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Sharma M, Tisarum R, Kohli RK, Batish DR, Cha-Um S, Singh HP. Inroads into saline-alkaline stress response in plants: unravelling morphological, physiological, biochemical, and molecular mechanisms. PLANTA 2024; 259:130. [PMID: 38647733 DOI: 10.1007/s00425-024-04368-4] [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: 10/26/2021] [Accepted: 02/22/2024] [Indexed: 04/25/2024]
Abstract
MAIN CONCLUSION This article discusses the complex network of ion transporters, genes, microRNAs, and transcription factors that regulate crop tolerance to saline-alkaline stress. The framework aids scientists produce stress-tolerant crops for smart agriculture. Salinity and alkalinity are frequently coexisting abiotic limitations that have emerged as archetypal mediators of low yield in many semi-arid and arid regions throughout the world. Saline-alkaline stress, which occurs in an environment with high concentrations of salts and a high pH, negatively impacts plant metabolism to a greater extent than either stress alone. Of late, saline stress has been the focus of the majority of investigations, and saline-alkaline mixed studies are largely lacking. Therefore, a thorough understanding and integration of how plants and crops rewire metabolic pathways to repair damage caused by saline-alkaline stress is of particular interest. This review discusses the multitude of resistance mechanisms that plants develop to cope with saline-alkaline stress, including morphological and physiological adaptations as well as molecular regulation. We examine the role of various ion transporters, transcription factors (TFs), differentially expressed genes (DEGs), microRNAs (miRNAs), or quantitative trait loci (QTLs) activated under saline-alkaline stress in achieving opportunistic modes of growth, development, and survival. The review provides a background for understanding the transport of micronutrients, specifically iron (Fe), in conditions of iron deficiency produced by high pH. Additionally, it discusses the role of calcium in enhancing stress tolerance. The review highlights that to encourage biomolecular architects to reconsider molecular responses as auxiliary for developing tolerant crops and raising crop production, it is essential to (a) close the major gaps in our understanding of saline-alkaline resistance genes, (b) identify and take into account crop-specific responses, and (c) target stress-tolerant genes to specific crops.
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Affiliation(s)
- Mansi Sharma
- Department of Environment Studies, Panjab University, Chandigarh, 160 014, India
- Department of Environmental Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, Uttar Pradesh, India
| | - Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ravinder Kumar Kohli
- Department of Botany, Panjab University, Chandigarh, 160014, India
- Amity University, Mohali Campus, Sector 82A, Mohali, 140306, Punjab, India
| | - Daizy R Batish
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Panjab University, Chandigarh, 160 014, India.
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2
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Mamrutha HM, Zeenat W, Kapil D, Budhagatapalli N, Tikaniya D, Rakesh K, Krishnappa G, Singh G, Singh GP. Evidence and opportunities for developing non-transgenic genome edited crops using site-directed nuclease 1 approach. Crit Rev Biotechnol 2023:1-11. [PMID: 37915126 DOI: 10.1080/07388551.2023.2270581] [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: 02/04/2022] [Accepted: 09/18/2023] [Indexed: 11/03/2023]
Abstract
The innovations and progress in genome editing/new breeding technologies have revolutionized research in the field of functional genomics and crop improvement. This revolution has expanded the horizons of agricultural research, presenting fresh possibilities for creating novel plant varieties equipped with desired traits that can effectively combat the challenges posed by climate change. However, the regulation and social acceptance of genome-edited crops still remain as major barriers. Only a few countries considered the site-directed nuclease 1 (SDN1) approach-based genome-edited plants under less or no regulation. Hence, the present review aims to comprise information on the research work conducted using SDN1 in crops by various genome editing tools. It also elucidates the promising candidate genes that can be used for editing and has listed the studies on non-transgenic crops developed through SDN1 either by Agrobacterium-mediated transformation or by ribo nucleoprotein (RNP) complex. The review also hoards the existing regulatory landscape of genome editing and provides an overview of globally commercialized genome-edited crops. These compilations will enable confidence in researchers and policymakers, across the globe, to recognize the full potential of this technology and reconsider the regulatory aspects associated with genome-edited crops. Furthermore, this compilation serves as a valuable resource for researchers embarking on the development of customized non-transgenic crops through the utilization of SDN1.
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Affiliation(s)
- H M Mamrutha
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Wadhwa Zeenat
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deswal Kapil
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Nagaveni Budhagatapalli
- Institute of Plant Biochemistry, Center for Plant Genome Engineering, Heinrich-Heine-University, Düsseldorf, Germany
| | - Divya Tikaniya
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Kumar Rakesh
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Gyanendra Singh
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - G P Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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3
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Yan H, Liu F, Zhang G, Liu S, Ma W, Yang T, Li Y, Yang J, Cui H. PlantCHRs: A comprehensive database of plant chromatin remodeling factors. Comput Struct Biotechnol J 2023; 21:4974-4987. [PMID: 37867975 PMCID: PMC10589754 DOI: 10.1016/j.csbj.2023.10.005] [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: 06/08/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
The Snf2 protein family is a group of ATP-dependent chromatin remodeling factors (CHRs) that play an essential role in gene expression regulation. In plants, Snf2 is involved in growth, development, as well as stress resistance. However, only a very limited number of experimentally validated Snf2 have been identified and reported, while the majority remaining undiscovered in most species . In this study, we predicted 3135 Snf2 proteins and 8398 chromatin remodeling complex (CRC) subunits in diverse plant species, and constructed the Plant Chromatin Remodeling Factors Database (PlantCHRs, http://www.functionalgenomics.cn/PlantCHRs/), which provide a comprehensive resource for researchers to access information about plant CHRs. We also developed an online tool capable of predicting CHRs and CRC subunits. Moreover, we investigated the distribution of Snf2 proteins in different species and observed a significant increase in the number of Snf2 proteins and the diversity of the Snf2 subfamily during the evolution, highlighting their evolutionary importance. By analyzing the expression patterns of the Snf2 genes in different tissues of maize and Arabidopsis, we found that the Snf2 proteins may show some conservation across different species in regulating plant growth and development. Over the all, we established a comprehensive database for plant CHRs, which will facilitate the researches on plant chromatin remodeling.
