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Wei J, Li H, Huang X, Zhao Y, Ouyang L, Wei M, Wang C, Wang J, Lu G. Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard. PeerJ 2024; 12:e17661. [PMID: 38978758 PMCID: PMC11229683 DOI: 10.7717/peerj.17661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/08/2024] [Indexed: 07/10/2024] Open
Abstract
Leaf mustard (Brassica juncea L. Czern & Coss), an important vegetable crop, experiences pronounced adversity due to seasonal drought stress, particularly at the seed germination stage. Although there is partial comprehension of drought-responsive genes, the role of long non-coding RNAs (lncRNAs) in adjusting mustard's drought stress response is largely unexplored. In this study, we showed that the drought-tolerant cultivar 'Weiliang' manifested a markedly lower base water potential (-1.073 MPa vs -0.437 MPa) and higher germination percentage (41.2% vs 0%) than the drought-susceptible cultivar 'Shuidong' under drought conditions. High throughput RNA sequencing techniques revealed a significant repertoire of lncRNAs from both cultivars during germination under drought stress, resulting in the identification of 2,087 differentially expressed lncRNAs (DELs) and their correspondingly linked 12,433 target genes. It was noted that 84 genes targeted by DEL exhibited enrichment in the photosynthesis pathway. Gene network construction showed that MSTRG.150397, a regulatory lncRNA, was inferred to potentially modulate key photosynthetic genes (Psb27, PetC, PetH, and PsbW), whilst MSTRG.107159 was indicated as an inhibitory regulator of six drought-responsive PIP genes. Further, weighted gene co-expression network analysis (WGCNA) corroborated the involvement of light intensity and stress response genes targeted by the identified DELs. The precision and regulatory impact of lncRNA were verified through qPCR. This study extends our knowledge of the regulatory mechanisms governing drought stress responses in mustard, which will help strategies to augment drought tolerance in this crop.
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Affiliation(s)
- Jinxing Wei
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Haibo Li
- Shaoguan University, Shaoguan, China
| | - Xiaoer Huang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Yongguo Zhao
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Lejun Ouyang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Mingken Wei
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Chun Wang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Junxia Wang
- South China Agricultural University, Guangzhou, China
| | - Guangyuan Lu
- Guangdong University of Petrochemical Technology, Maoming, China
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Li G, Manzoor MA, Wang G, Huang S, Ding X, Abdullah M, Zhang M, Song C. Comparative analysis of POD genes and their expression under multiple hormones in Pyrus bretschenedri. BMC Genom Data 2024; 25:41. [PMID: 38711007 DOI: 10.1186/s12863-024-01229-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Class III peroxidase (POD) enzymes play vital roles in plant development, hormone signaling, and stress responses. Despite extensive research on POD families in various plant species, the knowledge regarding the POD family in Chinese pear (Pyrus bretschenedri) is notably limited. RESULTS We systematically characterized 113 POD family genes, designated as PbPOD1 to PbPOD113 based on their chromosomal locations. Phylogenetic analysis categorized these genes into seven distinct subfamilies (I to VII). The segmental duplication events were identified as a prevalent mechanism driving the expansion of the POD gene family. Microsynteny analysis, involving comparisons with Pyrus bretschenedri, Fragaria vesca, Prunus avium, Prunus mume and Prunus persica, highlighted the conservation of duplicated POD regions and their persistence through purifying selection during the evolutionary process. The expression patterns of PbPOD genes were performed across various plant organs and diverse fruit development stages using transcriptomic data. Furthermore, we identified stress-related cis-acting elements within the promoters of PbPOD genes, underscoring their involvement in hormonal and environmental stress responses. Notably, qRT-PCR analyses revealed distinctive expression patterns of PbPOD genes in response to melatonin (MEL), salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA), reflecting their responsiveness to abiotic stress and their role in fruit growth and development. CONCLUSIONS In this study, we investigated the potential functions and evolutionary dynamics of PbPOD genes in Pyrus bretschenedri, positioning them as promising candidates for further research and valuable indicators for enhancing fruit quality through molecular breeding strategies.
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Affiliation(s)
- Guohui Li
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guoyu Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Shiping Huang
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Xiaoyuan Ding
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Muhammad Abdullah
- Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia
| | - Ming Zhang
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China.
| | - Cheng Song
- Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China.
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Fatima S, Khan MO, Iqbal N, Iqbal MM, Qamar H, Imtiaz M, Hundleby P, Wei Z, Ahmad N. Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species. Metabolites 2024; 14:179. [PMID: 38668307 PMCID: PMC11052333 DOI: 10.3390/metabo14040179] [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: 02/20/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
Brassica crops are well known for the accumulation of glucosinolates-secondary metabolites crucial for plants' adaptation to various stresses. Glucosinolates also functioning as defence compounds pose challenges to food quality due to their goitrogenic properties. Their disruption leaves plants susceptible to insect pests and diseases. Hence, a targeted reduction in seed glucosinolate content is of paramount importance to increase food acceptance. GLUCOSINOLATE TRANSPORTERS (GTRs) present a promising avenue for selectively reducing glucosinolate concentrations in seeds while preserving biosynthesis elsewhere. In this study, 54 putative GTR protein sequences found in Brassica were retrieved, employing Arabidopsis GTR1 and GTR2 templates. Comprehensive bioinformatics analyses, encompassing gene structure organization, domain analysis, motif assessments, promoter analysis, and cis-regulatory elements, affirmed the existence of transporter domains and stress-related regulatory elements. Phylogenetic analysis revealed patterns of conservation and divergence across species. Glucosinolates have been shown to increase under stress conditions, indicating a potential role in stress response. To elucidate the role of GTRs in glucosinolate transportation under NaCl stress in two distinct Brassica species, B. juncea and B. napus, plants were subjected to 0, 100, or 200 mM NaCl. Based on the literature, key GTR genes were chosen and their expression across various plant parts was assessed. Both species displayed divergent trends in their biochemical profiles as well as glucosinolate contents under elevated salt stress conditions. Statistical modelling identified significant contributors to glucosinolate variations, guiding the development of targeted breeding strategies for low-glucosinolate varieties. Notably, GTR2A2 exhibited pronounced expressions in stems, contributing approximately 52% to glucosinolate content variance, while GTR2B1/C2 displayed significant expression in flowers. Additionally, GTR2A1 and GTR1A2/B1 demonstrated noteworthy expression in roots. This study enhances our understanding of glucosinolate regulation under stress conditions, offering avenues to improve Brassica crop quality and resilience.
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Affiliation(s)
- Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Muhammad Omar Khan
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Nadia Iqbal
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Muhammad Mudassar Iqbal
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Huma Qamar
- Oilseeds Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan;
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Muhammad Imtiaz
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
| | - Penny Hundleby
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
| | - Zhengyi Wei
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute for Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan; (S.F.); (M.O.K.); (N.I.); (M.M.I.); (M.I.)
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Ma L, Tao X, Wang W, Jiao J, Pu Y, Yang G, Liu L, Fang Y, Wu J, Sun W. Genome-wide identification of RNA recognition motif (RRM1) in Brassica rapa and functional analysis of RNA-binding protein (BrRBP) under low-temperature stress. BMC PLANT BIOLOGY 2023; 23:621. [PMID: 38057714 DOI: 10.1186/s12870-023-04639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND The RNA recognition motif (RRM) is primarily engaged in the processing of mRNA and rRNA following gene transcription as well as the regulation of RNA transport; it is critical in preserving RNA stability. RESULTS In this study, we identified 102 members of the RRM1 gene family in Brassica rapa, which were dispersed across 10 chromosomes with the ninth chromosome being the most extensively distributed. The RRM1 gene family members of Brassica rapa and Arabidopsis thaliana were grouped into 14 subclades (I-XIV) using phylogenetic analysis. Moreover, the results of transcriptome analysis and RT-qPCR indicated that the expression of Brapa05T000840 was upregulated in the cultivars 'Longyou 7' and 'Longyou 99' following exposure to cold stress at a temperature of 4 °C for 24 h. The levels of expression in the leaves and growth cones of the 'Longyou 7' variety were found to be significantly higher than those observed in the 'Longyou 99' variety under conditions of low temperature and NaCl stress. It illustrates the involvement of the RRM1 gene in the physiological response to both low temperature and salt stress. In addition, it was observed that the survival rate of transgenic BrRBP (Brapa05T000840) Arabidopsis thaliana plants was notably higher compared to that of wild-type plants when subjected to varying durations of low temperature treatment. Furthermore, the expression of the BrRBP gene in transgenic plants exhibited an upward trend as the duration of low temperature treatment increased, reaching its peak at 24 h. The in-vivo enzymatic activity of reactive oxygen species-scavenging enzymes were found to be significantly elevated in comparison to wild-type plants, suggesting that the BrRBP gene may enhance the cold tolerance of Arabidopsis thaliana. CONCLUSIONS This study offers a significant foundation for comprehending the regulation mechanism of the RRM1 gene family in winter Brassica rapa subjected to cold stress, as well as for finding key genes associated with cold resistance.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaolei Tao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jintang Jiao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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Khan V, Umar S, Iqbal N. Synergistic action of Pseudomonas fluorescens with melatonin attenuates salt toxicity in mustard by regulating antioxidant system and flavonoid profile. PHYSIOLOGIA PLANTARUM 2023; 175:e14092. [PMID: 38148187 DOI: 10.1111/ppl.14092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 12/28/2023]
Abstract
Salt stress is an alarming abiotic stress that reduces mustard growth and yield. To attenuate salt toxicity effects, plant growth-promoting rhizobacteria (PGPR) offers a sustainable approach. Among the various PGPR, Pseudomonas fluorescens (P. fluorescens NAIMCC-B-00340) was chosen for its salt tolerance (at 100 mM NaCl) and for exhibiting various growth-promoting activities. Notably, P. fluorescens can produce auxin, which plays a role in melatonin (MT) synthesis. Melatonin is a pleiotropic molecule that acts as an antioxidant to scavenge reactive oxygen species (ROS), resulting in stress reduction. Owing to the individual role of PGPR and MT in salt tolerance, and their casual nexus, their domino effect was investigated in Indian mustard under salt stress. The synergistic action of P. fluorescens and MT under salt stress conditions was found to enhance the activity of antioxidative enzymes and proline content as well as promote the production of secondary metabolites. This led to reduced oxidative stress following effective ROS scavenging, maintained photosynthesis, and improved growth. In mustard plants treated with MT and P. fluorescens under salt stress, eight flavonoids showed significant increase. Kaempferol and cyanidin showed the highest concentrations and are reported to act as antioxidants with protective functions under stress. Thus, we can anticipate that strategies involved in their enhancement could provide a better adaptive solution to salt toxicity in mustard plants. In conclusion, the combination of P. fluorescens and MT affected antioxidant metabolism and flavonoid profile that could be used to mitigate salt-induced stress and bolster plant resilience.
