1
|
Lou T, Lv S, Wang J, Wang D, Lin K, Zhang X, Zhang B, Guo Z, Yi Z, Li Y. Cell size and xylem differentiation regulating genes from Salicornia europaea contribute to plant salt tolerance. PLANT, CELL & ENVIRONMENT 2024; 47:2640-2659. [PMID: 38558078 DOI: 10.1111/pce.14905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Cell wall is involved in plant growth and plays pivotal roles in plant adaptation to environmental stresses. Cell wall remodelling may be crucial to salt adaptation in the euhalophyte Salicornia europaea. However, the mechanism underlying this process is still unclear. Here, full-length transcriptome indicated cell wall-related genes were comprehensively regulated under salinity. The morphology and cell wall components in S. europaea shoot were largely modified under salinity. Through the weighted gene co-expression network analysis, SeXTH2 encoding xyloglucan endotransglucosylase/hydrolases, and two SeLACs encoding laccases were focused. Meanwhile, SeEXPB was focused according to expansin activity and the expression profiling. Function analysis in Arabidopsis validated the functions of these genes in enhancing salt tolerance. SeXTH2 and SeEXPB overexpression led to larger cells and leaves with hemicellulose and pectin content alteration. SeLAC1 and SeLAC2 overexpression led to more xylem vessels, increased secondary cell wall thickness and lignin content. Notably, SeXTH2 transgenic rice exhibited enhanced salt tolerance and higher grain yield. Altogether, these genes may function in the succulence and lignification process in S. europaea. This work throws light on the regulatory mechanism of cell wall remodelling in S. europaea under salinity and provides potential strategies for improving crop salt tolerance and yields.
Collapse
Affiliation(s)
- Tengxue Lou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Department of In Vitro Diagnostic Reagent, National Institutes for Food and Drug Control, Beijing, China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Jinhui Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zijing Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ze Yi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| |
Collapse
|
2
|
Jia W, Guo Z, Lv S, Lin K, Li Y. SbYS1 and SbWRKY72 regulate Cd tolerance and accumulation in sweet sorghum. PLANTA 2024; 259:100. [PMID: 38536457 DOI: 10.1007/s00425-024-04388-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/12/2024] [Indexed: 04/24/2024]
Abstract
MAIN CONCLUSION SbYS1 and its upstream transcription factor SbWRKY72 were involved in Cd tolerance and accumulation and are valuable for developing sweet sorghum germplasm with high-Cd tolerance or accumulation ability through genetic manipulation. Cadmium (Cd) is highly toxic and can severely affect human health. Sweet sorghum, as an energy crop, shows great potential in extracting cadmium from Cd-contaminated soils. However, its molecular mechanisms of Cd-tolerance and -accumulation remain largely unknown. Here, we isolated a YSL family gene SbYS1 from the sweet sorghum genotype with high Cd accumulation ability and the expression of SbYS1 in roots was induced by cadmium. GUS staining experiment exhibited that SbYS1 was expressed in the epidermis and parenchyma tissues of roots. Further subcellular localization analysis suggested that SbYS1 was localized in the endoplasmic reticulum and plasma membrane. Yeast transformed with SbYS1 exhibited a sensitive phenotype compared to the control when exposed to Cd-NA (chelates of cadmium and nicotianamine), indicating that SbYS1 may absorb cadmium in the form of Cd-NA. Arabidopsis overexpressing SbYS1 had a longer root length and accumulated less Cd in roots and shoots. SbWRKY72 bound to the promoter of SbYS1 and negatively regulated the expression of SbYS1. Transgenic Arabidopsis of SbWRKY72 showed higher sensitivity to cadmium and increased cadmium accumulation in roots. Our results provide references for improving the phytoremediation efficiency of sweet sorghum by genetic manipulation in the future.
Collapse
Affiliation(s)
- Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 401122, China
| | - Zijing Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
| |
Collapse
|
3
|
Kulkarni J, Sahoo SA, Herzyk P, Barvkar VT, Kumar SA, Ravichandran J, Samal A, Amtmann A, Borde M, Suprasanna P, Srivastava AK. Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.). PLANT, CELL & ENVIRONMENT 2024; 47:961-975. [PMID: 38044749 DOI: 10.1111/pce.14767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 11/04/2023] [Indexed: 12/05/2023]
Abstract
Sesuvium portulacastrum (L.) is a halophyte, adapted to grow naturally under saline environments. The ability to use Na and K interchangeably indicated its facultative halophyte nature. No significant growth reduction occurs in seedlings up to 250 mM NaCl, except for curling of the youngest leaf. Within 8 h of salt treatment, seedlings accumulate proline, glycine betaine and other amino acids in both root and shoot. Despite a continued increase of tissue Na content, the number of differentially expressed genes (DEGs) decreases between 8 and 24 h of salt exposure, indicating transcriptional restoration after the initial osmotic challenge. At 8 h, upregulated genes mainly encode transporters and transcription factors, while genes in growth-related pathways such as photosynthesis and ribosome-associated biogenesis are suppressed. Overexpression of SpRAB18 (an ABA-responsive dehydrin), one of the most strongly induced DEGs, in soybean was found to increase biomass in control conditions and the growth benefit was maintained when plants were grown in 100 mM NaCl, indicating conservation of function in halophyte and glycophyte. An open-access transcriptome database "SesuviumKB" (https://cb.imsc.res.in/sesuviumkb/) was developed to involve the scientific community in wide-scale functional studies of S. portulacastrum genes, that could pave the way to engineer salt tolerance in crops.