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Affiliation(s)
- Hengyu Yan
- College of Agronomy, Qingdao Agricultural University, China
| | - Fangyuan Liu
- College of Agronomy, Qingdao Agricultural University, China
| | - Guowei Zhang
- College of Agronomy, Qingdao Agricultural University, China
| | - Shuai Liu
- College of Agronomy, Qingdao Agricultural University, China
| | - Weiwei Ma
- College of Agronomy, Qingdao Agricultural University, China
| | - Ting Yang
- College of Agronomy, Qingdao Agricultural University, China
| | - Yubin Li
- College of Agronomy, Qingdao Agricultural University, China
| | - Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hailong Cui
- College of Economics and Management (Cooperative College), Qingdao Agricultural University, China
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4
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Xu N, Chen B, Cheng Y, Su Y, Song M, Guo R, Wang M, Deng K, Lan T, Bao S, Wang G, Guo Z, Yu L. Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean. Genes (Basel) 2023; 14:1294. [PMID: 37372474 DOI: 10.3390/genes14061294] [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: 05/17/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132-346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.
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Affiliation(s)
- Ning Xu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Bingru Chen
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yuxin Cheng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yufei Su
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Mengyuan Song
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Rongqiu Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Minghai Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Kunpeng Deng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Tianjiao Lan
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Shuying Bao
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Guifang Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Zhongxiao Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Lihe Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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Singh L, Pruthi R, Chapagain S, Subudhi PK. Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112206. [PMID: 37299185 DOI: 10.3390/plants12112206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants' growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of indica and japonica rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na+ concentration, shoot Na+:K+ ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, qSNK4, qSNC9, and qSKC10, which co-localized with the earlier reported QTLs, a novel QTL, qSNC7, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice.
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Affiliation(s)
- Lovepreet Singh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Rajat Pruthi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sandeep Chapagain
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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Zhang G, Bi Z, Jiang J, Lu J, Li K, Bai D, Wang X, Zhao X, Li M, Zhao X, Wang W, Xu J, Li Z, Zhang F, Shi Y. Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1170641. [PMID: 37251777 PMCID: PMC10213895 DOI: 10.3389/fpls.2023.1170641] [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: 02/21/2023] [Accepted: 04/10/2023] [Indexed: 05/31/2023]
Abstract
Introduction Saline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage. Methods To understand the genetic basis of saline-alkali tolerance and facilitate breeding efforts for developing saline-alkali tolerant rice varieties, the genetic basis of rice saline-alkali tolerance was dissected by phenotyping seven germination-related traits of 736 diverse rice accessions under the saline-alkali stress and control conditions using genome-wide association and epistasis analysis (GWAES). Results Totally, 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified as significantly associated with saline-alkali tolerance, which explained a significant portion of the total phenotypic variation of the saline-alkali tolerance traits in the 736 rice accessions. Most of these QTNs were located in genomic regions either harboring saline-alkali tolerance QTNs or known genes for saline-alkali tolerance reported previously. Epistasis as an important genetic basis of rice saline-alkali tolerance was validated by genomic best linear unbiased prediction in which inclusion of both main-effect and epistatic QTNs showed a consistently better prediction accuracy than either main-effect or epistatic QTNs alone. Candidate genes for two pairs of important epistatic QTNs were suggested based on combined evidence from the high-resolution mapping plus their reported molecular functions. The first pair included a glycosyltransferase gene LOC_Os02g51900 (UGT85E1) and an E3 ligase gene LOC_Os04g01490 (OsSIRP4), while the second pair comprised an ethylene-responsive transcriptional factor, AP59 (LOC_Os02g43790), and a Bcl-2-associated athanogene gene, OsBAG1 (LOC_Os09g35630) for salt tolerance. Detailed haplotype analyses at both gene promoter and CDS regions of these candidate genes for important QTNs identified favorable haplotype combinations with large effects on saline-alkali tolerance, which can be used to improve rice saline-alkali tolerance by selective introgression. Discussion Our findings provided saline-alkali tolerant germplasm resources and valuable genetic information to be used in future functional genomic and breeding efforts of rice saline-alkali tolerance at the germination stage.
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Affiliation(s)
- Guogen Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Bi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingbing Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Keyang Li
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Di Bai
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Xinchen Wang
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Xueyu Zhao
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
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Guo M, Zhao H, He Z, Zhang W, She Z, Mohammadi MA, Shi C, Yan M, Tian D, Qin Y. Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:910663. [PMID: 35712583 PMCID: PMC9194907 DOI: 10.3389/fpls.2022.910663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aqa Mohammadi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Dagang Tian
- Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
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8
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Mei S, Zhang G, Jiang J, Lu J, Zhang F. Combining Genome-Wide Association Study and Gene-Based Haplotype Analysis to Identify Candidate Genes for Alkali Tolerance at the Germination Stage in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:887239. [PMID: 35463411 PMCID: PMC9033254 DOI: 10.3389/fpls.2022.887239] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/22/2022] [Indexed: 06/01/2023]
Abstract
Salinity-alkalinity stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve the tolerance to salinity-alkalinity of rice varieties at the germination stage. Although we have a more comprehensive understanding of salt tolerance in rice, the genetic basis of alkali tolerance in rice is still poorly understood. In this study, we measured seven germination-related traits under alkali stress and control conditions using 428 diverse rice accessions. The alkali tolerance levels of rice germplasms varied considerably during germination. Xian/indica accessions had generally higher tolerance to alkali stress than Geng/japonica accessions at the germination stage. Using genome-wide association analysis, 90 loci were identified as significantly associated with alkali tolerance. Eight genes (LOC_Os01g12000, LOC_Os03g60240, LOC_Os03g08960, LOC_Os04g41410, LOC_Os09g25060, LOC_Os11g35350, LOC_Os12g09350, and LOC_Os12g13300) were selected as important candidate genes for alkali tolerance based on the gene functional annotation and gene-CDS-haplotype analysis. According to the expression levels of LOC_Os09g25060 (OsWRKY76), it is likely to play a negative regulatory role in alkali tolerance during rice germination. An effective strategy for improving rice alkali tolerance may be to pyramid alkali-tolerant haplotypes of multiple candidate genes to obtain the optimal haplotype combination. Our findings may provide valuable genetic information and expand the use of alkali tolerance germplasm resources in rice molecular breeding to improve the alkali tolerance at the germination stage.
