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Nabi B, Kumawat M, Ahlawat N, Ahlawat S. Molecular, Structural, and Functional Diversity of Universal Stress Proteins (USPs) in Bacteria, Plants, and Their Biotechnological Applications. Protein J 2024; 43:437-446. [PMID: 38492187 DOI: 10.1007/s10930-024-10192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Universal stress proteins (USPs) are widely distributed and play crucial roles in cellular responses to biotic and abiotic stresses. These roles include regulating cell growth and development, cell motility, hypoxia responses, and ion sequestration. With the increasing frequency and intensity of extreme weather events due to climate change, pathogens have developed different strategies to withstand environmental stresses, in which USPs play a significant role in their survival and virulence. In this study, we analyzed the importance of USPs in various organisms, such as archaea, plants, and fungi, as a parameter that influences their survival. We discussed the different types Of USPs and their role, aiming to carry out fundamental research in this field to identify significant constraints for better understanding of USP functions at molecular level. Additionally, we discussed concepts and research techniques that could help overcome these hurdles and facilitate new molecular approaches to better understand and target USPs as important stress adaptation and survival regulators. Although the precise characteristics of USPs are still unclear, numerous innovative uses have already been developed, tested, and implemented. Complementary approaches to basic research and applications, as well as new technology and analytical techniques, may offer insights into the cryptic but crucial activities of USPs in various living systems.
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Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India.
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Allahabad, 211007, India
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India.
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Qi T, He F, Zhang X, Wang J, Zhang Z, Jiang H, Zhao B, Du C, Che Y, Feng X, Wang Y, Li F. Genome-Wide Identification and Expression Profiling of Potato ( Solanum tuberosum L.) Universal Stress Proteins Reveal Essential Roles in Mechanical Damage and Deoxynivalenol Stress. Int J Mol Sci 2024; 25:1341. [PMID: 38279341 PMCID: PMC10816615 DOI: 10.3390/ijms25021341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Universal stress proteins (USPs) play an important regulatory role in responses to abiotic stress. Most of the research related to USPs so far has been conducted on plant models such as Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa L.), and cotton (Gossypium hirsutum L.). The potato (Solanum tuberosum L.) is one of the four major food crops in the world. The potato is susceptible to mechanical damage and infection by pathogenic fungi during transport and storage. Deoxynivalenol (DON) released by Fusarium can seriously degrade the quality of potatoes. As a result, it is of great significance to study the expression pattern of the potato StUSP gene family under abiotic stress conditions. In this study, a total of 108 USP genes were identified from the genome of the Atlantic potato, divided into four subgroups. Based on their genetic structure, the physical and chemical properties of their proteins and other aspects of their biological characteristics are comprehensively analyzed. Collinear analysis showed that the homologous genes of StUSPs and four other representative species (Solanum lycopersicum, Arabidopsis, Oryza sativa L., and Nicotiana attenuata) were highly conserved. The cis-regulatory elements of the StUSPs promoter are involved in plant hormones, environmental stress, mechanical damage, and light response. RNA-seq analysis showed that there are differences in the expression patterns of members of each subgroup under different abiotic stresses. A Weighted Gene Coexpression Network Analysis (WGCNA) of the central gene showed that the differential coexpression gene is mainly involved in the plant-pathogen response process, plant hormone signal transduction, and the biosynthesis process of secondary metabolites. Through qRT-PCR analysis, it was confirmed that StUSP13, StUSP14, StUSP15, and StUSP41 may be important candidate genes involved in the response to adversity stress in potatoes. The results of this study provide a basis for further research on the functional analysis of StUSPs in the response of potatoes to adversity stress.