Collapse
Affiliation(s)
- Jayant Kulkarni
- Department of Botany, Savitribai Phule Pune University, Pune, India
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sripati A Sahoo
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Pawel Herzyk
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Sanjukta A Kumar
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Janani Ravichandran
- The Institute of Mathematical Sciences (IMSc), Chennai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Anna Amtmann
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mahesh Borde
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashish K Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
4
|
Jordine A, Retzlaff J, Gens L, Ehrt B, Fürtauer L, van Dongen JT. Introducing the halophyte Salicornia europaea to investigate combined impact of salt and tidal submergence conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23228. [PMID: 38388483 DOI: 10.1071/fp23228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Tolerance mechanisms to single abiotic stress events are being investigated in different plant species, but how plants deal with multiple stress factors occurring simultaneously is still poorly understood. Here, we introduce Salicornia europaea as a species with an extraordinary tolerance level to both flooding and high salt concentrations. Plants exposed to 0.5MNaCl (mimicking sea water concentrations) grew larger than plants not exposed to salt. Adding more salt reduced growth, but concentrations up to 2.5MNaCl were not lethal. Regular tidal flooding with salt water (0.5MNaCl) did not affect growth or chlorophyll fluorescence, whereas continuous flooding stopped growth while plants survived. Quantitative polymerase chain reaction (qPCR) analysis of plants exposed to 1% oxygen in air revealed induction of selected hypoxia responsive genes, but these genes were not induced during tidal flooding, suggesting that S. europaea did not experience hypoxic stress. Indeed, plants were able to transport oxygen into waterlogged soil. Interestingly, sequential exposure to salt and hypoxic air changed the expression of several but not all genes as compared to their expression upon hypoxia only, demonstrating the potential to use S . europaea to investigate signalling-crosstalk between tolerance reactions to multiple environmental perturbations.
Collapse
Affiliation(s)
- Angelina Jordine
- Institute of Biology I, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen 52074, Germany
| | - Julia Retzlaff
- Institute of Biology I, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen 52074, Germany
| | - Lina Gens
- Institute of Biology I, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen 52074, Germany
| | - Brigitta Ehrt
- Institute of Biology I, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen 52074, Germany
| | - Lisa Fürtauer
- Institute of Biology III, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen 52074, Germany
| | - Joost T van Dongen
- Institute of Biology I, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen 52074, Germany
| |
Collapse
|
5
|
Ma YS, Jie HD, Zhao L, Lv XY, Liu XC, Tang YY, Zhang Y, He PL, Xing HC, Jie YC. Identification of the Xyloglucan Endotransglycosylase/Hydrolase ( XTH) Gene Family Members Expressed in Boehmeria nivea in Response to Cadmium Stress. Int J Mol Sci 2022; 23:ijms232416104. [PMID: 36555743 PMCID: PMC9785722 DOI: 10.3390/ijms232416104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Xyloglucan endotransglycosylase/hydrolase (XTH) genes play an important role in plant resistance to abiotic stress. However, systematic studies of the response of Boehmeria nivea (ramie) XTH genes (BnXTHs) to cadmium (Cd) stress are lacking. We sought to identify the BnXTH-family genes in ramie through bioinformatics analyses and to investigate their responses to Cd stress. We identified 19 members of the BnXTH gene family from the ramie genome, referred to as BnXTH1-19, among which BnXTH18 and BnXTH19 were located on no chromosomes and the remaining genes were unevenly distributed across 11 chromosomes. The 19 members were divided into four groups, Groups I/II/IIIA/IIIB, according to their phylogenetic relationships, and these groups were supported by analyses of intron-exon structure and conserved motif composition. A highly conserved catalytic site (HDEIDFEFLG) was observed in all BnXTH proteins. Additionally, three gene pairs (BnXTH6-BnXTH16, BnXTH8-BnXTH9, and BnXTH17-BnXTH18) were obtained with a fragment and tandem-repeat event analysis of the ramie genome. An analysis of cisregulatory elements revealed that BnXTH expression might be regulated by multiple hormones and abiotic and biotic stress responses. In particular, 17 cisregulatory elements related to abiotic and biotic stress responses and 11 cisregulatory elements related to hormone responses were identified. We also found that most BnXTH genes responded to Cd stress, and BnXTH1, BnXTH3, BnXTH6, and BnXTH15 were most likely to contribute to the Cd tolerance of ramie, as evidenced by the substantial increases in expression under Cd treatment. Heterologous expression of BnXTH1, BnXTH6, and BnXTH15 significantly enhanced the Cd tolerance of transgenic yeast cells. These results suggest that the BnXTH gene family is involved in Cd stress responses, laying a theoretical foundation for functional studies of BnXTH genes and the innovative breeding of Cd-tolerant ramie.
Collapse
Affiliation(s)
- Yu-Shen Ma
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hong-Dong Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Long Zhao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xue-Ying Lv
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xiao-Chun Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Yi Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Ying Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Peng-Liang He
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hu-Cheng Xing
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Engineering Research Center for Grass Crop Germplasm Innovation and Utilization, Changsha 410128, China
| | - Yu-Cheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Engineering Research Center for Grass Crop Germplasm Innovation and Utilization, Changsha 410128, China
- Correspondence:
| |
Collapse
|
6
|
Ranjbar G, Pirasteh-Anosheh H, Dehghanie F, Keshtkar S, Race M. Feasibility of growing Salicornia species in a coastal environment through planting date and density management in a direct seawater irrigation system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:47800-47809. [PMID: 35190989 DOI: 10.1007/s11356-022-19089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Two field experiments were conducted to evaluate six Salicornia species (Salicornia bigelovii Torr., S. europaea L., S. persica Gorgan ecotype, S. persica Urmia ecotype, S. sinus persica Bushehr ecotype, and S. persica Central Plateau ecotype) at different planting dates and densities under irrigation with Persian Gulf water. Evaluated planting dates were 14 November and 18 December 2016 and 16 January, 8 February, 8 March, and 28 March 2017. Examined planting densities included 13, 20, and 40 plant m-2. Only S. bigelovii and S. europaea produced measurable yield in all planting dates. The highest dry weight (651.1 gm-2) was obtained in S. sinus persica (Bu) planted on 8 February. Dry weight of S. bigelovii, S. europaea, S. sinus persica Bushehr, S. persica Central Plateau, S. persica Gorgan, and S. persica Urmia planted on 8 March were 174.2, 220.7, 542.5, 240.9, 158.0, and 147.5 g m-2, respectively. The ash contents of S. bigelovii, S. europaea, S. sinus persica Bushehr, S. persica Central Plateau, S. persica Gorgan, and S. persica Urmia were 46.3%, 45.0%, 49.6%, 49.6%, 50.0%, and 53.1%, respectively. Sodium and chloride contents of different Salicornia species varied from 13-15% and 16-17%, respectively. The oilseed content of S. bigelovii and S. sinus persica Bushehr was about 24.0% for both species. The highest and lowest dry weight, from the second experiment, were for S. sinus persica Bushehr and S. persica Central Plateau, respectively, in all planting density. The highest dry weight equal to 1336.2 gm-2 was obtained for S. sinus persica Bushehr in 40 plant m-2 density. Under such conditions, forage production potential of Salicornia is more achievable rather than seed production. Nevertheless, high ash content is a serious constraint to direct consumption by livestock; therefore, determining the nutritional value of Salicornia fodder requires further evaluations.