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Affiliation(s)
- Song Mei
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guogen Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jing Jiang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingbing Lu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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9
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Guo M, Zhang W, Mohammadi MA, He Z, She Z, Yan M, Shi C, Lin L, Wang A, Liu J, Tian D, Zhao H, Qin Y. OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:873993. [PMID: 35463416 PMCID: PMC9024357 DOI: 10.3389/fpls.2022.873993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aqa Mohammadi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingwei Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aqiong Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jindian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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10
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Singh D, Singh CK, Taunk J, Gaikwad K, Singh V, Sanwal SK, Karwa S, Singh D, Sharma PC, Yadav RK, Pal M. Linking genome wide RNA sequencing with physio-biochemical and cytological responses to catalogue key genes and metabolic pathways for alkalinity stress tolerance in lentil (Lens culinaris Medikus). BMC PLANT BIOLOGY 2022; 22:99. [PMID: 35247970 PMCID: PMC8897830 DOI: 10.1186/s12870-022-03489-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Alkaline soils cause low productivity in crop plants including lentil. Alkalinity adaptation strategies in lentil were revealed when morpho-anatomical and physio-biochemical observations were correlated with transcriptomics analysis in tolerant (PDL-1) and sensitive (L-4076) cultivars at seedling stage. RESULTS PDL-1 had lesser salt injury and performed better as compared to L-4076. Latter showed severe wilting symptoms and higher accumulation of Na+ and lower K+ in roots and shoots. PDL-1 performed better under high alkalinity stress which can be attributed to its higher mitotic index, more accumulation of K+ in roots and shoots and less aberrantly dividing cells. Also, antioxidant enzyme activities, osmolytes' accumulation, relative water content, membrane stability index and abscisic acid were higher in this cultivar. Differentially expressed genes (DEGs) related to these parameters were upregulated in tolerant genotypes compared to the sensitive one. Significantly up-regulated DEGs were found to be involved in abscisic acid (ABA) signalling and secondary metabolites synthesis. ABA responsive genes viz. dehydrin 1, 9-cis-epoxycarotenoid dioxygenase, ABA-responsive protein 18 and BEL1-like homeodomain protein 1 had log2fold change above 4.0. A total of 12,836 simple sequence repeats and 4,438 single nucleotide polymorphisms were identified which can be utilized in molecular studies. CONCLUSIONS Phyto-hormones biosynthesis-predominantly through ABA signalling, and secondary metabolism are the most potent pathways for alkalinity stress tolerance in lentil. Cultivar PDL-1 exhibited high tolerance towards alkalinity stress and can be used in breeding programmes for improving lentil production under alkalinity stress conditions.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute of Plant Biotechnology, 110012, New Delhi, India
| | - Vijayata Singh
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Satish Kumar Sanwal
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Sourabh Karwa
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deepti Singh
- Depatment of Botany, Meerut College, 250001, Meerut, India
| | - Parbodh Chander Sharma
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, 208002, Kanpur, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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11
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Tian T, Chen L, Ai Y, He H. Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq. Genes (Basel) 2022; 13:genes13020224. [PMID: 35205268 PMCID: PMC8871662 DOI: 10.3390/genes13020224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 02/04/2023] Open
Abstract
Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.
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Affiliation(s)
| | | | - Yufang Ai
- Correspondence: (Y.A.); (H.H.); Tel.: +86-0591-8378-9367 (H.H.)
| | - Huaqin He
- Correspondence: (Y.A.); (H.H.); Tel.: +86-0591-8378-9367 (H.H.)
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12
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In-on A, Thananusak R, Ruengjitchatchawalya M, Vongsangnak W, Laomettachit T. Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris. BIOLOGY 2022; 11:biology11010071. [PMID: 35053069 PMCID: PMC8773263 DOI: 10.3390/biology11010071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 01/17/2023]
Abstract
Cordyceps militaris is an edible fungus that produces many beneficial compounds, including cordycepin and carotenoid. In many fungi, growth, development and secondary metabolite production are controlled by crosstalk between light-signaling pathways and other regulatory cascades. However, little is known about the gene regulation upon light exposure in C. militaris. This study aims to construct a gene regulatory network (GRN) that responds to light in C. militaris. First, a genome-scale GRN was built based on transcription factor (TF)-target gene interactions predicted from the Regulatory Sequence Analysis Tools (RSAT). Then, a light-responsive GRN was extracted by integrating the transcriptomic data onto the genome-scale GRN. The light-responsive network contains 2689 genes and 6837 interactions. From the network, five TFs, Snf21 (CCM_04586), an AT-hook DNA-binding motif TF (CCM_08536), a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and a heat shock factor Hsf1 (CCM_05142), were identified as key regulators that co-regulate a large group of growth and developmental genes. The identified regulatory network and expression profiles from our analysis suggested how light may induce the growth and development of C. militaris into a sexual cycle. The light-mediated regulation also couples fungal development with cordycepin and carotenoid production. This study leads to an enhanced understanding of the light-responsive regulation of growth, development and secondary metabolite production in the fungi.
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Affiliation(s)
- Ammarin In-on
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; (A.I.-o.); (M.R.)
- School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Marasri Ruengjitchatchawalya
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; (A.I.-o.); (M.R.)
- Biotechnology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (W.V.); (T.L.)
| | - Teeraphan Laomettachit
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; (A.I.-o.); (M.R.)
- Theoretical and Computational Physics (TCP) Group, Center of Excellence in Theoretical and Computational Science (TaCS-CoE), King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
- Correspondence: (W.V.); (T.L.)
