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Méndez-Yáñez A, Sáez D, Rodríguez-Arriaza F, Letelier-Naritelli C, Valenzuela-Riffo F, Morales-Quintana L. Involvement of the GH38 Family Exoglycosidase α-Mannosidase in Strawberry Fruit Ripening. Int J Mol Sci 2024; 25:6581. [PMID: 38928287 PMCID: PMC11203768 DOI: 10.3390/ijms25126581] [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: 05/04/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Exoglycosidase enzymes hydrolyze the N-glycosylations of cell wall enzymes, releasing N-glycans that act as signal molecules and promote fruit ripening. Vesicular exoglycosidase α-mannosidase enzymes of the GH38 family (EC 3.2.1.24; α-man) hydrolyze N-glycans in non-reduced termini. Strawberry fruit (Fragaria × ananassa) is characterized by rapid softening as a result of cell wall modifications during the fruit ripening process. Enzymes acting on cell wall polysaccharides explain the changes in fruit firmness, but α-man has not yet been described in F. × ananassa, meaning that the indirect effects of N-glycan removal on its fruit ripening process are unknown. The present study identified 10 GH38 α-man sequences in the F. × ananassa genome with characteristic conserved domains and key residues. A phylogenetic tree built with the neighbor-joining method and three groups of α-man established, of which group I was classified into three subgroups and group III contained only Poaceae spp. sequences. The real-time qPCR results demonstrated that FaMAN genes decreased during fruit ripening, a trend mirrored by the total enzyme activity from the white to ripe stages. The analysis of the promoter regions of these FaMAN genes was enriched with ripening and phytohormone response elements, and contained cis-regulatory elements related to stress responses to low temperature, drought, defense, and salt stress. This study discusses the relevance of α-man in fruit ripening and how it can be a useful target to prolong fruit shelf life.
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Affiliation(s)
- Angela Méndez-Yáñez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Darwin Sáez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
- Programa de Doctorado en Ciencias Biomédicas, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Francisca Rodríguez-Arriaza
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Claudio Letelier-Naritelli
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Felipe Valenzuela-Riffo
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay s/n, Talca 3460000, Chile
| | - Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
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Amin A, Naim MD, Islam N, Mollah MNH. Genome-wide identification and characterization of DTX family genes highlighting their locations, functions, and regulatory factors in banana (Musa acuminata). PLoS One 2024; 19:e0303065. [PMID: 38843276 PMCID: PMC11156367 DOI: 10.1371/journal.pone.0303065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/19/2024] [Indexed: 06/09/2024] Open
Abstract
The detoxification efflux carriers (DTX) are a significant group of multidrug efflux transporter family members that play diverse functions in all kingdoms of living organisms. However, genome-wide identification and characterization of DTX family transporters have not yet been performed in banana, despite its importance as an economic fruit plant. Therefore, a detailed genome-wide analysis of DTX family transporters in banana (Musa acuminata) was conducted using integrated bioinformatics and systems biology approaches. In this study, a total of 37 DTX transporters were identified in the banana genome and divided into four groups (I, II, III, and IV) based on phylogenetic analysis. The gene structures, as well as their proteins' domains and motifs, were found to be significantly conserved. Gene ontology (GO) annotation revealed that the predicted DTX genes might play a vital role in protecting cells and membrane-bound organelles through detoxification mechanisms and the removal of drug molecules from banana cells. Gene regulatory analyses identified key transcription factors (TFs), cis-acting elements, and post-transcriptional regulators (miRNAs) of DTX genes, suggesting their potential roles in banana. Furthermore, the changes in gene expression levels due to pathogenic infections and non-living factor indicate that banana DTX genes play a role in responses to both biotic and abiotic stresses. The results of this study could serve as valuable tools to improve banana quality by protecting them from a range of environmental stresses.
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Affiliation(s)
- Al Amin
- Department of Statistics, Bioinformatics Laboratory, Faculty of Science, University of Rajshahi, Rajshahi, Bangladesh
- Department of Zoology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Nurul Islam
- Department of Zoology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Nurul Haque Mollah
- Department of Statistics, Bioinformatics Laboratory, Faculty of Science, University of Rajshahi, Rajshahi, Bangladesh
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Zhang X, Xue Y, Wang H, Nisa Z, Jin X, Yu L, Liu X, Yu Y, Chen C. Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean ( Glycine soja). PeerJ 2022; 10:e14451. [PMID: 36518280 PMCID: PMC9744164 DOI: 10.7717/peerj.14451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/01/2022] [Indexed: 12/05/2022] Open
Abstract
Background NDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress. Methods We identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR. Results In this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.