Collapse
Affiliation(s)
- Gholamhassan Ranjbar
- National Salinity Research Center (NSRC), Agricultural Research, Education and Extension Organization (AREEO), Yazd, Iran
| | - Hadi Pirasteh-Anosheh
- National Salinity Research Center (NSRC), Agricultural Research, Education and Extension Organization (AREEO), Yazd, Iran.
| | - Farhad Dehghanie
- National Salinity Research Center (NSRC), Agricultural Research, Education and Extension Organization (AREEO), Yazd, Iran
| | - Sardar Keshtkar
- Bushehr Agricultural and Natural Resources Research Center, Agricultural Research, Education and Extension Organization (AREEO), Bushehr, Iran
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, 03043, Cassino, Italy.
| |
Collapse
|
7
|
Salicornia europaea L. Functional Traits Indicate Its Optimum Growth. PLANTS 2022; 11:plants11081051. [PMID: 35448779 PMCID: PMC9033102 DOI: 10.3390/plants11081051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
Salicornia europaea L. grows in areas periodically flooded by salty or brackish water. It has potential economic value, because it can be used as food, forage, or biofuel, and has potential in pharmaceuticals and cosmetics. Increasing interest in S. europaea is due to its extreme salt tolerance and well growth in marginal saline soils. However, the variation in its functional traits in response to environmental conditions is still poorly studied. There are still questions regarding the optimal level of salinity for different traits. Therefore, we worked to address the question if S. europaea traits from different scales are controlled by salinity level. Based on performed pot experiment, we found that almost all traits are salinity dependent but affected in different ways. We demonstrated that morphological, biomass, and anatomical properties indicate optimum growth between 200 and 400 mM NaCl and growth limitations at 0, 800, and 1000 mM NaCl. Moreover, we found the most affected traits which include photosynthetic pigments and protein content, plant surface area, peroxidase activity, and anatomic traits related to cell shape. Our results significantly expanded the knowledge about S. europaea functional traits variation in response to salinity, which can be important for discovering regulating processes and for possible future agricultural applications.
Collapse
|
8
|
Wei J, Tiika RJ, Cui G, Ma Y, Yang H, Duan H. Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments. PeerJ 2022; 10:e12989. [PMID: 35261820 PMCID: PMC8898550 DOI: 10.7717/peerj.12989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
Background The KT/HAK/KUP (KUP) transporters play important roles in potassium (K+) uptake and translocation, regulation of osmotic potential, salt tolerance, root morphogenesis and plant development. However, the KUP family has not been systematically studied in the typical halophyte Salicornia europaea L., and the specific expression patterns of SeKUPs under NaCl condition and K+ deficiency are unknown. Methods In this study, SeKUPs were screened from PacBio transcriptome data of Salicornia europaea L. using bioinformatics. The identification, phylogenetic analysis and prediction of conserved motifs of SeKUPs were extensively explored. Moreover, the expression levels of 24 selected SeKUPs were assayed by real-time quantitative polymerase chain reaction (RT-qPCR). Results In this study, a total of 24 putative SeKUPs were identified in S. europaea. Nineteen SeKUPs with the fixed domain EA[ML]FADL were used to construct the phylogenetic tree, and they were divided into four clusters (clusters I-IV). MEME analysis identified 10 motifs in S. europaea, and the motif analysis suggested that 19 of the identified SeKUPs had at least four K+ transporter motifs existed in all SeKUPs (with the exception of SeKUP-2). The RT-qPCR analysis showed that the expression levels of most SeKUPs were significantly up-regulated in S. europaea when they were exposed to K+ deficiency and high salinity, implying that these SeKUPs may play a key role in the absorption and transport of K+ and Na+ in S. europaea. Discussions Our results laid the foundation for revealing the salt tolerance mechanism of SeKUPs, and provided key candidate genes for further studies on the function of KUP family in S. europaea.
Collapse
Affiliation(s)
- Jia Wei
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China,College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Richard John Tiika
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China,College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Yanjun Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| |
Collapse
|
9
|
Cárdenas-Pérez S, Niedojadło K, Mierek-Adamska A, Dąbrowska GB, Piernik A. Maternal salinity influences anatomical parameters, pectin content, biochemical and genetic modifications of two Salicornia europaea populations under salt stress. Sci Rep 2022; 12:2968. [PMID: 35194050 PMCID: PMC8863803 DOI: 10.1038/s41598-022-06385-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Salicornia europaea is among the most salt-tolerant of plants, and is widely distributed in non-tropical regions. Here, we investigated whether maternal habitats can influence different responses in physiology and anatomy depending on environmental conditions. We studied the influence of maternal habitat on S. europaea cell anatomy, pectin content, biochemical and enzymatic modifications under six different salinity treatments of a natural-high-saline habitat (~ 1000 mM) (Ciechocinek [Cie]) and an anthropogenic-lower-saline habitat (~ 550 mM) (Inowrocław [Inw]). The Inw population showed the highest cell area and roundness of stem water storing cells at high salinity and had the maximum proline, carotenoid, protein, catalase activity within salt treatments, and a maximum high and low methyl esterified homogalacturonan content. The Cie population had the highest hydrogen peroxide and peroxidase activity along with the salinity gradient. Gene expression analysis of SeSOS1 and SeNHX1 evidenced the differences between the studied populations and suggested the important role of Na+ sequestration into the vacuoles. Our results suggest that the higher salt tolerance of Inw may be derived from a less stressed maternal salinity that provides a better adaptive plasticity of S. europaea. Thus, the influence of the maternal environment may provide physiological and anatomical modifications of local populations.