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Affiliation(s)
- Varisha Khan
- Department of Botany, School of chemical and life sciences, Jamia Hamdard, New Delhi, India
| | - Shahid Umar
- Department of Botany, School of chemical and life sciences, Jamia Hamdard, New Delhi, India
| | - Noushina Iqbal
- Department of Botany, School of chemical and life sciences, Jamia Hamdard, New Delhi, India
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Chen H, Zhang S, Du K, Kang X. Genome-wide identification, characterization, and expression analysis of CCT transcription factors in poplar. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108101. [PMID: 37922648 DOI: 10.1016/j.plaphy.2023.108101] [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: 07/29/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
The CCT [CONSTANS (CO), CO-like, and TIMING OF CAB EXPRESSION1 (TOC1)] gene family is involved in photoperiodic flowering and adaptation to different environments. In this study, 39 CCT family genes from the poplar genome were identified and characterized, including 18 COL, 7 PRR, and 14 CMF TFs. Phylogenetics analysis showed that the PtrCCT gene family could be classified into five classes (Classes I-V) that have close relationships with Arabidopsis thaliana. Eight pairs of PtrCCTs had collinear relationships through interchromosomal synteny analysis in poplar, suggesting segmental duplication played a vital role in the expansion of the poplar CCT gene family. Besides, synteny analyses of the CCT members among poplar and different species provided more clues for PtrCCT gene family evolution. Cis-acting elements in the promoters of PtrCCTs predicted their involvement in light responses, hormone responses, biotic/abiotic stress responses, and plant growth and development. Eight members of the PpnCCT gene family were differentially expressed in the apical buds and leaves of triploid poplar compared to diploids. We then focused on PpnCCT39 upregulated in triploid poplars and showed that PpnCCT39 was localized in the nucleus, chloroplast, and cytoplasm and could interact with CLPP1 in the chloroplast. Overexpression of PpnCCT39 in poplar increased chlorophyll contents and enhanced photosynthetic rate. This study provided comprehensive information for the CCT gene family and set up a basis for its function identification in poplar.
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Affiliation(s)
- Hao Chen
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Shuwen Zhang
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Kang Du
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- National Key Laboratory of Forest Tree Genetics and Breeding, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
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7
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Zheng L, Assane Hamidou A, Zhao X, Ouyang Z, Lin H, Li J, Zhang X, Luo K, Chen Y. Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis. iScience 2023; 26:107801. [PMID: 37954140 PMCID: PMC10638475 DOI: 10.1016/j.isci.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.
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Affiliation(s)
- Linling Zheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Abdoulaye Assane Hamidou
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xuerui Zhao
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Zhiwei Ouyang
- HNU-ASU Joint International Tourism College, Hainan University, Haikou 570228, China
| | - Hongxin Lin
- Soil Fertilizer and Resources Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Junyi Li
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Kai Luo
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
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8
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Kim H, Woo OG, Kim JB, Yoon SY, Kim JS, Sul WJ, Hwang JY, Lee JH. Flavobacterium sp. strain GJW24 ameliorates drought resistance in Arabidopsis and Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1257137. [PMID: 37900757 PMCID: PMC10613084 DOI: 10.3389/fpls.2023.1257137] [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: 07/12/2023] [Accepted: 09/06/2023] [Indexed: 10/31/2023]
Abstract
Candidate strains that contribute to drought resistance in plants have been previously screened using approximately 500 plant growth-promoting rhizobacteria (PGPR) obtained from Gotjawal, South Korea, to further understand PGPR associated with plant drought tolerance. In this study, a selected PGPR candidate, Flavobacterium sp. strain GJW24, was employed to enhance plant drought tolerance. GJW24 application to Arabidopsis increased its survival rate under drought stress and enhanced stomatal closure. Furthermore, GJW24 promoted Arabidopsis survival under salt stress, which is highly associated with drought stress. GJW24 ameliorated the drought/salt tolerance of Brassica as well as Arabidopsis, indicating that the drought-resistance characteristics of GJW24 could be applied to various plant species. Transcriptome sequencing revealed that GJW24 upregulated a large portion of drought- and drought-related stress-inducible genes in Arabidopsis. Moreover, Gene Ontology analysis revealed that GJW24-upregulated genes were highly related to the categories involved in root system architecture and development, which are connected to amelioration of plant drought resistance. The hyper-induction of many drought/salt-responsive genes by GJW24 in Arabidopsis and Brassica demonstrated that the drought/salt stress tolerance conferred by GJW24 might be achieved, at least in part, through regulating the expression of the corresponding genes. This study suggests that GJW24 can be utilized as a microbial agent to offset the detrimental effects of drought stress in plants.
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Affiliation(s)
- Hani Kim
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - Og-Geum Woo
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - Ji Bin Kim
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - So-Young Yoon
- Department of Pharmacology and Neuroscience, Creighton University School of Medicine, Omaha, NE, United States
| | - Jong-Shik Kim
- Marine Industry Research Institute for East Sea Rim, Uljin, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Jee-Yeon Hwang
- Department of Pharmacology and Neuroscience, Creighton University School of Medicine, Omaha, NE, United States
| | - Jae-Hoon Lee
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
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9
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Waite JM, Kelly EA, Zhang H, Hargarten HL, Waliullah S, Altman NS, dePamphilis CW, Honaas LA, Kalcsits L. Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit. G3 (BETHESDA, MD.) 2023; 13:jkad120. [PMID: 37259608 PMCID: PMC10411604 DOI: 10.1093/g3journal/jkad120] [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: 12/20/2022] [Revised: 12/20/2022] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.
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Affiliation(s)
- Jessica M Waite
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Elizabeth A Kelly
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Huck Life Sciences Building, University Park, PA, 16802, USA
| | - Huiting Zhang
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
- Department of Horticulture, Washington State University, 251 Clark Hall, Pullman, WA, 99164, USA
| | - Heidi L Hargarten
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Sumyya Waliullah
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
- Department of Plant Pathology, University of Georgia, 2360 Rainwater Rd, Tifton, GA, 31798, USA
| | - Naomi S Altman
- Department of Statistics, The Huck Institutes of the Life Sciences, Pennsylvania State University, 312 Thomas Building, University Park, PA, 16802, USA
| | - Claude W dePamphilis
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Huck Life Sciences Building, University Park, PA, 16802, USA
| | - Loren A Honaas
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Lee Kalcsits
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
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10
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Wei J, Xu L, Shi Y, Cheng T, Tan W, Zhao Y, Li C, Yang X, Ouyang L, Wei M, Wang J, Lu G. Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107750. [PMID: 37210860 DOI: 10.1016/j.plaphy.2023.107750] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/14/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.
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Affiliation(s)
- Jinxing Wei
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Shi
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Tianfang Cheng
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenlan Tan
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yongguo Zhao
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Chunsheng Li
- Hubei Engineering University, Xiaogan, 432000, China
| | - Xinyu Yang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Lejun Ouyang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Mingken Wei
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Junxia Wang
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China.
| | - Guangyuan Lu
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China.
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11
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Li W, Zheng X, Cheng R, Zhong C, Zhao J, Liu TH, Yi T, Zhu Z, Xu J, Meksem K, Dai L, Liu S. Soybean ZINC FINGER PROTEIN03 targets two SUPEROXIDE DISMUTASE1s and confers resistance to Phytophthora sojae. PLANT PHYSIOLOGY 2023; 192:633-647. [PMID: 36782397 PMCID: PMC10152685 DOI: 10.1093/plphys/kiad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/22/2022] [Accepted: 01/19/2023] [Indexed: 05/03/2023]
Abstract
Phytophthora sojae causes Phytophthora root and stem rot disease of soybean (Glycine max), leading to huge annual yield loss worldwide, but resistance to Phytophthora sojae (Rps) genes remains elusive. Soybean cultivar "Yudou 29" is resistant to P. sojae strain PsMC1, and this study aimed to clone, identify, and characterize the Rps gene in Yudou 29 (RpsYD29) and clarify its functional mechanism. We map-based cloned RpsYD29 (ZINC FINGER PROTEIN03, GmZFP03) using the families of a cross between Yudou 29 and a P. sojae-susceptible soybean cultivar "Jikedou 2". P. sojae resistance of GmZFP03 was functionally validated by stable soybean genetic transformation and allele-phenotype association analysis. GmZFP03 was identified as a C2H2-type zinc finger protein transcription factor, showing 4 amino acid residue polymorphisms (V79F, G122-, G123-, and D125V) and remarkably different expression patterns between resistant and susceptible soybeans. Notably boosted activity and gene expression of superoxide dismutase (SOD) in resistant-type GmZFP03-expressed transgenic soybean, substantial enhancement of P. sojae resistance of wild-type soybean by exogenous SOD treatment, and GmZFP03 binding to and activation of 2 SOD1 (Glyma.03g242900 and Glyma.19g240400) promoters demonstrated the involvement of SOD1s in GmZFP03-mediated resistance to P. sojae strain PsMC1. Thus, this study cloned the soybean P. sojae-resistant GmZFP03, the product of which specifically targets 2 SOD1 promoters. GmZFP03 can be directly used for precise P. sojae-resistance soybean breeding.