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13
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Singh PK, Indoliya Y, Agrawal L, Awasthi S, Deeba F, Dwivedi S, Chakrabarty D, Shirke PA, Pandey V, Singh N, Dhankher OP, Barik SK, Tripathi RD. Genomic and proteomic responses to drought stress and biotechnological interventions for enhanced drought tolerance in plants. CURRENT PLANT BIOLOGY 2022; 29:100239. [DOI: 10.1016/j.cpb.2022.100239] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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14
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Kamran M, Ramesh SA, Gilliham M, Tyerman SD, Bose J. Role of TaALMT1 malate-GABA transporter in alkaline pH tolerance of wheat. PLANT, CELL & ENVIRONMENT 2020; 43:2443-2459. [PMID: 32666573 DOI: 10.1111/pce.13845] [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: 04/06/2020] [Revised: 06/11/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Malate exudation through wheat (Triticum aestivum L) aluminium-activated malate transporter 1 (TaALMT1) confers Al3+ tolerance at low pH, but is also activated by alkaline pH, and is regulated by and facilitates significant transport of gamma-aminobutyric acid (GABA, a zwitterionic buffer). Therefore, TaALMT1 may facilitate acidification of an alkaline rhizosphere by promoting exudation of both malate and GABA. Here, the performance of wheat near isogenic lines ET8 (Al+3 -tolerant, high TaALMT1 expression) and ES8 (Al+3 -sensitive, low TaALMT1 expression) are compared. Root growth (at 5 weeks) was higher for ET8 than ES8 at pH 9. ET8 roots exuded more malate and GABA at high pH and acidified the rhizosphere more rapidly. GABA and malate exudation was enhanced at high pH by the addition of aluminate in both ET8 and transgenic barley expressing TaALMT1. Xenopus laevis oocytes expressing TaALMT1 acidified an alkaline media more rapidly than controls corresponding to higher GABA efflux. TaALMT1 expression did not change under alkaline conditions but key genes involved in GABA turnover changed in accordance with a high rate of GABA synthesis. We propose that TaALMT1 plays a role in alkaline tolerance by exuding malate and GABA, possibly coupled to proton efflux.
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Affiliation(s)
- Muhammad Kamran
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia, Australia
| | - Sunita A Ramesh
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia, Australia
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Matthew Gilliham
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia, Australia
| | - Stephen D Tyerman
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia, Australia
| | - Jayakumar Bose
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, Glen Osmond, South Australia, Australia
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15
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Yang Y, Yang Y, Fan Q, Huang Z, Li J, Wu Q, Tang X, Ding J, Han N, Xu B. Molecular and Biochemical Characterization of Salt-Tolerant Trehalose-6-Phosphate Hydrolases Identified by Screening and Sequencing Salt-Tolerant Clones From the Metagenomic Library of the Gastrointestinal Tract. Front Microbiol 2020; 11:1466. [PMID: 32733411 PMCID: PMC7358406 DOI: 10.3389/fmicb.2020.01466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
The exploration and utilization of microbial salt-tolerant enzymatic and genetic resources are of great significance in the field of biotechnology and for the research of the adaptation of microorganisms to extreme environments. The presence of new salt-tolerant genes and enzymes in the microbial metagenomic library of the gastrointestinal tract has been confirmed through metagenomic technology. This paper aimed to identify and characterize enzymes that confer salt tolerance in the gastrointestinal tract microbe. By screening the fecal metagenomic library, 48 salt-tolerant clones were detected, of which 10 salt-tolerant clones exhibited stronger tolerance to 7% (wt/vol) NaCl and stability in different concentrations of NaCl [5%-9% (wt/vol)]. High-throughput sequencing and biological information analysis showed that 91 potential genes encoded proteins and enzymes that were widely involved in salt tolerance. Furthermore, two trehalose-6-phosphate hydrolase genes, namely, tre_P2 and tre_P3, were successfully cloned and expressed in Escherichia coli BL21 (DE3). By virtue of the substrate of p-nitrophenyl-α-D-glucopyranoside (pNPG) which can be specifically hydrolyzed by trehalose-6-phosphate hydrolase to produce glucose and p-nitrophenol, the two enzymes can act optimally at pH 7.5 and 30°C. Steady-state kinetics with pNPG showed that the K M and K cat values were 15.63 mM and 10.04 s-1 for rTRE_P2 and 12.51 mM and 10.71 s-1 for rTRE_P3, respectively. Characterization of enzymatic properties demonstrated that rTRE_P2 and rTRE_P3 were salt-tolerant. The enzymatic activity increased with increasing NaCl concentration, and the maximum activities of rTRE_P2 and rTRE_P3 were obtained at 4 and 3 M NaCl, respectively. The activities of rTRE_P2 increased by approximately 43-fold even after 24 h of incubation with 5 M NaCl. This study is the first to report the identification as well as molecular and biochemical characterization of salt-tolerant trehalose-6-phosphate hydrolase from the metagenomic library of the gastrointestinal tract. Results indicate the existence of numerous salt-tolerant genes and enzymes in gastrointestinal microbes and provide new insights into the salt-tolerant mechanisms in the gastrointestinal environment.
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Affiliation(s)
- Yanxia Yang
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yunjuan Yang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Qin Fan
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Junjun Li
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Qian Wu
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Xianghua Tang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Junmei Ding
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Nanyu Han
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Bo Xu
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
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16
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Li X, Zheng H, Wu W, Liu H, Wang J, Jia Y, Li J, Yang L, Lei L, Zou D, Zhao H. QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study. RICE (NEW YORK, N.Y.) 2020; 13:48. [PMID: 32676742 PMCID: PMC7364718 DOI: 10.1186/s12284-020-00412-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/08/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage. RESULTS A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of LOC_Os11g37390. CONCLUSION Based on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
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Affiliation(s)
- Xianwei Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Wenshen Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jiaming Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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17
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He Y, Dong Y, Yang X, Guo D, Qian X, Yan F, Wang Y, Li J, Wang Q. Functional activation of a novel R2R3-MYB protein gene, GmMYB68, confers salt-alkali resistance in soybean ( Glycine max L.). Genome 2020; 63:13-26. [PMID: 31550433 DOI: 10.1139/gen-2018-0132] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Soil salinity significantly reduces soybean (Glycine max L.) production worldwide. Plants resistance to stress conditions is a complex characteristic regulated by multiple signaling pathways. The v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF) plays a crucial role in plant development, secondary metabolism, and abiotic stress responses. GmMYB68-overexpression and RNA interference (RNAi) lines were established for examining the function of G. max GmMYB68 in plant responses to abiotic stresses. The predicted amino acid sequence of GmMYB68 was similar to that of R2R3-MYB proteins. Quantitative real-time PCR analysis revealed that GmMYB68 expression varied in response to abiotic stresses. GmMYB68-overexpression lines showed enhanced resistance to salt and alkali stresses and their osmotic adjustment and photosynthetic rates were also stronger than that of GmMYB68-RNAi and wild type plants. Although wild type and transgenic plants showed no significant differences in agronomic traits under normal conditions, the overexpression of GmMYB68 increased grain number and 100-grain weights under salt stress. Our study identified a valuable TF associated with stress response in soybean, as its overexpression might help improve salt and alkali tolerance in soybean and other crops.