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Affiliation(s)
- Tianshuai Qi
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Fumeng He
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Xinqi Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Jiaqi Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Zengli Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Heran Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China;
| | - Biao Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Chong Du
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Yunzhu Che
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Xu Feng
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Yingnan Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Fenglan Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
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Cui X, Zhang P, Chen C, Zhang J. VyUSPA3, a universal stress protein from the Chinese wild grape Vitis yeshanensis, confers drought tolerance to transgenic V. vinifera. PLANT CELL REPORTS 2023; 42:181-196. [PMID: 36318328 DOI: 10.1007/s00299-022-02943-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
VyUSPA3 from the Chinese wild grape Vitis yeshanensis interacts with ERF105, PUB24 and NF-YB3, and overexpression of the VyUSPA3 gene in V. vinifera cv. 'Thompson Seedless' confers drought tolerance. Drought is a major abiotic stress factor that seriously affects the growth and yield of grapevine. Although many drought-related genes have been identified in Arabidopsis and other plants, the functions of only a few of their counterparts have been revealed in grape. Here, a universal stress protein (USP) A from the Chinese wild grape Vitis yeshanensis, VyUSPA3, was identified and its function was subsequently characterized by overexpressing or silencing the VyUSPA3 gene in V. vinifera cv. 'Thompson Seedless' via Agrobacterium-mediated genetic transformation. After 21 d of the drought treatment, most leaves of the untransformed (UT) 'Thompson Seedless' lines wilted, yet UT lines were less damaged compared to the RNAi-VyUSPA3 lines, nonetheless, the OE-VyUSPA3 lines were mostly unaffected. Meanwhile, OE-VyUSPA3 lines showed smaller stomatal aperture, more developed roots, higher leaf relative water content, proline content, and antioxidant enzyme activities, as well as lower malondialdehyde, H2O2 and O2•- accumulation than UT lines, but this response pattern was reversed in the RNAi-VyUSPA3 lines. Besides, the transcript levels of four drought-related genes (RD22, RD29B, DREB2A, and NCED1) in OE-VyUSPA3 lines were greater than those in the RNAi-VyUSPA3 and UT lines. In addition, a yeast two-hybrid assay and a bimolecular fluorescence complementation assay confirmed that VyUSPA3 interacted with ERF105, PUB24, and NF-YB3, respectively. This study revealed that VyUSPA3 improved drought tolerance in transgenic grapevines possibly through interaction with the hormone signaling, ubiquitination system, ethylene-responsive element binding factor and nuclear factors.
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Affiliation(s)
- Xiaoyue Cui
- College of Horticulture, Northwest A&F University, Shaanxi, 712100, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Shaanxi, 712100, Yangling, China
| | - Pingying Zhang
- College of Horticulture, Northwest A&F University, Shaanxi, 712100, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Shaanxi, 712100, Yangling, China
| | - Chengcheng Chen
- College of Horticulture, Northwest A&F University, Shaanxi, 712100, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Shaanxi, 712100, Yangling, China
| | - Jianxia Zhang
- College of Horticulture, Northwest A&F University, Shaanxi, 712100, Yangling, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Shaanxi, 712100, Yangling, China.
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Hafeez MN, Khan MA, Sarwar B, Hassan S, Ali Q, Husnain T, Rashid B. Mutant Gossypium universal stress protein-2 (GUSP-2) gene confers resistance to various abiotic stresses in E. coli BL-21 and CIM-496-Gossypium hirsutum. Sci Rep 2021; 11:20466. [PMID: 34650178 PMCID: PMC8516947 DOI: 10.1038/s41598-021-99900-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022] Open
Abstract
Gossypium arboreum is considered a rich source of stress-responsive genes and the EST database revealed that most of its genes are uncharacterized. The full-length Gossypium universal stress protein-2 (GUSP-2) gene (510 bp) was cloned in E. coli and Gossypium hirsutum, characterized and point mutated at three positions, 352–354, Lysine to proline (M1-usp-2) & 214–216, aspartic acid to serine (M2-usp-2) & 145–147, Lysine to Threonine (M3-usp-2) to study its role in abiotic stress tolerance. It was found that heterologous expression of one mutant (M1-usp-2) provided enhanced tolerance against salt and osmotic stresses, recombinant cells have higher growth up to 10-5dilution in spot assay as compared to cells expressing W-usp-2 (wild type GUSP-2), M2-usp-2 and M3-usp-2 genes. M1-usp-2 gene transcript profiling exhibited significant expression (8.7 fold) in CIM-496-Gossypium hirsutum transgenic plants and enhance drought tolerance. However, little tolerance against heat and cold stresses in bacterial cells was observed. The results from our study concluded that the activity of GUSP-2 was enhanced in M1-usp-2 but wipe out in M2-usp-2 and M3-usp-2 response remained almost parallel to W-usp-2. Further, it was predicted through in silico analysis that M1-usp-2, W-usp-2 and M3-usp-2 may be directly involved in stress tolerance or function as a signaling molecule to activate the stress adaptive mechanism. However, further investigation will be required to ascertain its role in the adaptive mechanism of stress tolerance.