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Affiliation(s)
- Wei Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Xiang Zheng
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Rong Cheng
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Chanjuan Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Jie Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Tyler H Liu
- College of Letters and Science, University of Wisconsin, Madison, WI 53706, USA
| | - Tuyong Yi
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Zhendong Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jieting Xu
- Wimi Biotechnology Co., Ltd, Changzhou 213000, P. R. China
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Shiming Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
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12
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Sarcheshmeh MK, Abedi A, Aalami A. Genome-wide survey of catalase genes in Brassica rapa, Brassica oleracea, and Brassica napus: identification, characterization, molecular evolution, and expression profiling of BnCATs in response to salt and cadmium stress. PROTOPLASMA 2023; 260:899-917. [PMID: 36495350 DOI: 10.1007/s00709-022-01822-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Catalase (CAT, EC 1.11.1.6), one of the most important antioxidant enzymes, can control excess levels of H2O2 produced under oxidative stress in plants. In this study, 16, 8, and 7 CAT genes in the genome of Brassica napus, B. rapa, and B. oleracea were identified, respectively. Phylogenetic studies showed that CATs could be divided into two main groups, each containing specific monocotyledon and dicotyledon subgroups. Motifs, gene structure, and intron phase of CATs in B. napus, Brassica rapa, and Brassica oleracea are highly conserved. Analysis of codon usage bias showed the mutation pressure and natural selection of the codon usage of CATs. Segmental duplication and polyploid were major factors in the expansion of this gene family in B. napus, and genes have experienced negative selection during evolution. Existence of hormones and stress-responsive cis-elements and identifying miRNA molecules affecting CATs showed that these genes are complexly regulated at the transcriptional and posttranscriptional levels. Based on RNA-seq data, CATs are divided into two groups; the first group has moderate and specific expression in flowers, leaves, stems, and roots, while the second group shows expression in most tissues. qRT-PCR analysis showed that the expression of these genes is dynamic and has a specific expression consistent with other CAT genes in response to salinity and cadmium (Cd) stresses. These results provide information for further investigation of the function of CAT genes in response to stresses and the development of tolerant plants.
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Affiliation(s)
- Monavar Kanani Sarcheshmeh
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Amin Abedi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Ali Aalami
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
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Verma D, Kaushal N, Balhara R, Singh K. Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111620. [PMID: 36738937 DOI: 10.1016/j.plantsci.2023.111620] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.
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Affiliation(s)
- Deepika Verma
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Nishant Kaushal
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Rinku Balhara
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Kashmir Singh
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India.
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14
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Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study. Antioxidants (Basel) 2023; 12:antiox12030726. [PMID: 36978974 PMCID: PMC10045841 DOI: 10.3390/antiox12030726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Akebia trifoliata is a newly domesticated perennial fruit tree, and the lack of molecular research on stress resistance seriously affects its genetic improvement and commercial value development. Superoxide dismutase (SOD) can effectively eliminate the accumulation of reactive oxygen species (ROS) during the rapid growth of plant organs under biotic and abiotic stresses, maintaining a steady state of physiological metabolism. In this study, 13 SODs consisting of two FeSODs (FSDs), four MnSODs (MSDs) and seven Cu/ZnSODs (CSDs) were identified in the A. trifoliata genome. Structurally, the phylogeny, intron–exon pattern and motif sequences within these three subfamilies show high conservation. Evolutionarily, segmental/wide genome duplication (WGD) and dispersed duplication form the current SOD profile of A. trifoliata. Weighted gene coexpression network analysis (WGCNA) revealed the metabolic pathways of nine (69.2%) SODs involved in fruit development, among which AktMSD4 regulates fruit development and AktCSD4 participates in the stress response. In addition, under the stress of multiple pathogens, six (46.6%) SODs were continuously upregulated in the rinds of resistant lines; of these, three SODs (AktMSD1, AktMSD2 and AktMSD3) were weakly or not expressed in susceptible lines. The results pave the way for theoretical research on SODs and afford the opportunity for genetic improvement of A. trifoliata.
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15
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Bui QTN, Ki JS. Two novel superoxide dismutase genes (CuZnSOD and MnSOD) in the toxic marine dinoflagellate Alexandrium pacificum and their differential responses to metal stressors. CHEMOSPHERE 2023; 313:137532. [PMID: 36509186 DOI: 10.1016/j.chemosphere.2022.137532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Superoxide dismutase (SOD) is an important antioxidant enzyme that is involved in the first line of defense against reactive oxygen species (ROS) within cells. Herein, we determined two novel CuZnSOD and MnSOD genes from the toxic marine dinoflagellate Alexandrium pacificum (designated as ApCuZnSOD and ApMnSOD) and characterized their structural features and phylogenetic affiliations. In addition, we examined the relative gene expression and ROS levels following exposure to heavy metals. ApCuZnSOD encoded 358 amino acids (aa) with two CuZnSOD-conserved domains. ApMnSOD encoded 203 aa that contained a mitochondrial-targeting signal and a MnSOD signature motif but missed an N-terminal domain. Phylogenetic trees showed that ApCuZnSOD clustered with other dinoflagellates, whereas ApMnSOD formed a clade with green algae and plants. Based on the 72-h median effective concentration (EC50), A. pacificum showed toxic responses in the order of Cu, Ni, Cr, Zn, Cd, and Pb. SOD expression levels dramatically increased after 6 h of Pb (≥6.5 times) and 48 h of Cu treatment (≥3.9 times). These results are consistent with the significant increase in ROS production in the A. pacificum exposed to Pb and Cu. These suggest that the two ApSODs are involved in the antioxidant defense system but respond differentially to individual metals.
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Affiliation(s)
- Quynh Thi Nhu Bui
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea.
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16
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Yu W, Kong G, Chao J, Yin T, Tian H, Ya H, He L, Zhang H. Genome-wide identification of the rubber tree superoxide dismutase ( SOD) gene family and analysis of its expression under abiotic stress. PeerJ 2022; 10:e14251. [PMID: 36312747 PMCID: PMC9610661 DOI: 10.7717/peerj.14251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Background The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H2O2 and O2. However, the SOD gene family is not reported in rubber trees. Methods Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs' promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for further studies on the functions of HbSOD genes in rubber trees and stress response mechanisms.
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Affiliation(s)
- Wencai Yu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China,Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Guanghong Kong
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Jinquan Chao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China
| | - Hai Tian
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Huajin Ya
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Ligang He
- Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China
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Niu YF, Li GH, Zheng C, Liu ZY, Liu J. Insights to the superoxide dismutase genes and its roles in Hevea brasiliensis under abiotic stress. 3 Biotech 2022; 12:274. [PMID: 36110566 PMCID: PMC9468202 DOI: 10.1007/s13205-022-03328-7] [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: 12/15/2021] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
The superoxide dismutase (SOD) protein significantly influences the development and growth of plants and their reaction to abiotic stresses. However, little is known about the characteristics of rubber tree SOD genes and their expression changes under abiotic stresses. The present study recognized 11 SOD genes in the rubber tree genome, including 7 Cu/ZnSODs, 2 MnSODs, and 2 FeSODs. Except for HbFSD1, SODs were scattered on five chromosomes. The phylogenetic analysis of SOD proteins in rubber trees and a few other plants demonstrated that the SOD proteins contained three major subgroups. Moreover, the genes belonging to the same clade contained similar gene structures, which confirmed their classification further. The extension of the SOD gene family in the rubber tree was mainly induced by the segmental duplication events. The cis-acting components analysis showed that HbSODs were utilized in many biological procedures. The transcriptomics data indicated that the phosphorylation of the C-terminal domain of RNA polymerase II might control the cold response genes through the CBF pathway and activate the SOD system to respond to cold stress. The qRT-PCR results showed that the expression of HbCSD1 was significantly downregulated under drought and salt stresses, which might dominate the adaption capability to different stresses. Additionally, salt promoted the expression levels of HbMSD1 and HbMSD2, exhibiting their indispensable role in the salinity reaction. The study results will provide a theoretical basis for deep research on HbSODs in rubber trees. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03328-7.
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Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Guo-Hua Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Zi-Yan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
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18
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Wang Z, Wu J, Sun Z, Jiang W, Liu Y, Tang J, Meng X, Su X, Wu L, Wang L, Guo X, Peng D, Xing S. ICP-MS based metallomics and GC-MS based metabolomics reveals the physiological and metabolic responses of Dendrobium huoshanense plants exposed to Fe 3O 4 nanoparticles. Front Nutr 2022; 9:1013756. [PMID: 36245500 PMCID: PMC9558897 DOI: 10.3389/fnut.2022.1013756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
It is found that the growth of Dendrobium huoshanense was dependent on Fe3O4, while the bioavailability of plants to ordinary Fe3O4 was low on the earth. In order to improve the growth, quality and yield of D. huoshanense, we used Fe3O4 NPs (100 or 200 mg/L) that was easily absorbed by plants as nano-fertilizer to hydroponically treat seedlings of D. huoshanense for 3 weeks. Fe3O4 NPs induced not only earlier flowering and increased sugar content and photosynthesis, but also stressed to plants, increased MDA content and related antioxidant enzymes activities. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) revealed that Fe3O4 NPs caused a significant accumulation of Fe and some other nutrient elements (Mn, Co, B, Mo) in stems of D. huoshanense. Metabolomics revealed that the metabolites were reprogrammed in D. huoshanense when under Fe3O4 NPs exposure. Fe3O4 NPs inhibited antioxidant defense-related pathways, demonstrating that Fe3O4 NPs have antioxidant capacity to protect D. huoshanense from damage. As the first study associating Fe3O4 NPs with the quality of D. huoshanense, it provided vital insights into the molecular mechanisms of how D. huoshanense responds to Fe3O4 NPs, ensuring the reasonable use of Fe3O4 NPs as nano-fertilizer.