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Affiliation(s)
- Yuxuan He
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Yingshan Dong
- Jilin Academy of Agricultural Sciences, Changchun 130033, P.R. China
| | - Xiangdong Yang
- Jilin Academy of Agricultural Sciences, Changchun 130033, P.R. China
| | - Dongquan Guo
- Jilin Academy of Agricultural Sciences, Changchun 130033, P.R. China
| | - Xueyan Qian
- Jilin Academy of Agricultural Sciences, Changchun 130033, P.R. China
| | - Fan Yan
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Ying Wang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Jingwen Li
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China
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18
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Li N, Zheng H, Cui J, Wang J, Liu H, Sun J, Liu T, Zhao H, Lai Y, Zou D. Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage. RICE (NEW YORK, N.Y.) 2019; 12:24. [PMID: 30976929 PMCID: PMC6459459 DOI: 10.1186/s12284-019-0285-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Salinity-alkalinity stress is one of the major factors limiting rice production. The damage caused by alkaline salt stress to rice growth is more severe than that caused by neutral salt stress. At present, the genetic resources (quantitative trait loci (QTLs) and genes) that can be used by rice breeders to improve alkalinity tolerance are limited. Here, we assessed the alkalinity tolerance of rice at the seedling stage and performed a genome-wide association study (GWAS) based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 295 japonica rice varieties. RESULTS We used the score of alkalinity tolerance (SAT), the concentrations of Na+ and K+ in the shoots (SNC and SKC, respectively) and the Na+/K+ ratio of shoots (SNK) as indices to assess alkalinity tolerance at the seedling stage in rice. Based on population structure analysis, the japonica rice panel was divided into three subgroups. Linkage disequilibrium (LD) analysis showed that LD decay occurred at 109.77 kb for the whole genome and varied between 13.79 kb and 415.77 kb across the 12 chromosomes, at which point the pairwise squared correlation coefficient (r2) decreased to half of its maximum value. A total of eight QTLs significantly associated with the SAT, SNC and SNK were identified by genome-wide association mapping. A common QTL associated with the SAT, SNC and SNK on chromosome 3 at the position of 15.0 Mb, which explaining 13.36~13.64% of phenotypic variation, was selected for further analysis. The candidate genes were filtered based on LD decay, Gene Ontology (GO) enrichment, RNA sequencing data, and quantitative real-time PCR (qRT-PCR) analysis. Moreover, sequence analysis revealed one 7-bp insertion/deletion (indel) difference in LOC_Os03g26210 (OsIRO3) between the alkalinity-tolerant and alkalinity-sensitive rice varieties. OsIRO3 encodes a bHLH-type transcription factor and has been shown to be a negative regulator of the Fe-deficiency response in rice. CONCLUSION Based on these results, OsIRO3 maybe a novel functional gene associated with alkalinity tolerance in japonica rice. This study provides resources for improving alkalinity tolerance in rice, and the functional molecular marker could be verified to breed new rice varieties with alkalinity tolerance via marker-assisted selection (MAS).
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Affiliation(s)
- Ning Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Jingnan Cui
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Tongtong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yongcai Lai
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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19
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Dmitriev AA, Krasnov GS, Rozhmina TA, Zyablitsin AV, Snezhkina AV, Fedorova MS, Pushkova EN, Kezimana P, Novakovskiy RO, Povkhova LV, Smirnova MI, Muravenko OV, Bolsheva NL, Kudryavtseva AV, Melnikova NV. Flax (Linum usitatissimum L.) response to non-optimal soil acidity and zinc deficiency. BMC PLANT BIOLOGY 2019; 19:54. [PMID: 30813909 PMCID: PMC6393972 DOI: 10.1186/s12870-019-1641-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is grown for fiber and seed production. Unfavorable environments, such as nutrient deficiency and non-optimal soil acidity, decrease the quantity and quality of yield. Cultivation of tolerant to stress varieties can significantly reduce the crop losses. Understanding the mechanisms of flax response to the stresses and identification of resistance gene candidates will help in breeding of improved cultivars. In the present work, the response of flax plants to increased pH level and zinc (Zn) deficiency was studied. RESULTS We performed high-throughput transcriptome sequencing of two flax cultivars with diverse tolerance to increased pH level and Zn deficiency: Norlin (tolerant) and Mogilevsky (sensitive). Sixteen cDNA libraries were created from flax plants grown under control conditions, increased pH level, Zn deficiency, and both stresses simultaneously, and about 35 million reads were obtained for each experiment type. Unfavorable pH resulted in significantly stronger gene expression alterations compared to Zn deficiency. Ion homeostasis, oxidoreductase activity, cell wall, and response to stress Gene Ontology terms were the most affected by unfavorable pH and Zn deficiency both in tolerant and sensitive flax cultivars. Upregulation of genes encoding metal transporters was identified under increased pH level, Zn deficiency, and both stresses simultaneously. Under Zn deficiency, only in tolerant cultivar Norlin, we revealed the induction of several photosynthesis-related genes and, in this way, this tolerant genotype could overcome unfavorable effects of reduced Zn content. CONCLUSIONS We identified genes with expression alterations in flax under non-optimal soil acidity and Zn deficiency based on high-throughput sequencing data. These genes are involved in diverse processes, including ion transport, cell wall biogenesis, and photosynthesis, and could play an important role in flax response to the studied stresses. Moreover, genes with distinct expression changes between examined tolerant and sensitive genotypes could determine the mechanisms of flax tolerance to non-optimal soil acidity and Zn deficiency.