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Affiliation(s)
- Muhammad Nadeem Hafeez
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan. .,Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland. .,School of PhD Program in Cellular and Molecular Biotechnology, University of Teramo, Teramo, Italy. .,Department of Pharmacy, University of Chieti - Pescara "G. d'Annunzio", Chieti, Italy.
| | - Mohsin Ahmad Khan
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Bilal Sarwar
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Sameera Hassan
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan. .,Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan.
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
| | - Bushra Rashid
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Lahore, Pakistan
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Cui X, Zhang P, Hu Y, Chen C, Liu Q, Guan P, Zhang J. Genome-wide analysis of the Universal stress protein A gene family in Vitis and expression in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:57-70. [PMID: 34034161 DOI: 10.1016/j.plaphy.2021.04.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Universal Stress Protein A (USPA) plays critical roles in the regulation of growth, development and response to abiotic stress in plants. To date, most research related to the role of USPA in plants has been carried out in herbaceous models such as Arabidopsis, rice and soybean. Here, we used bioinformatics approaches to identify 21 USPA genes in the genome of Vitis vinifera L. Phylogenetic analysis revealed that VvUSPAs could be divided into eight clades. Based on predicted chromosomal locations, we identified 16 pairs of syntenic, orthologous genes between A. thaliana and V. vinifera. Further promoter cis-elements analysis, together with identification of potential microRNA (miRNA) binding sites, suggested that at least some of the VvUSPAs participate in response to phytohormones and abiotic stress. To add support for this, we analyzed the developmental and stress-responsive expression patterns of the homologous USPA genes in the drought-resistant wild Vitis yeshanensis accession 'Yanshan-1' and the drought-sensitive Vitis riparia accession 'He'an'. Most of the USPA genes were upregulated in different degrees in the two genotypes after drought stress and exposure to ethephon (ETH), abscisic acid (ABA) and methyl jasmonate (MeJA). Individual USPA genes showed various tissue-specific expression patterns. Heterologous expression of five selected genes (VvUSPA2, VvUSPA3, VvUSPA11, VvUSPA13 and VvUSPA16) in Escherichia coli (E. coli) enhanced resistance to drought stress. Our study provides a model for mapping gene function in response to abiotic stress and identified three candidate genes, VvUSPA3, VvUSPA11 and VvUSPA16, as regulators of drought response in V. vinifera.
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Affiliation(s)
- Xiaoyue Cui
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Pingying Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yafan Hu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Chengcheng Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Qiying Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Pingyin Guan
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg, 476131, Karlsruhe, Germany.
| | - Jianxia Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Arabia S, Sami AA, Akhter S, Sarker RH, Islam T. Comprehensive in silico Characterization of Universal Stress Proteins in Rice ( Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:712607. [PMID: 34394169 PMCID: PMC8355530 DOI: 10.3389/fpls.2021.712607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 06/10/2023]
Abstract
In a world where climate change is real and its consequences are unprecedented, understanding of the plant adaptive capacity and native stress-responsive machinery is crucial. In recent years, universal stress proteins (USPs) have received much attention in the field of plant science due to their stress-specific transcriptional regulation. This study focuses on the extensive characterization of the USP gene family members in the monocot crop rice (Oryza sativa L. var. japonica). Here, we report a total of 44 USP genes in the rice genome. In silico characterization of these genes showed that domain architecture played a major role in the functional diversification of the USP gene family which holds for all plant USPs. On top of that, a higher conservation of OsUSP members has been exhibited with a monocot genome (Zea mays L.) as compared to a dicot genome (Arabidopsis thaliana L.). Expression profiling of the identified genes led to the discovery of multiple OsUSP genes that showed pronounced transcript alteration under various abiotic stress conditions, indicating their potential role as multi-functional stress-specific modules. Furthermore, expression validation of OsUSP genes using qRT-PCR provided a strong evidence for the utility OsUSP genes in building multi-stress tolerant plants. Altogether, this study provides leads to suitable USP candidates that could be targeted for plant breeding and genetic engineering experiments to develop stress resilient crop species.