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Affiliation(s)
- Zhaojian Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zongping Sun
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, China
| | - Jun Tang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, United States
| | - Xinglong Su
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Liping Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Longhai Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, China
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Shamloo-Dashtpagerdi R, Lindlöf A, Tahmasebi S. Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis. PHYSIOLOGIA PLANTARUM 2022; 174:e13790. [PMID: 36169653 DOI: 10.1111/ppl.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Melatonin is a master regulator of diverse biological processes, including plant's abiotic stress responses and tolerance. Despite the extensive information on the role of melatonin in response to abiotic stress, how plants regulate endogenous melatonin content under stressful conditions remains largely unknown. In this study, we computationally mined Expressed Sequence Tag (EST) libraries of salinity-exposed Chinese cabbage (Brassica rapa) to identify the most reliable differentially expressed miRNA and its target gene(s). In light of these analyses, we found that miR168a potentially targets a key melatonin biosynthesis gene, namely O-METHYLTRANSFERASE 1 (OMT1). Accordingly, molecular and physiochemical evaluations were performed in a separate salinity experiment using contrasting B. rapa genotypes. Then, the association between B. rapa salinity tolerance and changes in measured molecular and physiochemical characteristics was determined. Results indicated that the expression profiles of miR168a and OMT1 significantly differed between B. rapa genotypes. Moreover, the expression profiles of miR168a and OMT1 significantly correlated with more melatonin content, robust antioxidant activities, and better ion homeostasis during salinity stress. Our results suggest that miR168a plausibly mediates melatonin biosynthesis, mainly through the OMT1 gene, under salinity conditions and thereby contributes to the salinity tolerance of B. rapa. To our knowledge, this is the first report on the role of miR168a and OMT1 in B. rapa salinity response.
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Affiliation(s)
| | | | - Sirous Tahmasebi
- Seed and Plant Improvement Research Department, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Shiraz, Iran
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20
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Molecular Evolution and Functional Divergence of Stress-Responsive Cu/Zn Superoxide Dismutases in Plants. Int J Mol Sci 2022; 23:ijms23137082. [PMID: 35806085 PMCID: PMC9266695 DOI: 10.3390/ijms23137082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 12/25/2022] Open
Abstract
Superoxide dismutases (SODs), a family of antioxidant enzymes, are the first line of defense against oxidative damage and are ubiquitous in every cell of all plant types. The Cu/Zn SOD, one of three types of SODs present in plant species, is involved in many of the biological functions of plants in response to abiotic and biotic stresses. Here, we carried out a comprehensive analysis of the Cu/Zn SOD gene family in different plant species, ranging from lower plants to higher plants, and further investigated their organization, sequence features, and expression patterns in response to biotic and abiotic stresses. Our results show that plant Cu/Zn SODs can be divided into two subfamilies (group I and group II). Group II appeared to be conserved only as single- or low-copy genes in all lineages, whereas group I genes underwent at least two duplication events, resulting in multiple gene copies and forming three different subgroups (group Ia, group Ib, and group Ic). We also found that, among these genes, two important events—the loss of introns and the loss of and variation in signal peptides—occurred over the long course of their evolution, indicating that they were involved in shifts in subcellular localization from the chloroplast to cytosol or peroxisome and underwent functional divergence. In addition, expression patterns of Cu/Zn SOD genes from Arabidopsis thaliana and Solanum lycopersicum were tested in different tissues/organs and developmental stages and under different abiotic stresses. The results indicate that the Cu/Zn SOD gene family possesses potential functional divergence and may play vital roles in ROS scavenging in response to various stresses in plants. This study will help establish a foundation for further understanding these genes’ function during stress responses.
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21
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Zameer R, Fatima K, Azeem F, ALgwaiz HIM, Sadaqat M, Rasheed A, Batool R, Shah AN, Zaynab M, Shah AA, Attia KA, AlKahtani MDF, Fiaz S. Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H 2O 2) Under Abiotic Stress Condition. FRONTIERS IN PLANT SCIENCE 2022; 13:870241. [PMID: 35783965 PMCID: PMC9246500 DOI: 10.3389/fpls.2022.870241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/08/2022] [Indexed: 05/27/2023]
Abstract
Superoxide dismutase (SOD) proteins are important antioxidant enzymes that help plants to grow, develop, and respond to a variety of abiotic stressors. SOD gene family has been identified in a number of plant species but not yet in Daucus carota. A total of 9 DcSOD genes, comprising 2 FeSODs, 2 MnSODs, and 5 Cu/ZnSODs, are identified in the complete genome of D. carota, which are dispersed in five out of nine chromosomes. Based on phylogenetic analysis, SOD proteins from D. carota were categorized into two main classes (Cu/ZnSODs and MnFeSODs). It was predicted that members of the same subgroups have the same subcellular location. The phylogenetic analysis was further validated by sequence motifs, exon-intron structure, and 3D protein structures, with each subgroup having a similar gene and protein structure. Cis-regulatory elements responsive to abiotic stresses were identified in the promoter region, which may contribute to their differential expression. Based on RNA-seq data, tissue-specific expression revealed that DcCSD2 had higher expression in both xylem and phloem. Moreover, DcCSD2 was differentially expressed in dark stress. All SOD genes were subjected to qPCR analysis after cold, heat, salt, or drought stress imposition. SODs are antioxidants and play a critical role in removing reactive oxygen species (ROS), including hydrogen peroxide (H2O2). DcSODs were docked with H2O2 to evaluate their binding. The findings of this study will serve as a basis for further functional insights into the DcSOD gene family.
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Affiliation(s)
- Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hussah I. M. ALgwaiz
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Asima Rasheed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Riffat Batool
- Department of Botany, GC Women University, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muneera D. F. AlKahtani
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
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22
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Chatterjee A, Nirwan S, Mohapatra S, Sharma P, Agnihotri A, Shrivastava N. Biochemical aspects of pathogenic variability in white rust infected Indian mustard. Mycologia 2022; 114:757-768. [PMID: 35648633 DOI: 10.1080/00275514.2022.2060007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
White rust caused by Albugo candida, an oomycete pathogen, is a devastating disease of Brassica juncea (Indian mustard) worldwide. There is a need to screen virulent white rust isolates to challenge the developed white rust-resistant B. juncea cultivars to screen their resistance potential. The current study explores pathogenic and biochemical response of Indian mustard to white rust isolates collected from three different geographic locations of India. The observations refine our understanding of the disease severity in India. Disease progression and biochemical responses were studied in the cotyledonary as well as true leaf stage of the B. juncea cultivar Varuna at different time points. The biochemical findings highlight the fluctuation of significant biochemical parameters such as total proteins, sugars, and phenols, superoxide dismutase, and hydrogen peroxide during the A. candida infection in B. juncea.
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Affiliation(s)
- Anupriya Chatterjee
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Shradha Nirwan
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Pankaj Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201303, India
| | - Abha Agnihotri
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Neeraj Shrivastava
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
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23
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Chauhan J, Srivastava JP, Singhal RK, Soufan W, Dadarwal BK, Mishra UN, Anuragi H, Rahman MA, Sakran MI, Brestic M, Zivcak M, Skalicky M, Sabagh AEL. Alterations of Oxidative Stress Indicators, Antioxidant Enzymes, Soluble Sugars, and Amino Acids in Mustard [ Brassica juncea (L.) Czern and Coss.] in Response to Varying Sowing Time, and Field Temperature. FRONTIERS IN PLANT SCIENCE 2022; 13:875009. [PMID: 35592568 PMCID: PMC9111527 DOI: 10.3389/fpls.2022.875009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/01/2022] [Indexed: 05/24/2023]
Abstract
The impact of elevated temperature at the reproductive stage of a crop is one of the critical limitations that influence crop growth and productivity globally. This study was aimed to reveal how sowing time and changing field temperature influence on the regulation of oxidative stress indicators, antioxidant enzymes activity, soluble sugars (SS), and amino acids (AA) in Indian Mustard. The current study was carried out during the rabi 2017-2018 and 2018-2019 where, five varieties of mustard viz. Pusa Mustard 25 (PM-25) (V1), PM-26 (V2), BPR-541-4 (V3), RH-406 (V4), and Urvashi (V5) were grown under the field conditions on October 30 (normal sowing; S1), November 18 (late sowing; S2) and November 30 (very late sowing; S3) situations. The S1 and S3 plants, at mid-flowering stage, showed a significant variation in accumulation of SS (8.5 and 17.3%), free AA (235.4 and 224.6%), and proline content (118.1 and 133%), respectively, and played a crucial role in the osmotic adjustment under stress. The results showed that S3 sowing, exhibited a significant induction of the hydrogen peroxide (H2O2) (110.2 and 86.6%) and malondialdehyde (23.5 and 47.5%) concentrations, respectively, which indicated the sign of oxidative stress in plants. Interestingly, the polyphenol oxidase, peroxidase, superoxide dismutase, and catalase enzyme activities were also significantly increased in S3 plants compared to S1 plants, indicating their significant roles in ameliorating the oxidative stress. Furthermore, the concentration of fatty acid levels such as palmitic, stearic, oleic, and linoleic acids level also significantly increased in S3 plants, which influenced the seed and oil quality. The study suggests that the late sowing significantly impaired the biochemical mechanisms in Indian mustard. Further, the mustard variety V4 (RH-406) was found to be effective for cultivation as well as environmental stress adoption in Indian soils, and it could be highly useful in breeding for developing heat-tolerant genotypes for ensuring the food security.