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Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- All-Russian Research Institute for Flax, Torzhok, Russia
| | | | | | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Parfait Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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20
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Cho SH, Lee CH, Gi E, Yim Y, Koh HJ, Kang K, Paek NC. The Rice Rolled Fine Striped (RFS) CHD3/Mi-2 Chromatin Remodeling Factor Epigenetically Regulates Genes Involved in Oxidative Stress Responses During Leaf Development. FRONTIERS IN PLANT SCIENCE 2018; 9:364. [PMID: 29616070 PMCID: PMC5870552 DOI: 10.3389/fpls.2018.00364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/05/2018] [Indexed: 05/20/2023]
Abstract
In rice (Oryza sativa), moderate leaf rolling increases photosynthetic competence and raises grain yield; therefore, this important agronomic trait has attracted much attention from plant biologists and breeders. However, the relevant molecular mechanism remains unclear. Here, we isolated and characterized Rolled Fine Striped (RFS), a key gene affecting rice leaf rolling, chloroplast development, and reactive oxygen species (ROS) scavenging. The rfs-1 gamma-ray allele and the rfs-2 T-DNA insertion allele of RFS failed to complement each other and their mutants had similar phenotypes, producing extremely incurved leaves due to defective development of vascular cells on the adaxial side. Map-based cloning showed that the rfs-1 mutant harbors a 9-bp deletion in a gene encoding a predicted CHD3/Mi-2 chromatin remodeling factor belonging to the SNF2-ATP-dependent chromatin remodeling family. RFS was expressed in various tissues and accumulated mainly in the vascular cells throughout leaf development. Furthermore, RFS deficiency resulted in a cell death phenotype that was caused by ROS accumulation in developing leaves. We found that expression of five ROS-scavenging genes [encoding catalase C, ascorbate peroxidase 8, a putative copper/zinc superoxide dismutase (SOD), a putative SOD, and peroxiredoxin IIE2] decreased in rfs-2 mutants. Western-blot and chromatin immunoprecipitation (ChIP) assays demonstrated that rfs-2 mutants have reduced H3K4me3 levels in ROS-related genes. Loss-of-function in RFS also led to multiple developmental defects, affecting pollen development, grain filling, and root development. Our results suggest that RFS is required for many aspects of plant development and its function is closely associated with epigenetic regulation of genes that modulate ROS homeostasis.
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Affiliation(s)
- Sung-Hwan Cho
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chung-Hee Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Eunji Gi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yehyun Yim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kiyoon Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Kiyoon Kang, Nam-Chon Paek,
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Crop Biotechnology Institute, Institutes of Green Bio Science & Technology, Seoul National University, Seoul, South Korea
- *Correspondence: Kiyoon Kang, Nam-Chon Paek,
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21
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Transcriptome analysis of genes involved in defense against alkaline stress in roots of wild jujube (Ziziphus acidojujuba). PLoS One 2017; 12:e0185732. [PMID: 28976994 PMCID: PMC5627934 DOI: 10.1371/journal.pone.0185732] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/18/2017] [Indexed: 11/19/2022] Open
Abstract
Wild jujube (Ziziphus acidojujuba Mill.) is highly tolerant to alkaline, saline and drought stress; however, no studies have performed transcriptome profiling to study the response of wild jujube to these and other abiotic stresses. In this study, we examined the tolerance of wild jujube to NaHCO3-NaOH solution and analyzed gene expression profiles in response to alkaline stress. Physiological experiments revealed that H2O2 content in leaves increased significantly and root activity decreased quickly during alkaline of pH 9.5 treatment. For transcriptome analysis, wild jujube plants grown hydroponically were treated with NaHCO3-NaOH solution for 0, 1, and 12 h and six transcriptomes from roots were built. In total, 32,758 genes were generated, and 3,604 differentially expressed genes (DEGs) were identified. After 1 h, 853 genes showed significantly different expression between control and treated plants; after 12 h, expression of 2,856 genes was significantly different. The expression pattern of nine genes was validated by quantitative real-time PCR. After gene annotation and gene ontology enrichment analysis, the genes encoding transcriptional factors, serine/threonine-protein kinases, heat shock proteins, cysteine-like kinases, calmodulin-like proteins, and reactive oxygen species (ROS) scavengers were found to be closely involved in alkaline stress response. These results will provide useful insights for elucidating the mechanisms underlying alkaline tolerance in wild jujube.
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22
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Zhang H, Liu XL, Zhang RX, Yuan HY, Wang MM, Yang HY, Ma HY, Liu D, Jiang CJ, Liang ZW. Root Damage under Alkaline Stress Is Associated with Reactive Oxygen Species Accumulation in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1580. [PMID: 28943882 PMCID: PMC5596797 DOI: 10.3389/fpls.2017.01580] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/29/2017] [Indexed: 05/19/2023]
Abstract
Alkaline stress (high pH) severely damages root cells, and consequently, inhibits rice (Oryza sativa L.) seedling growth. In this study, we demonstrate the accumulation of reactive oxygen species (ROS) in root cells under alkaline stress. Seedlings of two rice cultivars with different alkaline tolerances, 'Dongdao-4' (moderately alkaline-tolerant) and 'Jiudao-51' (alkaline-sensitive), were subjected to alkaline stress simulated by 15 mM sodium carbonate (Na2CO3). Alkaline stress greatly reduced seedling survival rate, shoot and root growth, and root vigor. Moreover, severe root cell damage was observed under alkaline stress, as shown by increased membrane injury, malondialdehyde accumulation, and Evan's Blue staining. The expression of the cell death-related genes OsKOD1, OsHsr203j, OsCP1, and OsNAC4 was consistently upregulated, while that of a cell death-suppressor gene, OsBI1, was downregulated. Analysis of the ROS contents revealed that alkaline stress induced a marked accumulation of superoxide anions ([Formula: see text]) and hydrogen peroxide (H2O2) in rice roots. The application of procyanidins (a potent antioxidant) to rice seedlings 24 h prior to alkaline treatment significantly alleviated alkalinity-induced root damage and promoted seedling growth inhibition, which were concomitant with reduced ROS accumulation. These results suggest that root cell damage, and consequently growth inhibition, of rice seedlings under alkaline stress is closely associated with ROS accumulation. The antioxidant activity of superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase increased under alkaline stress in the roots, probably in response to the cellular damage induced by oxidative stress. However, this response mechanism may be overwhelmed by the excess ROS accumulation observed under stress, resulting in oxidative damage to root cells. Our findings provide physiological insights into the molecular mechanisms of alkalinity-induced damage to root cells, and will contribute to the improvement of alkaline stress tolerance in rice plants.