Collapse
Affiliation(s)
- S Cárdenas-Pérez
- Chair of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
| | - K Niedojadło
- Department of Cellular and Molecular Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - A Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland
| | - G B Dąbrowska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - A Piernik
- Chair of Geobotany and Landscape Planning, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| |
Collapse
|
10
|
Tiika RJ, Wei J, Cui G, Ma Y, Yang H, Duan H. Transcriptome-wide characterization and functional analysis of Xyloglucan endo-transglycosylase/hydrolase (XTH) gene family of Salicornia europaea L. under salinity and drought stress. BMC PLANT BIOLOGY 2021; 21:491. [PMID: 34696719 PMCID: PMC8547092 DOI: 10.1186/s12870-021-03269-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 10/11/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Salicornia europaea is a halophyte that has a very pronounced salt tolerance. As a cell wall manipulating enzyme, xyloglucan endotransglycosylase/hydrolase (XTH) plays an important role in plant resistance to abiotic stress. However, no systematic study of the XTH gene family in S. europaea is well known. PacBio Iso-Seq transcriptome sequence data were used for bioinformatics and gene expression analysis using real-time quantitative polymerase chain reaction (RT-qPCR). RESULTS Transcriptome sequencing (PacBio Iso-Seq system) generated 16,465,671 sub-reads and after quality control of Iso-Seq, 29,520 isoforms were obtained with an average length of 2112 bp. A total of 24,869 unigenes, with 98% of which were obtained using coding sequences (CDSs), and 6398 possible transcription factors (TFs) were identified. Thirty-five (35) non-redundant potential SeXTH proteins were identified in S. europaea and categorized into group I/II and group III based on their genetic relatedness. Prediction of the conserved motif revealed that the DE(I/L/F/V)DF(I)EFLG domain was conserved in the S. europaea proteins and a potential N-linked glycosylation domain N(T)V(R/L/T/I)T(S/K/R/F/P)G was also located near the catalytic residues. All SeXTH genes exhibited discrete expression patterns in different tissues, at different times, and under different stresses. For example, 27 and 15 SeXTH genes were positively expressed under salt stress in shoots and roots at 200 mM NaCl in 24 h, and 34 SeXTH genes were also positively regulated under 48 h of drought stress in shoots and roots. This indicates their function in adaptation to salt and drought stress. CONCLUSION The present study discovered SeXTH gene family traits that are potential stress resistance regulators in S. europaea, and this provides a basis for future functional diversity research.
Collapse
Affiliation(s)
- Richard John Tiika
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Jia Wei
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yanjun Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| |
Collapse
|
11
|
Jia W, Lin K, Lou T, Feng J, Lv S, Jiang P, Yi Z, Zhang X, Wang D, Guo Z, Tang Y, Qiu R, Li Y. Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance. PLANTA 2021; 254:16. [PMID: 34185181 DOI: 10.1007/s00425-021-03669-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance. As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA-mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.
Collapse
Affiliation(s)
- Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, People's Republic of China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Tengxue Lou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
| | - Ze Yi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zijing Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yetao Tang
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Rongliang Qiu
- Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, People's Republic of China.
| |
Collapse
|
12
|
Lv S, Tai F, Guo J, Jiang P, Lin K, Wang D, Zhang X, Li Y. Phosphatidylserine Synthase from Salicornia europaea Is Involved in Plant Salt Tolerance by Regulating Plasma Membrane Stability. PLANT & CELL PHYSIOLOGY 2021; 62:66-79. [PMID: 33141223 PMCID: PMC7991898 DOI: 10.1093/pcp/pcaa141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/24/2020] [Indexed: 05/05/2023]
Abstract
Salinity-induced lipid alterations have been reported in many plant species; however, how lipid biosynthesis and metabolism are regulated and how lipids work in plant salt tolerance are much less studied. Here, a constitutively much higher phosphatidylserine (PS) content in the plasma membrane (PM) was found in the euhalophyte Salicornia europaea than in Arabidopsis. A gene encoding PS synthase (PSS) was subsequently isolated from S. europaea, named SePSS, which was induced by salinity. Multiple alignments and phylogenetic analysis suggested that SePSS belongs to a base exchange-type PSS, which localises to the endoplasmic reticulum. Knockdown of SePSS in S. europaea suspension cells resulted in reduced PS content, decreased cell survival rate, and increased PM depolarization and K+ efflux under 400 or 800 mM NaCl. By contrast, the upregulation of SePSS leads to increased PS and phosphatidylethanolamine levels and enhanced salt tolerance in Arabidopsis, along with a lower accumulation of reactive oxygen species, less membrane injury, less PM depolarization and higher K+/Na+ in the transgenic lines than in wild-type (WT). These results suggest a positive correlation between PS levels and plant salt tolerance, and that SePSS participates in plant salt tolerance by regulating PS levels, hence PM potential and permeability, which help maintain ion homeostasis. Our work provides a potential strategy for improving plant growth under multiple stresses.
Collapse
Affiliation(s)
- Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fang Tai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Laboratory of Genetics and Breeding of Marine Organism,�College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jie Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Linda Liu and Partners, Beijing 100000, China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kangqi Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duoliya Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Corresponding author: E-mail, ; Fax, +86 10 62836691
| |
Collapse
|
13
|
Soltabayeva A, Ongaltay A, Omondi JO, Srivastava S. Morphological, Physiological and Molecular Markers for Salt-Stressed Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:243. [PMID: 33513682 PMCID: PMC7912532 DOI: 10.3390/plants10020243] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022]
Abstract
Plant growth and development is adversely affected by different kind of stresses. One of the major abiotic stresses, salinity, causes complex changes in plants by influencing the interactions of genes. The modulated genetic regulation perturbs metabolic balance, which may alter plant's physiology and eventually causing yield losses. To improve agricultural output, researchers have concentrated on identification, characterization and selection of salt tolerant varieties and genotypes, although, most of these varieties are less adopted for commercial production. Nowadays, phenotyping plants through Machine learning (deep learning) approaches that analyze the images of plant leaves to predict biotic and abiotic damage on plant leaves have increased. Here, we review salinity stress related markers on molecular, physiological and morphological levels for crops such as maize, rice, ryegrass, tomato, salicornia, wheat and model plant, Arabidopsis. The combined analysis of data from stress markers on different levels together with image data are important for understanding the impact of salt stress on plants.
