhou University, Guiyang 550025, China
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Shalmani A, Ullah U, Muhammad I, Zhang D, Sharif R, Jia P, Saleem N, Gul N, Rakhmanova A, Tahir MM, Chen KM, An N. The TAZ domain-containing proteins play important role in the heavy metals stress biology in plants. ENVIRONMENTAL RESEARCH 2021; 197:111030. [PMID: 33774015 DOI: 10.1016/j.envres.2021.111030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
TAZ (transcriptional coactivator with PDZ-binding) zinc finger domains, also known as transcription adaptor putative zinc finger domains, that control diverse function in plant growth and development. Here, in the present study, we evaluated the role of the TAZ domain-containing gene in response to various heavy metals. Initially, we found a total of 3, 7, 8, 9, 9, 9, 7, 14, 6, 10, and 6 proteins containing TAZ domain in stiff brome, millet, sorghum, potato, pepper, maize, rice, apple, peach, pear, and tomato genome that could trigger the plant resistance against various heavy metals, respectively. Various in-silico approaches were applied such as duplication, phylogenetic analysis, and gene structure, to understand the basic features of the TAZ domain-containing genes in plants. Gene expression analyses were also performed under heavy metals (Cr, Zn, Ni, Cd, Co, Fe, Mn, and Pb). The results of quantitative real-time PCR analysis indicated that the TAZ gene family members were differentially expressed under different heavy metals. We further characterized the functions of the TAZ domain-containing gene under the heavy metal stresses by overexpressing the OsTAZ4 gene in Arabidopsis. The TAZ genes could promote plant resistance against various heavy metals by interacting with OsMYB34 and OsFHA9 transcription factors. The results will contribute to elucidate the relationship of TAZ proteins with heavy metals stresses and also ascertain the biological function in plant growth and development.
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Affiliation(s)
- Abdullah Shalmani
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Uzair Ullah
- Department of Genetics, Hazara University, Manshera, KPK, Pakistan.
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China; College of Agronomy, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Dong Zhang
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, PR China.
| | - Peng Jia
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Noor Saleem
- College of Agronomy, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Nazish Gul
- Department of Genetics, Hazara University, Manshera, KPK, Pakistan.
| | - Aizhan Rakhmanova
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi Province, 712100, China.
| | - Muhammad Mobeen Tahir
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Na An
- College of Horticulture, Northwest A and F University, Yangling, Shaanxi Province, 712100, China; College of Life Sciences, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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14
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Ali M, Muhammad I, ul Haq S, Alam M, Khattak AM, Akhtar K, Ullah H, Khan A, Lu G, Gong ZH. The CaChiVI2 Gene of Capsicum annuum L. Confers Resistance Against Heat Stress and Infection of Phytophthora capsici. FRONTIERS IN PLANT SCIENCE 2020; 11:219. [PMID: 32174952 PMCID: PMC7057250 DOI: 10.3389/fpls.2020.00219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/12/2020] [Indexed: 05/08/2023]
Abstract
Extreme environmental conditions seriously affect crop growth and development, resulting in substantial reduction in yield and quality. However, chitin-binding proteins (CBP) family member CaChiVI2 plays a crucial role in eliminating the impact of adverse environmental conditions, such as cold and salt stress. Here, for the first time it was discovered that CaChiVI2 (Capana08g001237) gene of pepper (Capsicum annuum L.) had a role in resistance to heat stress and physiological processes. The full-length open-reading frame (ORF) of CaChiVI2 (606-bp, encoding 201-amino acids), was cloned into TRV2:CaChiVI2 vector for silencing. The CaChiVI2 gene carries heat shock elements (HSE, AAAAAATTTC) in the upstream region, and thereby shows sensitivity to heat stress at the transcriptional level. The silencing effect of CaChiVI2 in pepper resulted in increased susceptibility to heat and Phytophthora capsici infection. This was evident from the severe symptoms on leaves, the increase in superoxide (O2 -) and hydrogen peroxide (H2O2) accumulation, higher malondialdehyde (MDA), relative electrolyte leakage (REL) and lower proline contents compared with control plants. Furthermore, the transcript level of other resistance responsive genes was also altered. In addition, the CaChiIV2-overexpression in Arabidopsis thaliana showed mild heat and drought stress symptoms and increased transcript level of a defense-related gene (AtHSA32), indicating its role in the co-regulation network of the plant. The CaChiVI2-overexpressed plants also showed a decrease in MDA contents and an increase in antioxidant enzyme activity and proline accumulation. In conclusion, the results suggest that CaChiVI2 gene plays a decisive role in heat and drought stress tolerance, as well as, provides resistance against P. capsici by reducing the accumulation of reactive oxygen species (ROS) and modulating the expression of defense-related genes. The outcomes obtained here suggest that further studies should be conducted on plants adaptation mechanisms in variable environments.