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Affiliation(s)
- Hui Zhang
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
| | - Xiao-Long Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Rui-Xue Zhang
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
| | - Hai-Yan Yuan
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
| | - Ming-Ming Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
| | - Hao-Yu Yang
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
| | - Hong-Yuan Ma
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
| | - Duo Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Chang-Jie Jiang
- Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Zheng-Wei Liang
- Northeast Institute of Geography and Agroecology, Chinese Academy of SciencesChangchun, China
- Da’an Sodic Land Experiment Station, Chinese Academy of Sciences, Da’anJilin, China
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23
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Wang J, Wang R, Wang Y, Zhang L, Zhang L, Xu Y, Yao S. Short and Solid Culm/RFL/APO2 for culm development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:85-96. [PMID: 28370563 DOI: 10.1111/tpj.13548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/20/2017] [Indexed: 05/14/2023]
Abstract
The culm development of rice is characterized by elongation and medullary cavity (MC) formation, which are determined by node formation meristem and residual meristem, respectively. Although many factors have been shown to affect culm elongation, molecules involved in MC formation remained to be identified. In this study, we show that a point mutation in SHORT and SOLID CULM (SSC), the rice homologue of Arabidopsis LFY, resulted in plants with drastically reduced culm length and completely abolished MC formation. Analysis of transgenic plants with moderately enhanced SSC expression revealed significant decreases in plant height and MC size in contrast to slight changes in heading date, indicating that the culm developmental process is much more tightly monitored by the gene. Transcriptomic analysis revealed the differential expression of knotted-1 like homeobox (KNOX) protein genes and gibberellin (GA) metabolic genes in the ssc mutant background, and most of the genes contained well-conserved LFY-binding cis-elements that could be effectively recognized by SSC. Genetic analysis found that the reduced culm length of the mutant could be largely rescued by the GA-accumulating mutation eui, whereas MC formation remained unchanged in the double mutant plants. Taken together, our results suggest that SSC affects culm elongation mainly through maintaining GA homeostasis, while functions in MC formation by mediating residual meristem activity possibly via the KNOX pathway. The present study provides a potential strategy for improving the culm morphology and plant architecture in rice by manipulating SSC and/or its downstream components.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruci Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yueming Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Li Zhang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Li Zhang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufang Xu
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanguo Yao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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24
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Guo M, Li S, Tian S, Wang B, Zhao X. Transcriptome analysis of genes involved in defense against alkaline stress in roots of wild jujube (Ziziphus acidojujuba). PLoS One 2017. [PMID: 28976994 DOI: 10.1371/journalpone0185732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Wild jujube (Ziziphus acidojujuba Mill.) is highly tolerant to alkaline, saline and drought stress; however, no studies have performed transcriptome profiling to study the response of wild jujube to these and other abiotic stresses. In this study, we examined the tolerance of wild jujube to NaHCO3-NaOH solution and analyzed gene expression profiles in response to alkaline stress. Physiological experiments revealed that H2O2 content in leaves increased significantly and root activity decreased quickly during alkaline of pH 9.5 treatment. For transcriptome analysis, wild jujube plants grown hydroponically were treated with NaHCO3-NaOH solution for 0, 1, and 12 h and six transcriptomes from roots were built. In total, 32,758 genes were generated, and 3,604 differentially expressed genes (DEGs) were identified. After 1 h, 853 genes showed significantly different expression between control and treated plants; after 12 h, expression of 2,856 genes was significantly different. The expression pattern of nine genes was validated by quantitative real-time PCR. After gene annotation and gene ontology enrichment analysis, the genes encoding transcriptional factors, serine/threonine-protein kinases, heat shock proteins, cysteine-like kinases, calmodulin-like proteins, and reactive oxygen species (ROS) scavengers were found to be closely involved in alkaline stress response. These results will provide useful insights for elucidating the mechanisms underlying alkaline tolerance in wild jujube.
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Affiliation(s)
- Mingxin Guo
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Shipeng Li
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Shan Tian
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Bei Wang
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
| | - Xusheng Zhao
- College of Life Science, Luoyang Normal University, Luoyang, Henan, China
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25
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Song L, Wang R, Zhang L, Wang Y, Yao S. CRR1 encoding callose synthase functions in ovary expansion by affecting vascular cell patterning in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:620-632. [PMID: 27464824 DOI: 10.1111/tpj.13287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
The ovary of rice undergoes rapid expansion immediately after fertilization, and this process determines the final sink strength potential of caryopses. To date, work on rice grain development has mainly focused on endosperm filling, whereas information on the essential elements for ovary expansion remains limited. We report here a functional analysis of the ovary expansion retarded mutant crr1 in rice. Map-based cloning revealed that CRR1 encodes a protein homologous to the Arabidopsis callose synthases AtGSL8 and AtGSL10. Point mutation in crr1 resulted in alternative splicing, which led to the formation of the truncated crr1 protein without the β-glucan synthase domain. Iodine staining showed that there were few starch granules and these were unevenly distributed in the pericarp of crr1, and a 5,6-carboxyfluorescein diacetate transport assay revealed that carbohydrates were less efficiently unloaded from the lateral vasculature into the developing caryopsis. CRR1 transcripts were detected in all plant organs, with the highest level found in receptacles, which are mainly composed of vascular tissues. Analysis of pCRR1::GUS transgenic plants showed that CRR1 was specifically expressed in vascular bundle cells. Consistently, loss of function of CRR1 led to disordered patterns of vascular cells in the ovaries and receptacles of the mutant. Furthermore, a small portion of cells in the vascular bundles of crr1 showed defective cell wall formation, and callose deposition was specifically reduced at the plasmodesmata (PD) of cells with aberrant walls. Our results suggest that CRR1 performs a pivotal role in determining initial ovary expansion in rice, possibly via the PD-mediated permeability of cell fate determinants for vascular cell differentiation.