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Liu Y, Pei L, Xiao S, Peng L, Liu Z, Li X, Yang Y, Wang J. AtPPRT1 negatively regulates salt stress response in Arabidopsis seedlings. PLANT SIGNALING & BEHAVIOR 2020; 15:1732103. [PMID: 32079457 PMCID: PMC7194377 DOI: 10.1080/15592324.2020.1732103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Salt stress is one of the environmental factors that negatively affect plant growth and development. We have previously reported a putative C3HC4 zinc-finger ubiquitin E3 ligase (AtPPRT1) negatively regulates Abscisic acid (ABA) and drought stress response. According to previous studies, the accumulation of ABA in plants can further regulate the salt stress response. Therefore, in this study, we further analyzed whether AtPPRT1 negatively regulates the salt stress response. The results showed that AtPPRT1 expression was induced by salt stress. Furthermore, under salt stress, the β-glucuronidase (GUS) gene driven by the AtPPRT1 promoter has shown increased activity in the hypocotyl and petioles of Arabidopsis seedlings. Additionally, seedlings of the T-DNA insertion mutant atpprt1 showed significant growth advantage under salt stress, whereas overexpressing AtPPRT1 (OE lines) in Arabidopsis seedlings displayed hypersensitive under salt stress. Etiolated atpprt1 seedlings also demonstrated significantly elongated hypocotyl lengths in salt stress. The elevated or reduced salt tolerance of atpprt1 and AtPPRT1 overexpressing lines was confirmed by the changes in chlorophyll content and 3,3'-Diaminobenzidine (DAB) staining. The above data suggest that AtPPRT1 has a negative effect on salt tolerance in Arabidopsis seedlings.
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Affiliation(s)
- Yu Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Linsen Pei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shuya Xiao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lu Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhibin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- CONTACT Jianmei Wang ; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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8
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Dossa K, Mmadi MA, Zhou R, Zhang T, Su R, Zhang Y, Wang L, You J, Zhang X. Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame ( Sesamum indicum L.). Int J Mol Sci 2019; 20:ijms20163930. [PMID: 31412539 PMCID: PMC6721054 DOI: 10.3390/ijms20163930] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/26/2019] [Accepted: 08/10/2019] [Indexed: 01/21/2023] Open
Abstract
Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Marie A Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Tianyuan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruqi Su
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Yujuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
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Chi YH, Koo SS, Oh HT, Lee ES, Park JH, Phan KAT, Wi SD, Bae SB, Paeng SK, Chae HB, Kang CH, Kim MG, Kim WY, Yun DJ, Lee SY. The Physiological Functions of Universal Stress Proteins and Their Molecular Mechanism to Protect Plants From Environmental Stresses. FRONTIERS IN PLANT SCIENCE 2019; 10:750. [PMID: 31231414 PMCID: PMC6560075 DOI: 10.3389/fpls.2019.00750] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/22/2019] [Indexed: 05/13/2023]
Abstract
Since the original discovery of a Universal Stress Protein (USP) in Escherichia coli, a number of USPs have been identified from diverse sources including archaea, bacteria, plants, and metazoans. As their name implies, these proteins participate in a broad range of cellular responses to biotic and abiotic stresses. Their physiological functions are associated with ion scavenging, hypoxia responses, cellular mobility, and regulation of cell growth and development. Consistent with their roles in resistance to multiple stresses, USPs show a wide range of structural diversity that results from the diverse range of other functional motifs fused with the USP domain. As well as providing structural diversity, these catalytic motifs are responsible for the diverse biochemical properties of USPs and enable them to act in a number of cellular signaling transducers and metabolic regulators. Despite the importance of USP function in many organisms, the molecular mechanisms by which USPs protect cells and provide stress resistance remain largely unknown. This review addresses the diverse roles of USPs in plants and how the proteins enable plants to resist against multiple stresses in ever-changing environment. Bioinformatic tools used for the collection of a set of USPs from various plant species provide more than 2,100 USPs and their functional diversity in plant physiology. Data from previous studies are used to understand how the biochemical activity of plant USPs modulates biotic and abiotic stress signaling. As USPs interact with the redox protein, thioredoxin, in Arabidopsis and reactive oxygen species (ROS) regulates the activity of USPs, the involvement of USPs in redox-mediated defense signaling is also considered. Finally, this review discusses the biotechnological application of USPs in an agricultural context by considering the development of novel stress-resistant crops through manipulating the expression of USP genes.