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Affiliation(s)
- Jyoti Chauhan
- Department of Plant Physiology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, India
| | - J. P. Srivastava
- Department of Plant Physiology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, India
| | - Rajesh Kumar Singhal
- Indian Council of Agricultural Research-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Walid Soufan
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh, Saudi Arabia
| | - Basant Kumar Dadarwal
- Department of Plant Physiology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, India
| | | | - Hirdayesh Anuragi
- Indian Council of Agricultural Research-Central Agroforestry Research Institute, Jhansi, India
| | - Md Atikur Rahman
- Grassland and Forage Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Mohamed I. Sakran
- Biochemistry Section, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Marian Brestic
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Marek Zivcak
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Ayman EL Sabagh
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
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24
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Plant Response to Cold Stress: Cold Stress Changes Antioxidant Metabolism in Heading Type Kimchi Cabbage (Brassica rapa L. ssp. Pekinensis). Antioxidants (Basel) 2022; 11:antiox11040700. [PMID: 35453385 PMCID: PMC9031148 DOI: 10.3390/antiox11040700] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
Cold stress is known as the important yield-limiting factor of heading type Kimchi cabbage (HtKc, Brassica rapa L. ssp. pekinensis), which is an economically important crop worldwide. However, the biochemical and molecular responses to cold stress in HtKc are largely unknown. In this study, we conducted transcriptome analyses on HtKc grown under normal versus cold conditions to investigate the molecular mechanism underlying HtKc responses to cold stress. A total of 2131 genes (936 up-regulated and 1195 down-regulated) were identified as differentially expressed genes and were significantly annotated in the category of “response to stimulus”. In addition, cold stress caused the accumulation of polyphenolic compounds, including p-coumaric, ferulic, and sinapic acids, in HtKc by inducing the phenylpropanoid pathway. The results of the chemical-based antioxidant assay indicated that the cold-induced polyphenolic compounds improved the free-radical scavenging activity and antioxidant capacity, suggesting that the phenylpropanoid pathway induced by cold stress contributes to resistance to cold-induced reactive oxygen species in HtKc. Taken together, our results will serve as an important base to improve the cold tolerance in plants via enhancing the antioxidant machinery.
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25
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Verma D, Upadhyay SK, Singh K. Characterization of APX and APX-R gene family in Brassica juncea and B. rapa for tolerance against abiotic stresses. PLANT CELL REPORTS 2022; 41:571-592. [PMID: 34115169 DOI: 10.1007/s00299-021-02726-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
APX and APX-R gene families were identified and characterized in two important oilseed species of Brassica. Gene expression under abiotic stress conditions, recombinant protein expression, and analysis further divulged their drought, heat, and salt-responsive behavior. Ascorbate peroxidases (APX) are heme-dependent enzymes that rid the cells of H2O2 and regulate diverse biological processes. In the present study, we performed APX gene family characterization in two Brassica sp. (B. juncea and B. rapa) as these are commercially important oilseed crops and affected severely by abiotic stresses. We identified 16 BjuAPX and 9 BraAPX genes and 2 APX-R genes each in B. juncea and B. rapa genomes, respectively. Phylogenetic analysis divided the APX genes into five distinct clades, which exhibited conservation in the gene structure, motif organization, and sub-cellular location within the clade. Structural analysis of APX and APX-R proteins revealed the amino acid substitutions in conserved domains of APX-R proteins. The expression profiling of BjuAPX and BraAPX genes showed that 3 BjuAPX, 7BraAPX, and 2 BraAPX-R genes were drought and heat responsive. Notably, BjuAAPX1a, BjuAPX1d, BjuAAPX6, BraAAPX1a, BraAAPX2, and BraAAPX3b showed high expression levels in RT-qPCR. Cis-regulatory elements in APX and APX-R gene promoters supported the differential behavior of these genes. Further, two stress-responsive genes BjuAPX1d and BraAAPX2 were cloned, characterized, and their roles were validated under heat, drought, salt, and cold stress in bacterial expression system. This study for the first time reports the presence of APX activity in dimeric and LMW form of purified BraAAPX2 protein. The study may help pave way for developing abiotic stress-tolerant Brassica crops.
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Affiliation(s)
- Deepika Verma
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh, 160014, India
| | | | - Kashmir Singh
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh, 160014, India.
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26
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Rehman S, Rashid A, Manzoor MA, Li L, Sun W, Riaz MW, Li D, Zhuge Q. Genome-Wide Evolution and Comparative Analysis of Superoxide Dismutase Gene Family in Cucurbitaceae and Expression Analysis of Lagenaria siceraria Under Multiple Abiotic Stresses. Front Genet 2022; 12:784878. [PMID: 35211150 PMCID: PMC8861505 DOI: 10.3389/fgene.2021.784878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Superoxide dismutase (SOD) is an important enzyme that serves as the first line of defense in the plant antioxidant system and removes reactive oxygen species (ROS) under adverse conditions. The SOD protein family is widely distributed in the plant kingdom and plays a significant role in plant growth and development. However, the comprehensive analysis of the SOD gene family has not been conducted in Cucurbitaceae. Subsequently, 43 SOD genes were identified from Cucurbitaceae species [Citrullus lanatus (watermelon), Cucurbita pepo (zucchini), Cucumis sativus (cucumber), Lagenaria siceraria (bottle gourd), Cucumis melo (melon)]. According to evolutionary analysis, SOD genes were divided into eight subfamilies (I, II, III, IV, V, VI, VII, VIII). The gene structure analysis exhibited that the SOD gene family had comparatively preserved exon/intron assembly and motif as well. Phylogenetic and structural analysis revealed the functional divergence of Cucurbitaceae SOD gene family. Furthermore, microRNAs 6 miRNAs were predicted targeting 3 LsiSOD genes. Gene ontology annotation outcomes confirm the role of LsiSODs under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Promoter regions of the SOD family revealed that most cis-elements were involved in plant development, stress response, and plant hormones. Evaluation of the gene expression showed that most SOD genes were expressed in different tissues (root, flower, fruit, stem, and leaf). Finally, the expression profiles of eight LsiSOD genes analyzed by qRT-PCR suggested that these genetic reserves responded to drought, saline, heat, and cold stress. These findings laid the foundation for further study of the role of the SOD gene family in Cucurbitaceae. Also, they provided the potential for its use in the genetic improvement of Cucurbitaceae.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Arif Rashid
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | | | - Lingling Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
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Aleem M, Aleem S, Sharif I, Wu Z, Aleem M, Tahir A, Atif RM, Cheema HMN, Shakeel A, Lei S, Yu D, Wang H, Kaushik P, Alyemeni MN, Bhat JA, Ahmad P. Characterization of SOD and GPX Gene Families in the Soybeans in Response to Drought and Salinity Stresses. Antioxidants (Basel) 2022; 11:antiox11030460. [PMID: 35326109 PMCID: PMC8944523 DOI: 10.3390/antiox11030460] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 12/31/2022] Open
Abstract
Plant stresses causing accumulation of reactive oxidative species (ROS) are scavenged by effective antioxidant defense systems. Therefore, the present study performed genome-wide identification of superoxide dismutase (SOD) and glutathione peroxidase (GPX) gene families in cultivated and wild soybeans, and 11 other legume species. We identified a total of 101 and 95 genes of SOD and GPX, respectively, across thirteen legume species. The highest numbers of SODs and GPXs were identified in cultivated (Glycine max) and wild (Glycine soja). A comparative phylogenetic study revealed highest homology among the SODs and GPXs of cultivated and wild soybeans relative to other legumes. The exon/intron structure, motif and synteny blocks were conserved in both soybean species. According to Ka/Ks, purifying the selection played the major evolutionary role in these gene families, and segmental duplication are major driving force for SODs and GPXs expansion. In addition, the qRT-PCR analysis of the G. max and G. soja SOD and GPX genes revealed significant differential expression of these genes in response to oxidative, drought and salinity stresses in root tissue. In conclusion, our study provides new insights for the evolution of SOD and GPX gene families in legumes, and provides resources for further functional characterization of these genes for multiple stresses.
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Affiliation(s)
- Muqadas Aleem
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan;
| | - Saba Aleem
- Barani Agricultural Research Station, Fatehjang 43350, Pakistan;
| | - Iram Sharif
- Cotton Research Station, Ayub Agricultural Research Institute, Faisalabad 38040, Pakistan;
| | - Zhiyi Wu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
| | - Maida Aleem
- Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Ammara Tahir
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
| | - Rana Muhammad Atif
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan;
| | - Hafiza Masooma Naseer Cheema
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38040, Pakistan; (H.M.N.C.); (A.S.)
| | - Amir Shakeel
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38040, Pakistan; (H.M.N.C.); (A.S.)
| | - Sun Lei
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
| | - Hui Wang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; (M.A.); (Z.W.); (A.T.); (S.L.)
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Mohammed Nasser Alyemeni
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 12546, Saudi Arabia;
| | - Javaid Akhter Bhat
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 12546, Saudi Arabia;
- Correspondence: (D.Y.); (H.W.); (J.A.B.); (P.A.)
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28
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Shahzad B, Rehman A, Tanveer M, Wang L, Park SK, Ali A. Salt Stress in Brassica: Effects, Tolerance Mechanisms, and Management. JOURNAL OF PLANT GROWTH REGULATION 2022. [PMID: 0 DOI: 10.1007/s00344-021-10338-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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29
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Ma L, Qi W, Bai J, Li H, Fang Y, Xu J, Xu Y, Zeng X, Pu Y, Wang W, Liu L, Li X, Sun W, Wu J. Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress. Front Genet 2022; 12:753624. [PMID: 35126448 PMCID: PMC8814366 DOI: 10.3389/fgene.2021.753624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/24/2021] [Indexed: 11/29/2022] Open
Abstract
Winter Brassica rapa (B. rapa) is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. Ascorbate peroxidase (APX) plays important roles in the response of this plant to abiotic stress and in scavenging free radicals. In this study, the roles of APX proteins in the cold response and superoxide metabolism pathways in rapeseed species were investigated, and a comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profiles in the APX gene family was conducted. Most BrAPX genes were specifically expressed under cold stress and behaved significantly differently in cold-tolerant and weakly cold-resistant varieties. Quantitative real-time-PCR (qRT-PCR) was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress. The expression of five BrAPX genes was significantly upregulated in growth cones at 3 h of cold stress, while their expression was significantly lower at 24 h than at 3 h. The expression of Bra015403 and Bra003918 was significantly higher in “Longyou-7” growth cones than in other treatments. Five BrAPXs (Bra035235, Bra003918, Bra033040, Bra017120, and Bra031934) were closely associated with abiotic stress responses in B. rapa. These candidate genes may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Weiliang Qi
- College of Agriculture and Forestry, Longdong University, Qingyang, China
| | - Jing Bai
- Zhangye Academy of Agricultural Sciences, Zhangye, China
| | - Haiyun Li
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jia Xu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yaozhao Xu
- College of Agronomy and Biotechnology, Hexi University, Zhangye, China
| | - Xiucun Zeng
- College of Agronomy and Biotechnology, Hexi University, Zhangye, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xuecai Li
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Wancang Sun, ; Junyan Wu,
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Wancang Sun, ; Junyan Wu,
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Safder I, Shao G, Sheng Z, Hu P, Tang S. Genome-wide identification studies - A primer to explore new genes in plant species. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:9-22. [PMID: 34558163 DOI: 10.1111/plb.13340] [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: 02/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Genome data have accumulated rapidly in recent years, doubling roughly after every 6 months due to the influx of next-generation sequencing technologies. A plethora of plant genomes are available in comprehensive public databases. This easy access to data provides an opportunity to explore genome datasets and recruit new genes in various plant species not possible a decade ago. In the past few years, many gene families have been published using these public datasets. These genome-wide studies identify and characterize gene members, gene structures, evolutionary relationships, expression patterns, protein interactions and gene ontologies, and predict putative gene functions using various computational tools. Such studies provide meaningful information and an initial framework for further functional elucidation. This review provides a concise layout of approaches used in these gene family studies and demonstrates an outline for employing various plant genome datasets in future studies.