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Affiliation(s)
- Longzhen Song
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruci Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Li Zhang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yueming Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shanguo Yao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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26
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Chen W, Zhu Q, Liu Y, Zhang Q. Chromatin Remodeling and Plant Immunity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 106:243-260. [PMID: 28057214 DOI: 10.1016/bs.apcsb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance?
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Affiliation(s)
- W Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Y Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, College of Life Sciences, South China Agricultural University, Guangzhou, China.
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27
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Chen L, Zhang YH, Huang T, Cai YD. Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities. Mol Genet Genomics 2016; 291:913-34. [PMID: 26728152 DOI: 10.1007/s00438-015-1157-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 12/08/2015] [Indexed: 01/18/2023]
Abstract
Studies of protein phenotypes represent a central challenge of modern genetics in the post-genome era because effective and accurate investigation of protein phenotypes is one of the most critical procedures to identify functional biological processes in microscale, which involves the analysis of multifactorial traits and has greatly contributed to the development of modern biology in the post genome era. Therefore, we have developed a novel computational method that identifies novel proteins associated with certain phenotypes in yeast based on the protein-protein interaction network. Unlike some existing network-based computational methods that identify the phenotype of a query protein based on its direct neighbors in the local network, the proposed method identifies novel candidate proteins for a certain phenotype by considering all annotated proteins with this phenotype on the global network using a shortest path (SP) algorithm. The identified proteins are further filtered using both a permutation test and their interactions and sequence similarities to annotated proteins. We compared our method with another widely used method called random walk with restart (RWR). The biological functions of proteins for each phenotype identified by our SP method and the RWR method were analyzed and compared. The results confirmed a large proportion of our novel protein phenotype annotation, and the RWR method showed a higher false positive rate than the SP method. Our method is equally effective for the prediction of proteins involving in all the eleven clustered yeast phenotypes with a quite low false positive rate. Considering the universality and generalizability of our supporting materials and computing strategies, our method can further be applied to study other organisms and the new functions we predicted can provide pertinent instructions for the further experimental verifications.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China. .,College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People's Republic of China.
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China.
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28
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Wang Y, Cheng ZZ, Chen X, Zheng Q, Yang ZM. CrGNAT gene regulates excess copper accumulation and tolerance in Chlamydomonas reinhardtii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:120-129. [PMID: 26475193 DOI: 10.1016/j.plantsci.2015.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Abstract
Excess copper (Cu) in environment affects the growth and metabolism of plants and green algae. However, the molecular mechanism for regulating plant tolerance to excess Cu is not fully understood. Here, we report a gene CrGNAT enconding an acetyltransferase in Chlamydomonas reinhardtii and identified its role in regulating tolerance to Cu toxicity. Expression of CrGNAT was significantly induced by 75-400μM Cu. The top induction occurred at 100μM. Transgenic algae overexpressing CrGNAT (35S::CrGNAT) in C. reinhardtii showed high tolerance to excess Cu, with improved cell population, chlorophyll accumulation and photosynthesis efficiency, but with low degree of oxidation with regard to reduced hydrogen peroxide, lipid peroxides and non-protein thiol compounds. In contrast, CrGNAT knock-down lines with antisense led to sensitivity to Cu stress. 35S::CrGNAT algae accumulated more Cu and other metals (Zn, Fe, Cu, Mn and Mg) than wild-type, whereas the CrGNAT down-regulated algae (35S::AntiCrGNAT) had moderate levels of Cu and Mn, but no effects on Zn, Fe and Mg accumulation as compared to wild-type. The elevated metal absorption in CrGNAT overexpression algae implies that the metals can be removed from water media. Quantitative RT-PCR analysis revealed that expression of two genes encoding N-lysine histone methyltransferases was repressed in 35S::CrGNAT algae, suggesting that CrGNAT-regulated algal tolerance to Cu toxicity is likely associated with histone methylation and chromatin remodeling. The present work provided an example a basis to develop techniques for environmental restoration of metal-contaminated aquatic ecosystems.
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Affiliation(s)
- Ye Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhen Zhen Cheng
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xi Chen
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Qi Zheng
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China.
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Donà M, Mittelsten Scheid O. DNA Damage Repair in the Context of Plant Chromatin. PLANT PHYSIOLOGY 2015; 168:1206-18. [PMID: 26089404 PMCID: PMC4528755 DOI: 10.1104/pp.15.00538] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/17/2015] [Indexed: 05/03/2023]
Abstract
The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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Esters of the marine-derived triterpene sipholenol A reverse P-GP-mediated drug resistance. Mar Drugs 2015; 13:2267-86. [PMID: 25874923 PMCID: PMC4413211 DOI: 10.3390/md13042267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/10/2015] [Accepted: 03/25/2015] [Indexed: 12/16/2022] Open
Abstract
Our previous studies showed that several sipholane triterpenes, sipholenol A, sipholenone E, sipholenol L and siphonellinol D, have potent reversal effect for multidrug resistance (MDR) in cancer cells that overexpressed P-glycoprotein (P-gp/ABCB1). Through comparison of cytotoxicity towards sensitive and multi-drug resistant cell lines, we identified that the semisynthetic esters sipholenol A-4-O-acetate and sipholenol A-4-O-isonicotinate potently reversed P-gp-mediated MDR but had no effect on MRP1/ABCC1 and BCRP/ABCG2-mediated MDR. The results from [3H]-paclitaxel accumulation and efflux studies suggested that these two triterpenoids were able to increase the intracellular accumulation of paclitaxel by inhibiting its active efflux. In addition, western blot analysis revealed that these two compounds did not alter the expression levels of P-gp when treated up to 72 h. These sipholenol derivatives also stimulated the ATPase activity of P-gp membranes, which suggested that they might be substrates of P-gp. Moreover, in silico molecular docking studies revealed the virtual binding modes of these two compounds into human homology model of P-gp. In conclusion, sipholenol A-4-O-acetate and sipholenol A-4-O-isonicotinate efficiently inhibit the P-gp and may represent potential reversal agents for the treatment of multidrug resistant cancers.
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