Collapse
Affiliation(s)
- Aigerim Soltabayeva
- Biology Department, School of Science and Humanities, Nazarbayev University, Nur Sultan Z05H0P9, Kazakhstan;
| | - Assel Ongaltay
- Biology Department, School of Science and Humanities, Nazarbayev University, Nur Sultan Z05H0P9, Kazakhstan;
| | - John Okoth Omondi
- International Institute of Tropical Agriculture, PO Box 30258 Lilongwe 3, Malawi; or
| | - Sudhakar Srivastava
- Beijing Advanced Innovative Center For Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China;
| |
Collapse
|
14
|
Vahidi MF, Gharechahi J, Behmanesh M, Ding XZ, Han JL, Hosseini Salekdeh G. Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen. PeerJ 2021; 9:e10463. [PMID: 33510967 PMCID: PMC7808268 DOI: 10.7717/peerj.10463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023] Open
Abstract
Background The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen. Method We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota. Results Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen. Conclusion Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.
Collapse
Affiliation(s)
- Mohammad Farhad Vahidi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China, Institute of Animal Science, Beijing, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| |
Collapse
|
15
|
Gazara RK, Khan S, Iqrar S, Ashrafi K, Abdin MZ. Comparative transcriptome profiling of rice colonized with beneficial endophyte, Piriformospora indica, under high salinity environment. Mol Biol Rep 2020; 47:7655-7673. [PMID: 32979167 DOI: 10.1007/s11033-020-05839-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/10/2020] [Indexed: 01/20/2023]
Abstract
The salinity stress tolerance in plants has been studied enormously, reflecting its agronomic relevance. Despite the extensive research, limited success has been achieved in relation to the plant tolerance mechanism. The beneficial interaction between Piriformospora indica and rice could essentially improve the performance of the plant during salt stress. In this study, the transcriptomic data between P. indica treated and untreated rice roots were compared under control and salt stress conditions. Overall, 661 salt-responsive differentially expressed genes (DEGs) were detected with 161 up- and 500 down-regulated genes in all comparison groups. Gene ontology analyses indicated the DEGs were mainly enriched in "auxin-activated signaling pathway", "water channel activity", "integral component of plasma membrane", "stress responses", and "metabolic processes". Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the DEGs were primarily related to "Zeatin biosynthesis", "Fatty acid elongation", "Carotenoid biosynthesis", and "Biosynthesis of secondary metabolites". Particularly, genes related to cell wall modifying enzymes (e.g. invertase/pectin methylesterase inhibitor protein and arabinogalactans), phytohormones (e.g. Auxin-responsive Aux/IAA gene family, ent-kaurene synthase, and 12-oxophytodienoate reductase) and receptor-like kinases (e.g. AGC kinase and receptor protein kinase) were induced in P. indica colonized rice under salt stress condition. The differential expression of these genes implies that the coordination between hormonal crosstalk, signaling, and cell wall dynamics contributes to the higher growth and tolerance in P. indica-inoculated rice. Our results offer a valuable resource for future functional studies on salt-responsive genes that should improve the resilience and adaptation of rice against salt stress.
Collapse
Affiliation(s)
- Rajesh K Gazara
- Centro de Bioiências e Biotecnologia, Universidade Estadual do Norte Fluminense "Darcy Ribeiro" University, Campos dos goytacazes, Rio de Janeiro, Brazil
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
- Department of Electrical Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Shazia Khan
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110062, India
| | - Sadia Iqrar
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110062, India
| | - Kudsiya Ashrafi
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110062, India
| | - Malik Z Abdin
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110062, India.
| |
Collapse
|
16
|
Furtado BU, Nagy I, Asp T, Tyburski J, Skorupa M, Gołębiewski M, Hulisz P, Hrynkiewicz K. Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation. BMC PLANT BIOLOGY 2019; 19:427. [PMID: 31619171 PMCID: PMC6794796 DOI: 10.1186/s12870-019-2032-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 09/12/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Salicornia europaea, a succulent obligatory halophyte is the most salt-tolerant plant species in the world. It survives salt concentrations of more than 1 M. Therefore, it is a suitable model plant to identify genes involved in salt tolerance mechanisms that can be used for the improvement of crops. The changes in a plant's gene expression in response to abiotic stresses may depend on factors like soil conditions at the site, seasonality, etc. To date, experiments were performed to study the gene expression of S. europaea only under controlled conditions. Conversely, the present study investigates the transcriptome and physicochemical parameters of S. europaea shoots and roots from two different types of saline ecosystems growing under natural conditions. RESULTS The level of soil salinity was higher at the naturally saline site than at the anthropogenic saline site. The parameters such as ECe, Na+, Cl-, Ca+, SO42- and HCO3- of the soils and plant organs significantly varied according to sites and seasons. We found that Na+ mainly accumulated in shoots, whereas K+ and Ca2+ levels were higher in roots throughout the growing period. Moreover, changes in S. europaea gene expression were more prominent in seasons, than sites and plant organs. The 30 differentially expressed genes included enzymes for synthesis of S-adenosyl methionine, CP47 of light-harvesting complex II, photosystem I proteins, Hsp70 gene, ATP-dependent Clp proteases, ribulose bisphosphate carboxylase/oxygenase (Rubisco), phenylalanine ammonia-lyase (PAL), cytochrome c oxidase (COX) and ATP synthase. CONCLUSION The comparisons made based on two seasons, plant organs and two different sites suggest the importance of seasonal variations in gene expression of S. europaea. We identify the genes that may play an important role in acclimation to season-dependent changes of salinity. The genes were involved in processes such as osmotic adjustment, energy metabolism and photosynthesis.