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Affiliation(s)
- Yong Hun Chi
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Sung Sun Koo
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Hun Taek Oh
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Eun Seon Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Joung Hun Park
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Kieu Anh Thi Phan
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Seong Dong Wi
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Su Bin Bae
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Chang Ho Kang
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Institute of Agricultural and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- *Correspondence: Sang Yeol Lee,
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Gorshkova DS, Getman IA, Voronkov AS, Chizhova SI, Kuznetsov VV, Pojidaeva ES. The Gene Encoding the Universal Stress Protein AtUSP is Regulated by Phytohormones and Involved in Seed Germination of Arabidopsis thaliana. DOKL BIOCHEM BIOPHYS 2018; 479:105-107. [DOI: 10.1134/s1607672918020151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 11/22/2022]
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Functional Characterization of Selected Universal Stress Protein from Salvia miltiorrhiza (SmUSP) in Escherichia coli. Genes (Basel) 2017; 8:genes8090224. [PMID: 28885603 PMCID: PMC5615357 DOI: 10.3390/genes8090224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/20/2017] [Accepted: 09/05/2017] [Indexed: 12/21/2022] Open
Abstract
The multigene universal stress protein (USP) family is evolutionarily conserved. Members play indispensable roles in plant tolerance to abiotic stresses. Although relatively well-characterized in model plants, such as Arabidopsis thaliana and Oryzasativa, this family has not been investigated in Salvia miltiorrhiza, an important herbal plant for which yields can be limited by various abiotic stresses. Here, we identified 32 USP family members in the S. miltiorrhiza genome, and used phylogenetic analysis to sort these SmUSPs into four groups. Groups A and B belong to the ATP-binding class whereas Groups C and D are in the non-ATP-binding class. Motif analysis and multiple sequence alignment hinted that members of group A and B were able to bind ATP. Our qRT-PCR data from different tissues/organs and under salt and heat stresses provided an overall expression pattern for those genes. Three SmUSPs (SmUSP1, SmUSP8, and SmUSP27) were cloned from S. miltiorrhiza and functionally characterized in Escherichiacoli. Compared with the control cells, those that expressed SmUSPs exhibited enhanced tolerance to salt, heat, and a combination of the two. This suggested that the protein has a protective role in cells when exposed to single-stress and multiple-stress conditions. Our findings provide valuable information that helps improve our understanding of the evolutionary and functional conservation and diversity associated with the USP gene family in S. miltiorrhiza.