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Affiliation(s)
- Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling, China
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Izhar Muhammad
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Saeed ul Haq
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Mukhtar Alam
- Department of Agriculture, The University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Mateen Khattak
- Department of Horticulture, The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Kashif Akhtar
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hidayat Ullah
- Department of Agriculture, The University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Gang Lu
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling, China
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15
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Shalmani A, Muhammad I, Sharif R, Zhao C, Ullah U, Zhang D, Jing XQ, Amin B, Jia P, Mobeen Tahir M, Xu Z, Chen KM, An N. Zinc Finger-Homeodomain Genes: Evolution, Functional Differentiation, and Expression Profiling Under Flowering-Related Treatments and Abiotic Stresses in Plants. Evol Bioinform Online 2019; 15:1176934319867930. [PMID: 31523124 PMCID: PMC6728664 DOI: 10.1177/1176934319867930] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/11/2019] [Indexed: 11/15/2022] Open
Abstract
Zinc finger-homeodomain (ZHD) proteins constitute a plant-specific transcription factor family that play important roles in plant growth, development, and stress responses. In this study, we investigated a total of 10, 17, and 31 ZHD gene members in the peach, Arabidopsis, and apple genome, respectively. The phylogenetic tree divided the identified ZHD genes into 4 subfamilies based on their domain organization, gene structure, and motif distribution with minor variations. The ZHD gene family members were unevenly distributed throughout in apple, peach, and Arabidopsis genomes. Segmental duplication was observed for 14 pairs of genes in apple. Transcript analysis found that ZHD genes mostly expressed in various tissues, particularly in leaves and flowers. Moreover, the transcript of most ZHD genes was significantly affected at different time points in response to various flowering-related exogenous hormones (sugar, gibberellin [GA], and 6-benzylaminopurine [6-BA]), signifying their possible role in the flowering induction in apple. Furthermore, the transcripts of CaZHD6, CaZHD7, CaZHD3, and CaZHD8 have induced in response to abiotic stresses including heat, drought, salt, and cold, indicating their possible involvement in response to abiotic stresses. Our research work systemically presents the different roles of ZHD genes. We believe that this study will provide a platform for future functional characterization of ZHD genes and to deeply unfold their roles in the regulation of flowering induction in plants.
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Affiliation(s)
- Abdullah Shalmani
- College of Horticulture, Northwest
A&F University, Yangling, China
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Rahat Sharif
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - CaiPing Zhao
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Uzair Ullah
- Department of Agriculture, Hazara
University, Mansehra, KPK, Pakistan
| | - Dong Zhang
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Bakht Amin
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Peng Jia
- College of Horticulture, Northwest
A&F University, Yangling, China
| | | | - Ze Xu
- College of Horticulture, Northwest
A&F University, Yangling, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
| | - Na An
- College of Horticulture, Northwest
A&F University, Yangling, China
- State Key Laboratory of Crop Stress
Biology in Arid Areas, College of Life Sciences, Northwest A&F University,
Yangling, China
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16
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Muhammad I, Li WQ, Jing XQ, Zhou MR, Shalmani A, Ali M, Wei XY, Sharif R, Liu WT, Chen KM. A systematic in silico prediction of gibberellic acid stimulated GASA family members: A novel small peptide contributes to floral architecture and transcriptomic changes induced by external stimuli in rice. JOURNAL OF PLANT PHYSIOLOGY 2019; 234-235:117-132. [PMID: 30784850 DOI: 10.1016/j.jplph.2019.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 05/08/2023]
Abstract