Collapse
Affiliation(s)
- Bliss Ursula Furtado
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, 4200 Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, 4200 Slagelse, Denmark
| | - Jarosław Tyburski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Monika Skorupa
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Marcin Gołębiewski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences and Spatial Management, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| |
Collapse
|
17
|
Szymańska S, Borruso L, Brusetti L, Hulisz P, Furtado B, Hrynkiewicz K. Bacterial microbiome of root-associated endophytes of Salicornia europaea in correspondence to different levels of salinity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:25420-25431. [PMID: 29951760 PMCID: PMC6133108 DOI: 10.1007/s11356-018-2530-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/11/2018] [Indexed: 05/26/2023]
Abstract
The halophytes have evolved several strategies to survive in saline environments; however, an additional support from their associated microbiota helps combat adverse conditions. Hence, our driving interests to investigate the endophytic bacterial community richness, diversity, and composition associated to roots of Salicornia europaea from two test sites with different origins of soil salinity. We assumed that salinity will have a negative effect on the diversity of endophytes but simultaneously will permit the high occurrence of halophylic bacteria. Further, to establish the role of the host and its external environment in determining the endophytic diversity, we analyzed the physico-chemical parameters of root zone soil and the concentration of salt ions in the plant roots. The results based on the Miseq Illumina sequencing approach revealed a higher number of endophytic bacterial OTUs at naturally saline test site with a higher level of soil salinity. Proteobacteria and Bacteriodetes were the dominant endophytic phyla at both analyzed sites; additionally, the high occurrence of Planctomycetes and Acidobacteria at more saline site and the occurrence of Firmicutes, Actinobacteria, and Chloroflexi at less saline site were recorded. The salinity in the root zone soil was crucial in structuring the endophytic community of S. europaea, and the significant prevalence of representatives from the phyla Deltaproteobacteria, Acidobacteria, Caldithrix, Fibrobacteres, and Verrucomicrobia at the more saline test site suggest domination of halophylic bacteria with potential role in mitigation of salt stress of halophytes.
Collapse
Affiliation(s)
- Sonia Szymańska
- Department of Microbiology, Faculty of Biology and Environmental Protection, N. Copernicus University in Torun, Lwowska 1, Toruń, Poland
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen - Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen - Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences, N. Copernicus University in Torun, Lwowska 1, Toruń, Poland
| | - Bliss Furtado
- Department of Microbiology, Faculty of Biology and Environmental Protection, N. Copernicus University in Torun, Lwowska 1, Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, N. Copernicus University in Torun, Lwowska 1, Toruń, Poland.
| |
Collapse
|
18
|
Evolutionary adaptation of Kluyveromyces marxianus strain for efficient conversion of whey lactose to bioethanol. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
19
|
Tai F, Lv S, Jiang P, Wang J, Feng J, Li Y. Establishment of a gene function analysis system for the euhalophyte Salicornia europaea L. PLANT CELL REPORTS 2017; 36:1251-1261. [PMID: 28466186 DOI: 10.1007/s00299-017-2150-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/25/2017] [Indexed: 06/07/2023]
Abstract
A Salicornia europaea L. in vitro cell transformation system was developed and further applied to SeNHX1 function investigation. The exploration of salt-tolerant genes from halophyte has seriously been limited by the lack of self-dependent transformation system. Here, an Agrobacterium tumefaciens-mediated in vitro cell transformation system of euhalophyte Salicornia europaea L. was developed. Calli derived from hypocotyl of S. europaea were co-cultured for 3 days with Agrobacterium at OD600 ranging from 1.0 to 1.5 and then selected with 25 mg/L hygromycin (Hyg). The transformed cells were identified from Hyg positive calli by GUS assay and qRT-PCR, and the transformation efficiency was up to 74.4%. The practicality of this system was further tested via genetic manipulation of S. europaea Na+/H+ antiporter 1 (SeNHX1) gene by creating the overexpressing, silencing, and empty vector cells. Survival ratio and Na+ distribution under salt treatment showed obvious differences in SeNHX1-overexpressing, -silencing, and empty vector cells, indicating the feasibility of this system to analyze gene function. This investigation is enlightening for studies in other non-model plants lacking of self-dependent transformation system.
Collapse
Affiliation(s)
- Fang Tai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jinhui Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
| |
Collapse
|
20
|
Salinity Response in Chloroplasts: Insights from Gene Characterization. Int J Mol Sci 2017; 18:ijms18051011. [PMID: 28481319 PMCID: PMC5454924 DOI: 10.3390/ijms18051011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 11/17/2022] Open
Abstract
Salinity is a severe abiotic stress limiting agricultural yield and productivity. Plants have evolved various strategies to cope with salt stress. Chloroplasts are important photosynthesis organelles, which are sensitive to salinity. An understanding of molecular mechanisms in chloroplast tolerance to salinity is of great importance for genetic modification and plant breeding. Previous studies have characterized more than 53 salt-responsive genes encoding important chloroplast-localized proteins, which imply multiple vital pathways in chloroplasts in response to salt stress, such as thylakoid membrane organization, the modulation of photosystem II (PS II) activity, carbon dioxide (CO2) assimilation, photorespiration, reactive oxygen species (ROS) scavenging, osmotic and ion homeostasis, abscisic acid (ABA) biosynthesis and signaling, and gene expression regulation, as well as protein synthesis and turnover. This review presents an overview of salt response in chloroplasts revealed by gene characterization efforts.