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Bhuria M, Goel P, Kumar S, Singh AK. The Promoter of AtUSP Is Co-regulated by Phytohormones and Abiotic Stresses in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1957. [PMID: 28083000 PMCID: PMC5183650 DOI: 10.3389/fpls.2016.01957] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/09/2016] [Indexed: 05/29/2023]
Abstract
Universal stress proteins (USPs) are known to be expressed in response to various abiotic stresses in a wide variety of organisms, such as bacteria, archaebacteria, protists, algae, fungi, plants, and animals. However, in plants, biological function of most of the USPs still remains obscure. In the present study, Arabidopsis USP gene (AtUSP) showed induction in response to abscisic acid (ABA) and various abiotic stresses viz. heat, dehydration, salt, osmotic, and cold stresses. Additionally, in silico analysis of AtUSP promoter identified several cis-elements responsive to phytohormones and abiotic stresses such as ABRE, ERE, DRE, and HSE, etc. To functionally validate the AtUSP promoter, the 1115 bp region of promoter was characterized under phytohormone and abiotic stress treatments. Deletion analysis of promoter was carried out by cloning the full length promoter (D0) and its three 5' deletion derivatives, D1 (964 bp), D2 (660 bp), and D3 (503 bp) upstream of the β-glucuronidase (GUS) reporter gene, which were then stably transformed in Arabidopsis plants. The AtUSP promoter (D0) showed minimal activity under non-stress conditions which was enhanced in response to phytohormone treatments (ABA and ACC) and abiotic stresses such as dehydration, heat, cold, salt, and osmotic stresses. The seedlings harboring D1 and D2 deletion fragments showed constitutive GUS expression even under control condition with increased activity almost under all the treatments. However, D3 seedlings exhibited complete loss of activity under control condition with induction under ACC treatment, dehydration, heat, oxidative, salt, and osmotic stresses. Thus, present study clearly showed that AtUSP promoter is highly inducible by phytohormones and multiple abiotic stresses and it can be exploited as stress inducible promoter to generate multi-stress tolerant crops with minimal effects on their other important traits.
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Affiliation(s)
- Monika Bhuria
- Council of Scientific and Industrial Research – Institute of Himalayan Bioresource TechnologyPalampur, India
- Academy of Scientific and Innovative ResearchNew Delhi, India
| | - Parul Goel
- Council of Scientific and Industrial Research – Institute of Himalayan Bioresource TechnologyPalampur, India
- Academy of Scientific and Innovative ResearchNew Delhi, India
| | - Sanjay Kumar
- Council of Scientific and Industrial Research – Institute of Himalayan Bioresource TechnologyPalampur, India
- Academy of Scientific and Innovative ResearchNew Delhi, India
| | - Anil K. Singh
- Council of Scientific and Industrial Research – Institute of Himalayan Bioresource TechnologyPalampur, India
- Academy of Scientific and Innovative ResearchNew Delhi, India
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Udawat P, Jha RK, Sinha D, Mishra A, Jha B. Overexpression of a Cytosolic Abiotic Stress Responsive Universal Stress Protein (SbUSP) Mitigates Salt and Osmotic Stress in Transgenic Tobacco Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:518. [PMID: 27148338 PMCID: PMC4838607 DOI: 10.3389/fpls.2016.00518] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/01/2016] [Indexed: 05/21/2023]
Abstract
The universal stress protein (USP) is a ubiquitous protein and plays an indispensable role in plant abiotic stress tolerance. The genome of Salicornia brachiata contains two homologs of intron less SbUSP gene which encodes for salt and osmotic responsive USP. In vivo localization reveals that SbUSP is a membrane bound cytosolic protein. The role of the gene was functionally validated by developing transgenic tobacco and compared with control [wild-type (WT) and vector control (VC)] plants under different abiotic stress condition. Transgenic lines (T1) exhibited higher chlorophyll, relative water, proline, total sugar, reducing sugar, free amino acids, polyphenol contents, osmotic potential, membrane stability, and lower electrolyte leakage and lipid peroxidation (malondialdehyde content) under stress treatments than control (WT and VC) plants. Lower accumulation of H2O2 and [Formula: see text] radicals was also detected in transgenic lines compared to control plants under stress conditions. Present study confers that overexpression of the SbUSP gene enhances plant growth, alleviates ROS buildup, maintains ion homeostasis and improves the physiological status of the plant under salt and osmotic stresses. Principal component analysis exhibited a statistical distinction of plant response to salinity stress, and a significant response was observed for transgenic lines under stress, which provides stress endurance to the plant. A possible signaling role is proposed that some downstream genes may get activated by abiotic stress responsive cytosolic SbUSP, which leads to the protection of cell from oxidative damages. The study unveils that ectopic expression of the gene mitigates salt or osmotic stress by scavenging ROS and modulating the physiological process of the plant.