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Affiliation(s)
- I Safder
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - G Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Z Sheng
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - P Hu
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - S Tang
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
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Azeem F, Zameer R, Rehman Rashid MA, Rasul I, Ul-Allah S, Siddique MH, Fiaz S, Raza A, Younas A, Rasool A, Ali MA, Anwar S, Siddiqui MH. Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:110-122. [PMID: 34864561 DOI: 10.1016/j.plaphy.2021.11.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Potassium (K+) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K+ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K+ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K+ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.
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Affiliation(s)
- Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | | | - Ijaz Rasul
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahauddin Zakariya University, Bahadur Sub-Campus, Layyah, Pakistan
| | | | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, 22620, Haripir, Pakistan.
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, 350002, China
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Asima Rasool
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Sultana Anwar
- Department of Agronomy, University of Florida, Gainesville, USA
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Yang Z, Zhang R, Zhou Z. The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:911761. [PMID: 35783982 PMCID: PMC9243642 DOI: 10.3389/fpls.2022.911761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/31/2022] [Indexed: 05/04/2023]
Abstract
Xyloglucan endotransglucosylase/hydrolase (XTH), belonging to glycoside hydrolase family 16, is one of the key enzymes in plant cell wall remodeling. Schima superba is an important timber and fireproof tree species in southern China. However, little is known about XTHs in S. superba. In the present study, a total of 34 SsuXTHs were obtained, which were classified into three subfamilies based on the phylogenetic relationship and unevenly distributed on 18 chromosomes. Furthermore, the intron-exon structure and conserved motif composition of them supported the classification and the members belonging to the same subfamily shared similar gene structures. Segmental and tandem duplication events did not lead to SsuXTH gene family expansion, and strong purifying selection pressures during evolution led to similar structure and function of SsuXTH gene family. The interaction network and cis-acting regulatory elements analysis revealed the SsuXTH expression might be regulated by multiple hormones, abiotic stresses and transcription factors. Finally, expression profiles and GO enrichment analysis showed most of the tandem repeat genes were mainly expressed in the phloem and xylem and they mainly participated in glycoside metabolic processes through the transfer and hydrolysis of xyloglucan in the cell wall and then regulated fiber elongation.
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Affiliation(s)
- Zhongyi Yang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, China
| | - Rui Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, China
- *Correspondence: Rui Zhang,
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, China
- Zhichun Zhou,
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Paul A, Chatterjee A, Subrahmanya S, Shen G, Mishra N. NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:777884. [PMID: 34987532 PMCID: PMC8720784 DOI: 10.3389/fpls.2021.777884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants, such as Arabidopsis thaliana and cotton; however, not much is known about NHXs in tea plant. In the present study, NHX genes of tea were obtained through a genome-wide search using A. thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER; CsNHX8) and plasma membrane (PM; CsNHX9), respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location, and protein-conserved motifs and domains were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes is subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in Camellia sinensis based on the orthologous genes in A. thaliana. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.
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Affiliation(s)
| | | | | | - Guoxin Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Neelam Mishra
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, India
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Pi B, Pan J, Xiao M, Hu X, Zhang L, Chen M, Liu B, Ruan Y, Huang Y. Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance. BMC PLANT BIOLOGY 2021; 21:555. [PMID: 34814855 PMCID: PMC8609832 DOI: 10.1186/s12870-021-03340-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/10/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND CCCH zinc finger family is one of the largest transcription factor families related to multiple biotic and abiotic stresses. Brassica napus L., an allotetraploid oilseed crop formed by natural hybridization between two diploid progenitors, Brassica rapa and Brassica oleracea. A systematic identification of rapeseed CCCH family genes is missing and their functional characterization is still in infancy. RESULTS In this study, 155 CCCH genes, 81 from its parent B. rapa and 74 from B. oleracea, were identified and divided into 15 subfamilies in B. napus. Organization and syntenic analysis explained the distribution and collinearity relationship of CCCH genes, the selection pressure and evolution of duplication gene pairs in B. napus genome. 44 diploid duplication gene pairs and 4 triple duplication gene groups were found in B. napus of CCCH family and the segmental duplication is attributed to most CCCH gene duplication events in B. napus. Nine types of CCCH motifs exist in B. napus CCCH family members, and motif C-X7/8-C-X5-C-X3-H is the most common and a new conserved CCH motif (C-X5-C-X3-H) has been identified. In addition, abundant stress-related cis-elements exist in promoters of 27 subfamily IX (RR-TZF) genes and their expression profiles indicated that RR-TZF genes could be involved in responses to hormone and abiotic stress. CONCLUSIONS The results provided a foundation to understand the basic characterization and genes evolution of CCCH gene family in B. napus, and provided potential targets for genetic engineering in Brassicaceae crops in pursuit of stress-tolerant traits.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Jiao Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Mu Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Xinchang Hu
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Min Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Boyu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128, China.
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Liu J, Xu L, Shang J, Hu X, Yu H, Wu H, Lv W, Zhao Y. Genome-wide analysis of the maize superoxide dismutase (SOD) gene family reveals important roles in drought and salt responses. Genet Mol Biol 2021; 44:e20210035. [PMID: 34606562 PMCID: PMC8493800 DOI: 10.1590/1678-4685-gmb-2021-0035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
Superoxide dismutase proteins (SODs) are antioxidant enzymes with important roles in abiotic stress responses. The SOD gene family has been systematically analyzed in many plants; however, it is still poorly understood in maize. Here, a bioinformatics analysis of maize SOD gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, gene duplications, promoter cis-elements and GO annotations. In total, 13 SOD genes were identified in maize and five members were involved in segmental duplication. Phylogenetic analysis indicated that SODs from maize and other plants comprised two groups, which could be further classified into different subgroups, with most members in the same subgroup having the same subcellular localization. The ZmSOD promoters contained 2-10 stress-responsive cis-elements with different distributions. Heatmap analysis indicated that ZmSODs were expressed in most of the detected tissues and organs. The expression patterns of ZmSODs were investigated under drought and salt treatments by qRT-PCR, and most members were responsive to drought or salt stress, especially some ZmSODs with significant expression changes were identified, such as ZmCSD2 and ZmMSD2, suggesting the important roles of ZmSODs in abiotic stress responses. Our results provide an important basis for further functional study of ZmSODs in future study.
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Affiliation(s)
- Jing Liu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Lijuan Xu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Jian Shang
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Xiaolin Hu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Haitao Yu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Hongying Wu
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
| | - Wenben Lv
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China
| | - Yang Zhao
- Anhui Agricultural University, School of Life Sciences, National Engineering Laboratory of Crop Stress Resistance Breeding, Hefei, China.,Anhui Agricultural University, Maize Engineering Technology Research Center of Anhui Province, School of Life Sciences, Hefei, China
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Iqbal Qureshi AM, Sofi MU, Dar NA, Khan MH, Mahdi SS, Dar ZA, Bangroo S, El-Serehy HA, Hefft DI, Popescu SM. Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa. Saudi J Biol Sci 2021; 28:5526-5537. [PMID: 34588862 PMCID: PMC8459115 DOI: 10.1016/j.sjbs.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/18/2021] [Accepted: 08/01/2021] [Indexed: 01/17/2023] Open
Abstract
Superoxide Dismutase SODs are defense associated proteins that detoxify ROS and primarily serve as scavengers. They have been described in numerous plant species, but their in-depth characterization in Brassica rapa has not been reported. Therefore, the present investigation on genome wide study of SOD gene family was conducted to identify BrSOD genes, their domain-based organization, gene structure analysis, phylogenetic analysis, intron-exon structure of genes and expression analysis. The sequence characterization of Super oxide dismutase gene family in Brassica rapa, their syntenic associateship of conserved motifs and phylogenetic correlationship, prediction of cis-elements and determing the expression analysis in distinct tissues namely plant callus, root, stem, leaf, flower, and silique under abiotic conditions have been analysed using different software’s. The study on SOD gene family identified 17 BrSOD genes which were grouped into eight BrCu-ZnSODs and nine BrFe-MnSODs domain-based organization. Furthermore, the conserved character of BrSODs were confirmed by intron-exon organisation, motif arrangements and domain architectural investigations. Expression analysis using RNA Sequence data of different developmental stages proclaimed that genes were manifested in all six tissues with an exception of BrCu-ZnSOD3, which was not manifested in roots; however, whose transcript was detected in all other tested tissues. The study has genome wide insight into the occurrence and functional specifications of BrSOD gene family in Brassica rapa that can be potentially utilized in breeding program for resilience to climate change and abiotic stresses tolerance Brassica variety.