Collapse
|
21
|
De novo transcriptome sequencing of Acer palmatum and comprehensive analysis of differentially expressed genes under salt stress in two contrasting genotypes. Mol Genet Genomics 2015; 291:575-86. [PMID: 26475609 DOI: 10.1007/s00438-015-1127-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/30/2015] [Indexed: 01/15/2023]
Abstract
Maple (Acer palmatum) is an important species for landscape planting worldwide. Salt stress affects the normal growth of the Maple leaf directly, leading to loss of esthetic value. However, the limited availability of Maple genomic information has hindered research on the mechanisms underlying this tolerance. In this study, we performed comprehensive analyses of the salt tolerance in two genotypes of Maple using RNA-seq. Approximately 146.4 million paired-end reads, representing 181,769 unigenes, were obtained. The N50 length of the unigenes was 738 bp, and their total length over 102.66 Mb. 14,090 simple sequence repeats and over 500,000 single nucleotide polymorphisms were identified, which represent useful resources for marker development. Importantly, 181,769 genes were detected in at least one library, and 303 differentially expressed genes (DEGs) were identified between salt-sensitive and salt-tolerant genotypes. Among these DEGs, 125 were upregulated and 178 were downregulated genes. Two MYB-related proteins and one LEA protein were detected among the first 10 most downregulated genes. Moreover, a methyltransferase-related gene was detected among the first 10 most upregulated genes. The three most significantly enriched pathways were plant hormone signal transduction, arginine and proline metabolism, and photosynthesis. The transcriptome analysis provided a rich genetic resource for gene discovery related to salt tolerance in Maple, and in closely related species. The data will serve as an important public information platform to further our understanding of the molecular mechanisms involved in salt tolerance in Maple.
Collapse
|
22
|
Massange-Sanchez JA, Palmeros-Suarez PA, Martinez-Gallardo NA, Castrillon-Arbelaez PA, Avilés-Arnaut H, Alatorre-Cobos F, Tiessen A, Délano-Frier JP. The novel and taxonomically restricted Ah24 gene from grain amaranth (Amaranthus hypochondriacus) has a dual role in development and defense. FRONTIERS IN PLANT SCIENCE 2015; 6:602. [PMID: 26300899 PMCID: PMC4524895 DOI: 10.3389/fpls.2015.00602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 07/21/2015] [Indexed: 05/03/2023]
Abstract
Grain amaranths tolerate stress and produce highly nutritious seeds. We have identified several (a)biotic stress-responsive genes of unknown function in Amaranthus hypochondriacus, including the so-called Ah24 gene. Ah24 was expressed in young or developing tissues; it was also strongly induced by mechanical damage, insect herbivory and methyl jasmonate and in meristems and newly emerging leaves of severely defoliated plants. Interestingly, an in silico analysis of its 1304 bp promoter region showed a predominance of regulatory boxes involved in development, but not in defense. The Ah24 cDNA encodes a predicted cytosolic protein of 164 amino acids, the localization of which was confirmed by confocal microscopy. Additional in silico analysis identified several other Ah24 homologs, present almost exclusively in plants belonging to the Caryophyllales. The possible function of this gene in planta was examined in transgenic Ah24 overexpressing Arabidopsis thaliana and Nicotiana tabacum plants. Transformed Arabidopsis showed enhanced vegetative growth and increased leaf number with no penalty in one fitness component, such as seed yield, in experimental conditions. Transgenic tobacco plants, which grew and reproduced normally, had increased insect herbivory resistance. Modified vegetative growth in transgenic Arabidopsis coincided with significant changes in the expression of genes controlling phytohormone synthesis or signaling, whereas increased resistance to insect herbivory in transgenic tobacco coincided with higher jasmonic acid and proteinase inhibitor activity levels, plus the accumulation of nicotine and several other putative defense-related metabolites. It is proposed that the primary role of the Ah24 gene in A. hypochondriacus is to contribute to a rapid recovery post-wounding or defoliation, although its participation in defense against insect herbivory is also plausible.
Collapse
Affiliation(s)
- Julio A. Massange-Sanchez
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad IrapuatoIrapuato, México
| | - Paola A. Palmeros-Suarez
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad IrapuatoIrapuato, México
| | - Norma A. Martinez-Gallardo
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad IrapuatoIrapuato, México
| | - Paula A. Castrillon-Arbelaez
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad IrapuatoIrapuato, México
| | - Hamlet Avilés-Arnaut
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo LeónSan Nicolás de los Garza, México
| | | | - Axel Tiessen
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad IrapuatoIrapuato, México
| | - John P. Délano-Frier
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad IrapuatoIrapuato, México
| |
Collapse
|
23
|
Nie L, Feng J, Fan P, Chen X, Guo J, Lv S, Bao H, Jia W, Tai F, Jiang P, Wang J, Li Y. Comparative proteomics of root plasma membrane proteins reveals the involvement of calcium signalling in NaCl-facilitated nitrate uptake in Salicornia europaea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4497-510. [PMID: 25956883 PMCID: PMC4507759 DOI: 10.1093/jxb/erv216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Improving crop nitrogen (N) use efficiency under salinity is essential for the development of sustainable agriculture in marginal lands. Salicornia europaea is a succulent euhalophyte that can survive under high salinity and N-deficient habitat conditions, implying that a special N assimilation mechanism may exist in this plant. In this study, phenotypic and physiological changes of S. europaea were investigated under different nitrate and NaCl levels. The results showed that NaCl had a synergetic effect with nitrate on the growth of S. europaea. In addition, the shoot nitrate concentration and nitrate uptake rate of S. europaea were increased by NaCl treatment under both low N and high N conditions, suggesting that nitrate uptake in S. europaea was NaCl facilitated. Comparative proteomic analysis of root plasma membrane (PM) proteins revealed 81 proteins, whose abundance changed significantly in response to NaCl and nitrate. These proteins are involved in metabolism, cell signalling, transport, protein folding, membrane trafficking, and cell structure. Among them, eight proteins were calcium signalling components, and the accumulation of seven of the above-mentioned proteins was significantly elevated by NaCl treatment. Furthermore, cytosolic Ca(2+) concentration ([Ca(2+)]cyt) was significantly elevated in S. europaea under NaCl treatment. The application of the Ca(2+) channel blocker LaCl3 not only caused a decrease in nitrate uptake rate, but also attenuated the promoting effects of NaCl on nitrate uptake rates. Based on these results, a possible regulatory network of NaCl-facilitated nitrate uptake in S. europaea focusing on the involvement of Ca(2+) signalling was proposed.