The GASA (GA-stimulated Arabidopsis) gene family is highly specific to plants, signifying a crucial role in plant growth and development. Herein, we retrieved 119 GASA genes in 10 different plant species in two major lineages (monocots and eudicots). Further, in the phylogenetic tree we classified these genes into four well-conserved subgroups. All the proteins contain a conserved GASA domain with similar characteristics and a highly specific 12-cysteine residue of the C-terminus position. According to the global microarray data and qRT-PCR based analysis, the OsGASA gene family was dominantly expressed in the seedling and transition phase of floral stages. Despite this, OsGASA genes profoundly contribute to rice grain size and length, whereas the highest abundance of transcript level was noticed in stage-2 (Inf 6, 3.0-cm-long spikelet) and stage-3 (Inf 7, 5.0-cm-long spikelet) under GA treatment during panicle formation. Additionally, the maximum expression level of these genes was recorded in response to GA and ABA in young seedlings. Further, in response to abiotic stresses, OsGASA1/8/10 was up- regulated by salt, OsGASA2/5/7 by drought, OsGASA3/6 by cold, and OsGASA4/9 by heat stress. With the exception of OsGASA4, the higher transcription levels of all the other GASA genes were induced by Cd and Cr metal stresses (8-10 fold changes) at various time points. Finally, the GO ontology analysis of GASAs revealed the biological involvement in the GA-mediated signaling pathway and abiotic stresses. Prominently, most of these proteins are localized in cellular components such as the cell wall and extracellular region, where the molecular functions such as ATP binding and protein binding were observed. These results imply that GASAs are significantly involved in rice panicle developmental stages, responses to external stimuli, and hormones.
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Affiliation(s)
- Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Meng-Ru Zhou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xiao-Yong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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17
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Shalmani A, Jing XQ, Shi Y, Muhammad I, Zhou MR, Wei XY, Chen QQ, Li WQ, Liu WT, Chen KM. Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants. BMC Genomics 2019; 20:27. [PMID: 30626335 PMCID: PMC6327500 DOI: 10.1186/s12864-018-5336-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background B-box (BBX) proteins play important roles in plant growth regulation and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses. Results In the present study we retrieved total 131 BBX members from five Poaceae species including 36 from maize, 30 from rice, 24 from sorghum, 22 from stiff brome, and 19 from Millet. All the BBX genes were grouped into five subfamilies on the basis of their phylogenetic relationships and structural features. The expression profiles of 12 OsBBX genes in different tissues were evaluated through qRT-PCR, and we found that most rice BBX members showed high expression level in the heading stage compared to seedling and booting stages. The expression of OsBBX1, OsBBX2, OsBBX8, OsBBX19, and OsBBX24 was strongly induced by abiotic stresses such as drought, cold and salt stresses. Furthermore, the expression of OsBBX2, OsBBX7, OsBBX17, OsBBX19, and OsBBX24 genes was up-regulated under GA, SA and MeJA hormones at different time points. Similarly, the transcripts level of OsBBX1, OsBBX7, OsBBX8, OsBBX17, and OsBBX19 genes were significantly affected by heavy metals such as Fe, Ni, Cr and Cd. Conclusion Change in the expression pattern of BBX members in response to abiotic, hormone and heavy metal stresses signifies their potential roles in plant growth and development and in response to multivariate stresses. The findings suggest that BBX genes could be used as potential genetic markers for the plants, particularly in functional analysis and determining their roles under multivariate stresses. Electronic supplementary material The online version of this article (10.1186/s12864-018-5336-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yi Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Meng-Ru Zhou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Xiao-Yong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Qiong-Qiong Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
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18
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Ali M, Luo DX, Khan A, Haq SU, Gai WX, Zhang HX, Cheng GX, Muhammad I, Gong ZH. Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications. Int J Mol Sci 2018; 19:E2216. [PMID: 30060631 PMCID: PMC6121964 DOI: 10.3390/ijms19082216] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 11/26/2022] Open
Abstract
Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (Capsicum annuum L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. Phytophthora capsici post inoculation, most of the CaChi (CaChiI3, CaChiIII1, CaChiIII2, CaChiIII4, CaChiIII6, CaChiIII7, CaChiIV1, CaChiVI1 and CaChiVI2) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the CaChiIII2, CaChiIII7, CaChiVI1 and CaChiVI2 were upregulated by abiotic stress, while CaChiI1, CaChiIII7, CaChiIV1 and CaChiIV2 responded to hormonal treatments. Furthermore, CaChiIV1-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.
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Affiliation(s)
- Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - De-Xu Luo
- Xuhuai Region Huaiyin Institute of Agricultural Sciences, Huaian 223001, China.
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Guo-Xin Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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