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Affiliation(s)
- Asif M Iqbal Qureshi
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Mehraj Uddin Sofi
- HMAARI, Leh, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - N A Dar
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - M H Khan
- ARSSSS, Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - S S Mahdi
- Division of Agronomy, FoA Wadura, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Zahoor A Dar
- DARS, Rangreth, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Shabir Bangroo
- Division of Soil Sciences, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology Shalimar Kashmir, India
| | - Hamed A El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyad, 11451, Saudi Arabia
| | - Daniel Ingo Hefft
- University Centre Reaseheath, Reaseheath College, Nantwich CW5 6DF, UK
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, 200585, Romania
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Su W, Raza A, Gao A, Jia Z, Zhang Y, Hussain MA, Mehmood SS, Cheng Y, Lv Y, Zou X. Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed ( Brassica napus L.) under Different Hormones and Abiotic Stress Conditions. Antioxidants (Basel) 2021; 10:1182. [PMID: 34439430 PMCID: PMC8389029 DOI: 10.3390/antiox10081182] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 01/25/2023] Open
Abstract
Superoxide dismutase (SOD) is an important enzyme that acts as the first line of protection in the plant antioxidant defense system, involved in eliminating reactive oxygen species (ROS) under harsh environmental conditions. Nevertheless, the SOD gene family was yet to be reported in rapeseed (Brassica napus L.). Thus, a genome-wide investigation was carried out to identify the rapeseed SOD genes. The present study recognized 31 BnSOD genes in the rapeseed genome, including 14 BnCSDs, 11 BnFSDs, and six BnMSDs. Phylogenetic analysis revealed that SOD genes from rapeseed and other closely related plant species were clustered into three groups based on the binding domain with high bootstrap values. The systemic analysis exposed that BnSODs experienced segmental duplications. Gene structure and motif analysis specified that most of the BnSOD genes displayed a relatively well-maintained exon-intron and motif configuration within the same group. Moreover, we identified five hormones and four stress- and several light-responsive cis-elements in the promoters of BnSODs. Thirty putative bna-miRNAs from seven families were also predicted, targeting 13 BnSODs. Gene ontology annotation outcomes confirm the BnSODs role under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Twelve BnSOD genes exhibited higher expression profiles in numerous developmental tissues, i.e., root, leaf, stem, and silique. The qRT-PCR based expression profiling showed that eight genes (BnCSD1, BnCSD3, BnCSD14, BnFSD4, BnFSD5, BnFSD6, BnMSD2, and BnMSD10) were significantly up-regulated under different hormones (ABA, GA, IAA, and KT) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. The predicted 3D structures discovered comparable conserved BnSOD protein structures. In short, our findings deliver a foundation for additional functional investigations on the BnSOD genes in rapeseed breeding programs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yan Lv
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (W.S.); (A.R.); (A.G.); (Z.J.); (Y.Z.); (M.A.H.); (S.S.M.); (Y.C.)
| | - Xiling Zou
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China; (W.S.); (A.R.); (A.G.); (Z.J.); (Y.Z.); (M.A.H.); (S.S.M.); (Y.C.)
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Fesharaki-Esfahani M, Shahpiri A, Kazemi-Nasab A. A highly efficient, thermo stable and broad pH adaptable copper-zinc super oxide dismutase (AmSOD1) mediates hydrogen peroxide tolerance in Avicennia marina. PHYTOCHEMISTRY 2021; 187:112766. [PMID: 33878605 DOI: 10.1016/j.phytochem.2021.112766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Avicennia marina is a widely distributed mangrove species with high tolerance to salt, oxidative stress and heavy metals. In the preset work, we found that superoxide dismutase (SOD) activity increases in Avicennia marina leaves in response to salt and hydrogen peroxide. Monitoring the SOD using Western blot analysis revealed that the accumulation of SOD increased in response to hydrogen peroxide but not in response to salinity stress. Here we also isolated and cloned a gene encoding AmSOD1 which was classified into the group of plant CuZnSODs based on amino acid sequence analysis. AmSOD1 was heterologously expressed in the soluble fraction of E. coli strain Rosetta (DE3). The cells expressing His-AmSOD1 were more tolerant in response to hydrogen peroxide treatment but not salt stress, suggesting the involvement of AmSOD1 in hydrogen peroxide tolerance. The enzyme His-AmSOD1 exhibited a molecular mass of 38 kDa, but it could be monomer in reducing conditions indicating a double-strand protein with intra-molecular disulfide bridge. There are two copper and two zinc moles per mole of dimer form of His-AmSOD1 suggesting the binding of one copper and one zinc ions to each monomer. The Pure His-AmSOD1 was highly active in vitro and its activity was considerably enhanced when the growth medium of the cells producing AmSOD1 was supplemented with Cu2+. The high stability of the recombinant AmSOD1 after incubation in a broad range pH and high temperature is a distinctive feature for AmSOD1, which may open new insights for application of AmSOD1 as a protein drug in different medical purposes.
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Affiliation(s)
- Monireh Fesharaki-Esfahani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Akram Kazemi-Nasab
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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Abstract
Nowadays, crop insufficiency resulting from soil salinization is threatening the world. On the basis that soil salinization has become a worldwide problem, studying the mechanisms of plant salt tolerance is of great theoretical and practical significance to improve crop yield, to cultivate new salt-tolerant varieties, and to make full use of saline land. Based on previous studies, this paper reviews the damage of salt stress to plants, including suppression of photosynthesis, disturbance of ion homeostasis, and membrane peroxidation. We have also summarized the physiological mechanisms of salt tolerance, including reactive oxygen species (ROS) scavenging and osmotic adjustment. Four main stress-related signaling pathways, salt overly sensitive (SOS) pathway, calcium-dependent protein kinase (CDPK) pathway, mitogen-activated protein kinase (MAPKs) pathway, and abscisic acid (ABA) pathway, are included. We have also enumerated some salt stress-responsive genes that correspond to physiological mechanisms. In the end, we have outlined the present approaches and techniques to improve salt tolerance of plants. All in all, we reviewed those aspects above, in the hope of providing valuable background knowledge for the future cultivation of agricultural and forestry plants.
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Ji HS, Bang SG, Ahn MA, Kim G, Kim E, Eom SH, Hyun TK. Molecular Cloning and Functional Characterization of Heat Stress-Responsive Superoxide Dismutases in Garlic ( Allium sativum L.). Antioxidants (Basel) 2021; 10:antiox10050815. [PMID: 34065356 PMCID: PMC8161062 DOI: 10.3390/antiox10050815] [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: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/26/2022] Open
Abstract
Superoxide dismutases (SODs) are key antioxidant enzymes that can detoxify the superoxide radicals generated by various stresses. Although various plant SODs have been suggested to improve stress tolerance, SODs in garlic, an economically important vegetable grown worldwide, remain relatively unknown. In this study, we found that heat stress strongly induced the activities of Cu/ZnSODs, FeSODs, and MnSODs in garlic leaves. In addition, we cloned four garlic SODs (AsSODs) and suggest that heat stress-increased SOD activity was reflected at least by the induction of these AsSODs. The results of the agro-infiltration assay suggested that the cloned AsSODs encoded functional SOD enzymes belonging to the Cu/ZnSOD and MnSOD families. As a first step toward understanding the enzymatic antioxidant system in garlic plants, our results provide a solid foundation for an in-depth analysis of the physiological functions of the AsSOD family.
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Zhang G, Ding Q, Wei B. Genome-wide identification of superoxide dismutase gene families and their expression patterns under low-temperature, salt and osmotic stresses in watermelon and melon. 3 Biotech 2021; 11:194. [PMID: 33927985 DOI: 10.1007/s13205-021-02726-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/10/2021] [Indexed: 12/01/2022] Open
Abstract
The growth and development of watermelon and melon are affected by abiotic stresses such as cold, salinity and drought. Plant superoxide dismutase (SOD) proteins exerted great effects on plant growth, development and response to abiotic stresses. However, little is known about the characteristics of watermelon and melon SOD gene families and their expression patterns under abiotic stresses. In this study, the genome-wide identification of SOD genes and their expression patterns under abiotic stresses has been done in watermelon and melon. Seven SODs were identified in watermelon and melon, respectively. Chromosome location indicated that the SODs were dispersedly distributed on 4-6 chromosomes. Almost all the SOD proteins contained 300 amino acids or less and the intron numbers of SODs ranged from 5 to 7. On the basis of phylogenetic analysis, the SODs were classified into six sub-groups which was also verified by similar motif composition, gene structure and sub-cellular location. Gene ontology analysis displayed that many SOD proteins participated in binding, catalytic, antioxidant activity and stimulus-response. Cis-regulatory elements related to stresses and hormones were found in the promoters of the SODs. Based on the quantitative real-time PCR, most of CmSOD and ClSOD genes showed obvious up-regulation under low-temperature, NaCl and PEG6000 treatments. The abiotic stress-responsive SOD genes were identified to improve watermelon and melon tolerance against abiotic stresses. This was a preliminary study to describe the genome-wide analysis of SOD gene family in watermelon and melon, and the results would facilitate further study of gene cloning and functional verification of SOD genes response to abiotic stresses in watermelon and melon. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02726-7.