Collapse
Affiliation(s)
- Lingling Nie
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Pengxiang Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
| | - Xianyang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Jie Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Hexigeduleng Bao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China Shanghai Center for Plant Stress Biology (PSC), Chinese Academy of Sciences, No. 3888 Chenhua Road, Songjiang District, Shanghai 201602, PR China
| | - Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Fang Tai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Jinhui Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| |
Collapse
|
24
|
Diray-Arce J, Clement M, Gul B, Khan MA, Nielsen BL. Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics 2015; 16:353. [PMID: 25943316 PMCID: PMC4422317 DOI: 10.1186/s12864-015-1553-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 04/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of Suaeda fruticosa, a halophyte that has the ability to sequester salts in its leaves. Suaeda fruticosa is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores. This plant is an obligate halophyte that grows optimally from 200-400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. De novo assembly of the transcriptome and analysis has allowed identification of differentially expressed and unique genes present in this non-conventional crop. RESULTS Twelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of Suaeda fruticosa. The transcriptome was assembled de novo using Velvet and Oases k-45 and clustered using CDHIT-EST. There are 54,526 unigenes; among these 475 genes are downregulated and 44 are upregulated when samples from plants grown under optimal salt are compared with those grown without salt. BLAST analysis identified the differentially expressed genes, which were categorized in gene ontology terms and their pathways. CONCLUSIONS This work has identified potential genes involved in salt tolerance in Suaeda fruticosa, and has provided an outline of tools to use for de novo transcriptome analysis. The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression and identification of genes that may be involved in salt tolerance. The transcriptome may serve as a reference sequence for study of other succulent halophytes.
Collapse
Affiliation(s)
- Joann Diray-Arce
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA.
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, 84602, USA.
| | - Bilquees Gul
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan.
| | - M Ajmal Khan
- College of Arts and Sciences, Qatar University, Doha, Qatar.
| | - Brent L Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA.
| |
Collapse
|
25
|
Feng J, Wang J, Fan P, Jia W, Nie L, Jiang P, Chen X, Lv S, Wan L, Chang S, Li S, Li Y. High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea. BMC PLANT BIOLOGY 2015; 15:63. [PMID: 25848810 PMCID: PMC4349674 DOI: 10.1186/s12870-015-0451-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/06/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far. RESULTS Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE. CONCLUSIONS Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis.
Collapse
Affiliation(s)
- Juanjuan Feng
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Jinhui Wang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Pengxiang Fan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
- />Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson road, East Lansing, MI 48824 USA
| | - Weitao Jia
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lingling Nie
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ping Jiang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Xianyang Chen
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sulian Lv
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lichuan Wan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sandra Chang
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Yinxin Li
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| |
Collapse
|
26
|
Le Gall H, Philippe F, Domon JM, Gillet F, Pelloux J, Rayon C. Cell Wall Metabolism in Response to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2015; 4:112-66. [PMID: 27135320 PMCID: PMC4844334 DOI: 10.3390/plants4010112] [Citation(s) in RCA: 581] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 12/17/2022]
Abstract
This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions.
Collapse
Affiliation(s)
- Hyacinthe Le Gall
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Florian Philippe
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Jean-Marc Domon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Françoise Gillet
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Jérôme Pelloux
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| | - Catherine Rayon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039 Amiens, France.
| |
Collapse
|
27
|
Vera-Estrella R, Barkla BJ, Pantoja O. Comparative 2D-DIGE analysis of salinity responsive microsomal proteins from leaves of salt-sensitive Arabidopsis thaliana and salt-tolerant Thellungiella salsuginea. J Proteomics 2014; 111:113-27. [PMID: 24892798 DOI: 10.1016/j.jprot.2014.05.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 12/18/2022]
Abstract
UNLABELLED Halophytes have evolved unique molecular strategies to overcome high soil salinity but we still know very little about the main mechanisms that these plants use to complete their lifecycle under salinity stress. One useful approach to further our understanding in this area is to directly compare the response to salinity of two closely related species which show diverse levels of salt tolerance. Here we present a comparative proteomic study using DIGE of leaf microsomal proteins to identify salt-responsive membrane associated proteins in Arabidopsis thaliana (a glycophyte) and Thellungiella salsuginea (a halophyte). While a small number of distinct protein abundance changes were observed upon salt stress in both species, the most notable differences were observed between species and specifically, in untreated plants with a total of 36 proteins displaying significant abundance changes. Gene ontology (GO) term enrichment analysis showed that the majority of these proteins were distributed into two functional categories; transport (31%) and carbohydrate metabolism (17%). Results identify several novel salt responsive proteins in this system and support the theory that T. salsuginea shows a high degree of salt-tolerance because molecular mechanisms are primed to deal with the stress. This intrinsic ability to anticipate salinity stress distinguishes it from the glycophyte A. thaliana. BIOLOGICAL SIGNIFICANCE There is significant interest in understanding the molecular mechanisms that plants use to tolerate salinity as soil salinization is becoming an increasing concern for agriculture with high soil Na(+) levels leading to reduced yields and economic loss. Much of our knowledge on the molecular mechanisms employed by plants to combat salinity stress has come from work on salt-sensitive plants, but studies on naturally occurring highly salt-resistant plants, halophytes, and direct comparisons between closely related glycophytes and halophytes, could help to further our understanding of salinity tolerance mechanisms. In this study, employing two closely related species which differ markedly in their salt-tolerance, we carried out a quantitative proteomic approach using 2D-DIGE to identify salt-responsive proteins and compare and contrast the differences between the two plant species. Our work complements a previous study using iTRAQ technology (34) and highlights the benefits of using alternative technologies and approaches to gain a broader representation of the salt-responsive proteome in these species.
Collapse
Affiliation(s)
- Rosario Vera-Estrella
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos CP 62210, Mexico.
| | - Bronwyn J Barkla
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos CP 62210, Mexico
| | - Omar Pantoja
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos CP 62210, Mexico
| |
Collapse
|