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Affiliation(s)
- Pushpika Udawat
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Rajesh K. Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Dinkar Sinha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
| | - Avinash Mishra
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
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Udawat P, Jha RK, Sinha D, Mishra A, Jha B. Overexpression of a Cytosolic Abiotic Stress Responsive Universal Stress Protein (SbUSP) Mitigates Salt and Osmotic Stress in Transgenic Tobacco Plants. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 27148338 DOI: 10.3389/flps.2016.00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The universal stress protein (USP) is a ubiquitous protein and plays an indispensable role in plant abiotic stress tolerance. The genome of Salicornia brachiata contains two homologs of intron less SbUSP gene which encodes for salt and osmotic responsive USP. In vivo localization reveals that SbUSP is a membrane bound cytosolic protein. The role of the gene was functionally validated by developing transgenic tobacco and compared with control [wild-type (WT) and vector control (VC)] plants under different abiotic stress condition. Transgenic lines (T1) exhibited higher chlorophyll, relative water, proline, total sugar, reducing sugar, free amino acids, polyphenol contents, osmotic potential, membrane stability, and lower electrolyte leakage and lipid peroxidation (malondialdehyde content) under stress treatments than control (WT and VC) plants. Lower accumulation of H2O2 and [Formula: see text] radicals was also detected in transgenic lines compared to control plants under stress conditions. Present study confers that overexpression of the SbUSP gene enhances plant growth, alleviates ROS buildup, maintains ion homeostasis and improves the physiological status of the plant under salt and osmotic stresses. Principal component analysis exhibited a statistical distinction of plant response to salinity stress, and a significant response was observed for transgenic lines under stress, which provides stress endurance to the plant. A possible signaling role is proposed that some downstream genes may get activated by abiotic stress responsive cytosolic SbUSP, which leads to the protection of cell from oxidative damages. The study unveils that ectopic expression of the gene mitigates salt or osmotic stress by scavenging ROS and modulating the physiological process of the plant.
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Affiliation(s)
- Pushpika Udawat
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India; Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Rajesh K Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India; Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Dinkar Sinha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute Bhavnagar, India
| | - Avinash Mishra
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India; Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research InstituteBhavnagar, India; Academy of Scientific and Innovative Research, Council of Scientific and Industrial ResearchNew Delhi, India
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15
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He Q, Zhu S, Zhang B. MicroRNA-target gene responses to lead-induced stress in cotton (Gossypium hirsutum L.). Funct Integr Genomics 2014; 14:507-15. [PMID: 24879091 DOI: 10.1007/s10142-014-0378-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/27/2014] [Accepted: 05/12/2014] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) play key roles in plant responses to various metal stresses. To investigate the miRNA-mediated plant response to heavy metals, cotton (Gossypium hirsutum L.), the most important fiber crop in the world, was exposed to different concentrations (0, 25, 50, 100, and 200 µM) of lead (Pb) and then the toxicological effects were investigated. The expression patterns of 16 stress-responsive miRNAs and 10 target genes were monitored in cotton leaves and roots by quantitative real-time PCR (qRT-PCR); of these selected genes, several miRNAs and their target genes are involved in root development. The results show a reciprocal regulation of cotton response to lead stress by miRNAs. The characterization of the miRNAs and the associated target genes in response to lead exposure would help in defining the potential roles of miRNAs in plant adaptation to heavy metal stress and further understanding miRNA regulation in response to abiotic stress.
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Affiliation(s)
- Qiuling He
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
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Ashraf MA, Shahid AA, Rao AQ, Bajwa KS, Husnain T. Functional characterization of a bidirectional plant promoter from cotton leaf curl Burewala virus using an Agrobacterium-mediated transient assay. Viruses 2014; 6:223-42. [PMID: 24424501 PMCID: PMC3917440 DOI: 10.3390/v6010223] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/14/2013] [Accepted: 12/24/2013] [Indexed: 11/16/2022] Open
Abstract
The C1 promoter expressing the AC1 gene, and V1 promoter expressing the AV1 gene are located in opposite orientations in the large intergenic region of the Cotton leaf curl Burewala virus (CLCuBuV) genome. Agro-infiltration was used to transiently express putative promoter constructs in Nicotiana tabacum and Gossypium hirsutum leaves, which was monitored by a GUS reporter gene, and revealed that the bidirectional promoter of CLCuBuV transcriptionally regulates both the AC1 and AV1 genes. The CLCuBuV C1 gene promoter showed a strong, consistent transient expression of the reporter gene (GUS) in N. tabacum and G. hirsutum leaves and exhibited GUS activity two- to three-fold higher than the CaMV 35S promoter. The CLCuBuV bidirectional gene promoter is a nearly constitutive promoter that contains basic conserved elements. Many cis-regulatory elements (CREs) were also analyzed within the bidirectional plant promoters of CLCuBuV and closely related geminiviruses, which may be helpful in understanding the transcriptional regulation of both the virus and host plant.