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Affiliation(s)
- Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu China
| | - Qian Ding
- College of Floriculture, Weifang Engineering Vocational College, Qingzhou, 262500 Shandong China
| | - Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu China
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Joshi S, Kaur K, Khare T, Srivastava AK, Suprasanna P, Kumar V. Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na +/H +) antiporters under salinity stress in soybean. 3 Biotech 2021; 11:16. [PMID: 33442515 DOI: 10.1007/s13205-020-02555-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/12/2020] [Indexed: 11/25/2022] Open
Abstract
This study was aimed at the genome-wide identification, a comprehensive in silico characterization of NHX genes from soybean (Glycine max L.) and their tissue-specific expression under varied levels (0-200 mM NaCl) of salinity stress. A total of nine putative NHX genes were identified from soybean. The phylogenetic analysis confirmed a total of five sub-groups and GmNHXs were distributed in three of them. Bioinformatics analyses confirmed all GmNHXs as ion transporters in nature, and all were localized on the vacuolar membrane. Several cis-acting regulatory elements involved in hormonal signal-responsiveness and abiotic stress including salinity responses were identified in the promoter regions of GmNHXs. Amiloride, which is a known Na+/H+ exchanger activity inhibitor, binding motifs were observed in all the GmNHXs. Furthermore, the identified GmNHXs were predicted-targets of 75 different miRNA candidates. To gain an insight into the functional divergence of GmNHX transporters, qRT-PCR based gene expression analysis was done in control and salt-treated root, stem and leaf tissues of two contrasting Indian soybean varieties MAUS-47 (tolerant) and Gujosoya-2 (sensitive). The gene up-regulation was tissue-specific and varied amongst the soybean varieties, with higher induction in tolerant variety. Maximum induction was observed in GmNHX2 in root tissues of MAUS-47 at 200 mM NaCl stress. Overall, identified GmNHXs may be explored further as potential gene candidates for soybean improvement.
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Affiliation(s)
- Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
| | - Kawaljeet Kaur
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
- Department of Environmental Science, Savitribai Phule Pune University, Pune, 411007 India
| | - Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Mumbai, 400094 India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Mumbai, 400094 India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
- Department of Environmental Science, Savitribai Phule Pune University, Pune, 411007 India
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Das Laha S, Dutta S, Schäffner AR, Das M. Gene duplication and stress genomics in Brassicas: Current understanding and future prospects. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153293. [PMID: 33181457 DOI: 10.1016/j.jplph.2020.153293] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.
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Affiliation(s)
- Shayani Das Laha
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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Mustard Leaf Extract Suppresses Psychological Stress in Chronic Restraint Stress-Subjected Mice by Regulation of Stress Hormone, Neurotransmitters, and Apoptosis. Nutrients 2020; 12:nu12123640. [PMID: 33256231 PMCID: PMC7760211 DOI: 10.3390/nu12123640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 12/27/2022] Open
Abstract
Mustard leaf (Brassica juncea var. crispifolia L. H. Bailey) has been reported to have psychological properties such as anti-depressant activities. However, studies on chronic stress and depression caused by restraint have not been conducted. Therefore, this study aimed to evaluate the effects of a mustard leaf (ML) extract on chronic restraint stress (CRS) in mice. Male mice were subjected to a CRS protocol for a period of four weeks to induce stress. The results showed that the ML extract (100 and 500 mg/kg/perorally administered for four weeks) significantly decreased corticosterone levels and increased neurotransmitters levels in stressed mice. Apoptosis by CRS exposure was induced by Bcl-2 and Bax expression regulation and was suppressed by reducing caspase-3 and poly (ADP-ribose) polymerase expression after treatment with the ML extract. Our results confirmed that apoptosis was regulated by increased expression of brain-derived neurotrophic factor (BDNF). Additionally, cytokine levels were regulated by the ML extract. In conclusion, our results showed that the ML extract relieved stress effects by regulating hormones and neurotransmitters in CRS mice, BDNF expression, and apoptosis in the brain. Thus, it can be suggested that the studied ML extract is an agonist that can help relieve stress and depression.
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Qin L, Chen E, Li F, Yu X, Liu Z, Yang Y, Wang R, Zhang H, Wang H, Liu B, Guan Y, Ruan Y. Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet ( Setaria italica L.). Int J Mol Sci 2020; 21:ijms21228520. [PMID: 33198267 PMCID: PMC7696101 DOI: 10.3390/ijms21228520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.
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Affiliation(s)
- Ling Qin
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China;
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Erying Chen
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Feifei Li
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Xiao Yu
- College of Life Science, Shandong Normal University, Jinan 250014, China;
| | - Zhenyu Liu
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Yanbing Yang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Runfeng Wang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Huawen Zhang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Hailian Wang
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Bin Liu
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
| | - Yan’an Guan
- Featured Crops Engineering Laboratory of Shandong Province, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (E.C.); (F.L.); (Z.L.); (Y.Y.); (R.W.); (H.Z.); (H.W.); (B.L.)
- College of Life Science, Shandong Normal University, Jinan 250014, China;
- Correspondence: (Y.G.); (Y.R.); Tel.: +86-531-6665-8115 (Y.G.); +86-731-8467-3684 (Y.R.)
| | - Ying Ruan
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China;
- Correspondence: (Y.G.); (Y.R.); Tel.: +86-531-6665-8115 (Y.G.); +86-731-8467-3684 (Y.R.)
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Fu X, Lu Z, Wei H, Zhang J, Yang X, Wu A, Ma L, Kang M, Lu J, Wang H, Yu S. Genome-Wide Identification and Expression Analysis of the NHX (Sodium/Hydrogen Antiporter) Gene Family in Cotton. Front Genet 2020; 11:964. [PMID: 32973884 PMCID: PMC7461838 DOI: 10.3389/fgene.2020.00964] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/31/2020] [Indexed: 01/17/2023] Open
Abstract
The sodium/hydrogen antiporter (NHX) gene family with the Na+/H+ exchange protein domain is a transporter of sodium and hydrogen ions and plays an important role in the response of plants to salt stress. Studying the response of cotton to salt stress through comprehensive identification and analysis of NHX genes in several species and their roles in salt tolerance mechanisms is of great significance. In this study, 23, 24, 12, and 12 NHX genes were identified from Gossypium hirsutum (Gh), G. barbadense, G. arboreum and G. raimondii, respectively. Phylogenetic analysis showed that these genes were mainly divided into three clades with significant subcellular localization, namely, endosome (Endo-class), plasma membrane (PM-class) and vacuole (Vac-class). By analyzing the structure of NHX genes and proteins, each branch of the NHX gene family was found to be structurally conserved, and collinearity analysis showed that NHX genes were mainly expressed through whole genome and segmental duplication. The non-synonymous (Ka)/synonymous (Ks) values showed that the NHX gene family experienced strong purifying selection during long-term evolution. Cis-acting element analysis showed that the NHX gene family may be related to the regulation of abscisic acid (ABA) and methyl jasmonate (MeJA) hormones. Additionally, transcriptomic data analysis and qRT-PCR showed that GhNHXs exhibited different expression patterns in each tissue and under different salinities. These results provide an important reference for us to further understand and analyze the molecular regulation mechanism of cotton NHX genes.
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Affiliation(s)
- Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xu Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Meng Kang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Schmidt SB, Eisenhut M, Schneider A. Chloroplast Transition Metal Regulation for Efficient Photosynthesis. TRENDS IN PLANT SCIENCE 2020; 25:817-828. [PMID: 32673582 DOI: 10.1016/j.tplants.2020.03.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/14/2020] [Accepted: 03/04/2020] [Indexed: 05/24/2023]
Abstract
Plants require sunlight, water, CO2, and essential nutrients to drive photosynthesis and fulfill their life cycle. The photosynthetic apparatus resides in chloroplasts and fundamentally relies on transition metals as catalysts and cofactors. Accordingly, chloroplasts are particularly rich in iron (Fe), manganese (Mn), and copper (Cu). Owing to their redox properties, those metals need to be carefully balanced within the cell. However, the regulation of transition metal homeostasis in chloroplasts is poorly understood. With the availability of the arabidopsis genome information and membrane protein databases, a wider catalogue for searching chloroplast metal transporters has considerably advanced the study of transition metal regulation. This review provides an updated overview of the chloroplast transition metal requirements and the transporters involved for efficient photosynthesis in higher plants.
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Affiliation(s)
- Sidsel Birkelund Schmidt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Marion Eisenhut
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Anja Schneider
- Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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Global Landscapes of the Na+/H+ Antiporter (NHX) Family Members Uncover their Potential Roles in Regulating the Rapeseed Resistance to Salt Stress. Int J Mol Sci 2020; 21:ijms21103429. [PMID: 32408717 PMCID: PMC7279160 DOI: 10.3390/ijms21103429] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Soil salinity is a main abiotic stress in agriculture worldwide. The Na+/H+ antiporters (NHXs) play pivotal roles in intracellular Na+ excretion and vacuolar Na+ compartmentalization, which are important for plant salt stress resistance (SSR). However, few systematic analyses of NHXs has been reported in allotetraploid rapeseed so far. Here, a total of 18 full-length NHX homologs, representing seven subgroups (NHX1-NHX8 without NHX5), were identified in the rapeseed genome (AnAnCnCn). Number variations of BnaNHXs might indicate their significantly differential roles in the regulation of rapeseed SSR. BnaNHXs were phylogenetically divided into three evolutionary clades, and the members in the same subgroups had similar physiochemical characteristics, gene/protein structures, and conserved Na+ transport motifs. Darwin´s evolutionary pressure analysis suggested that BnaNHXs suffered from strong purifying selection. The cis-element analysis revealed the differential transcriptional regulation of NHXs between the model Arabidopsis and B. napus. Differential expression of BnaNHXs under salt stress, different nitrogen forms (ammonium and nitrate), and low phosphate indicated their potential involvement in the regulation of rapeseed SSR. Global landscapes of BnaNHXs will give an integrated understanding of their family evolution and molecular features, which will provide elite gene resources for the genetic improvement of plant SSR through regulating the NHX-mediated Na+ transport.
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Zang Y, Chen J, Li R, Shang S, Tang X. Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress. PeerJ 2020; 8:e9063. [PMID: 32411532 PMCID: PMC7207209 DOI: 10.7717/peerj.9063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/05/2020] [Indexed: 11/25/2022] Open
Abstract
Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.
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Affiliation(s)
- Yu Zang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ruoxi Li
- School of Life Science, Southwest University, Chongqing, China
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Silva SAF, Silva FLB, Ribas AF, de Souza SGH, dos Santos TB. Genome-wide in silico analysis of SOD genes in common bean (Phaseolus vulgaris L.). ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s12892-020-00030-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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