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Affiliation(s)
- Muhammad Aleem Ashraf
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Ahmad Ali Shahid
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Abdul Qayyum Rao
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Kamran Shehzad Bajwa
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Tayyab Husnain
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
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Martínez-Esteso MJ, Sellés-Marchart S, Lijavetzky D, Pedreño MA, Bru-Martínez R. A DIGE-based quantitative proteomic analysis of grape berry flesh development and ripening reveals key events in sugar and organic acid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:2521-69. [PMID: 21576399 DOI: 10.1093/jxb/erq434] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components, such as sugars, acids, flavours, anthocyanins, tannins, etc., are accumulated during the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance the understanding of the berry development and ripening processes. Here, the developmental analysis of V. vinifera cv. Muscat Hamburg berries is reported at protein level, from fruit set to full ripening. A top-down proteomic approach based on differential in-gel electrophoresis (DIGE) followed by tandem mass spectrometry led to identification and quantification of 156 and 61 differentially expressed proteins in green and ripening phases, respectively. Two key points in development, with respect to changes in protein level, were detected: end of green development and beginning of ripening. The profiles of carbohydrate metabolism enzymes were consistent with a net conversion of sucrose to malate during green development. Pyrophosphate-dependent phosphofructokinase is likely to play a key role to allow an unrestricted carbon flow. The well-known change of imported sucrose fate at the beginning of ripening from accumulation of organic acid (malate) to hexoses (glucose and fructose) was well correlated with a switch in abundance between sucrose synthase and soluble acid invertase. The role of the identified proteins is discussed in relation to their biological function, grape berry development, and to quality traits. Another DIGE experiment comparing fully ripe berries from two vintages showed very few spots changing, thus indicating that protein changes detected throughout development are specific.
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Affiliation(s)
- Maria José Martínez-Esteso
- Grupo de Proteómica y Genómica Funcional de Plantas, Dept. Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain
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Mendisco F, Keyser C, Hollard C, Seldes V, Nielsen AE, Crubézy E, Ludes B. Application of the iPLEX™ Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: benefits for ancient population studies. Electrophoresis 2011; 32:386-93. [PMID: 21298665 DOI: 10.1002/elps.201000483] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/16/2010] [Accepted: 11/17/2010] [Indexed: 11/06/2022]
Abstract
Important developments in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique have generated new perspectives regarding SNP genotyping, which are particularly promising for ancient population-based studies. The main aim of the present study was to investigate the application of a MALDI-TOF MS-based SNP genotyping technique, called iPLEX(®) Gold, to analyze Amerindian ancient DNA samples. The first objective was to test the sensitivity of the method, which is recommended for DNA quantities between 10 and 5 ng, for ancient biological samples containing DNA molecules that were degraded and present in minute quantities. The second objective was to detail the advantages of this technique for studies on ancient populations. Two multiplexes were designed, allowing the major Amerindian mitochondrial and Y haplogroups to be determined simultaneously. This analysis has never been described before. Results demonstrated the reliability and accuracy of the method; data were obtained for both mitochondrial and nuclear DNA using picogram (pg) quantities of nucleic acid. This technique has the advantages of both MS and minisequencing techniques; thus, it should be included in the protocols for future ancient DNA studies.
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Affiliation(s)
- Fanny Mendisco
- Laboratoire d'Anthropologie Moléculaire, Université de Strasbourg, Institut de Médecine Légale, Strasbourg, France.
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