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Affiliation(s)
- Xu Zhang
- Harbin Normal University, Harbin, Heilongjiang, China
| | - Yongguo Xue
- Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Haihang Wang
- Harbin Normal University, Harbin, Heilongjiang, China
| | | | - Xiaoxia Jin
- Harbin Normal University, Harbin, Heilongjiang, China
| | - Lijie Yu
- Harbin Normal University, Harbin, Heilongjiang, China
| | - Xinlei Liu
- Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yang Yu
- Shenyang University, Shenyang, China
| | - Chao Chen
- Harbin Normal University, Harbin, Heilongjiang, China
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Zhao J, Pu X, Li W, Li M. Characterization and evolutionary diversification of the phospholipase D gene family in mosses. Front Genet 2022; 13:1015393. [PMID: 36313445 PMCID: PMC9607936 DOI: 10.3389/fgene.2022.1015393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Plant phospholipase D (PLD) exerts important roles in various biological processes, such as intracellular signaling and morphological development. Our knowledge about early land plant PLDs is still underdeveloped. In this study, we identified 84 PLD genes in six mosses, i.e., Physcomitrella patens, Ceratodon purpureus, Fontinalis antipyretica, Pleurozium schreberi, Sphagnum magellanicum, and Sphagnum fallax. These PLDs were classified into four clades (I-IV). We showed that PLD underwent rapid expansion in mosses. A total of six conserved domains and two core HKD motifs were detected. Structure analysis uncovered that the moss PLDs from within a clade generally exhibited similar exon-intron organization. Cis-elements prediction and expression analyses indicated that P. patens PLDs had key roles in stress responsiveness and plant development. Particularly, about half of the P. patens PLDs (e.g., PpPLD1, PpPLD2, and PpPLD5) were differentially expressed under biotic and abiotic stresses. We also determined the expression pattern of P. patens PLD genes in various tissues and at different stages of development. Although the moss, clubmoss, liverwort, and fern PLDs evolved largely under functional constraints, we found episodic positive selection in the moss PLDs, e.g., C. purpureus PLD2 and P. patens PLD11. We infer that the evolutionary force acting on the PLDs may have facilitated moss colonization of land. Our work provides valuable insights into the diversification of moss PLD genes, and can be used for future studies of their functions.
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Affiliation(s)
- Jinjie Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Xinyuan Pu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Wenfei Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Meng Li
- Yunnan Academy of Tobacco Science, Kunming, Yunnan, China
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Genomic Survey and Cold-Induced Expression Patterns of bHLH Transcription Factors in Liriodendron chinense (Hemsl) Sarg. FORESTS 2022. [DOI: 10.3390/f13040518] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
bHLH transcription factors play an animated role in the plant kingdom during growth and development, and responses to various abiotic stress. In this current study, we conducted, the genome-wide survey of bHLH transcription factors in Liriodendron chinense (Hemsl) Sarg., 91 LcbHLH family members were identified. Identified LcbHLH gene family members were grouped into 19 different subfamilies based on the conserved motifs and phylogenetic analysis. Our results showed that LcbHLH genes clustered in the same subfamily exhibited a similar conservative exon-intron pattern. Hydrophilicity value analysis showed that all LcbHLH proteins were hydrophilic. The Molecular weight (Mw) of LcbHLH proteins ranged from 10.19 kD (LcbHLH15) to 88.40 kD (LcbHLH50). A greater proportion, ~63%, of LcbHLH proteins had a theoretical isoelectric point (pI) less than seven. Additional analysis on the collinear relationships within species and among dissimilar species illustrated that tandem and fragment duplication are the foremost factors of amplification of this family in the evolution process, and they are all purified and selected. RNA-seq and real-time quantitative PCR analysis of LcbHLH members showed that the expression of LcbHLH35, 55, and 86 are up-regulated, and the expression of LcbHLH9, 20, 39, 54, 56, and 69 is down-regulated during cold stress treatments while the expression of LcbHLH24 was up-regulated in the short term and then later down-regulated. From our results, we concluded that LcbHLH genes might participate in cold-responsive processes of L. chinense. These findings provide the basic information of bHLH gene in L. chinense and their regulatory roles in plant development and cold stress response.
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Tang W, Wang X, Kou M, Yan H, Gao R, Li C, Song W, Zhang Y, Wang X, Liu Y, Li Z, Li Q. The sweetpotato GIGANTEA gene promoter is co-regulated by phytohormones and abiotic stresses in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:143-154. [PMID: 34628175 DOI: 10.1016/j.plaphy.2021.08.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/19/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
GIGANTEA (GI) is known to play significant roles in various molecular pathways. Nevertheless, the underlying mechanism of the transcriptional regulation of GI remains obscure in sweetpotato. In the present study, a 1518-bp promoter sequence was obtained from the Ipomoea batatas GIGANTEA (IbGI) gene, and several potential cis-elements responsive to light, phytohormones and abiotic stresses were identified by in silico analysis. In order to functionally validate the IbGI promoter, the 5' deletion analysis of the promoter was performed by cloning the full-length promoter (D0) and its four deletion fragments, D1 (1235 bp), D2 (896 bp), D3 (549 bp) and D4 (286 bp), upstream of the β-glucuronidase (GUS) reporter gene. Then, these were stably transformed in Arabidopsis plants. All transgenic seedlings exhibited stable GUS activity in the condition of control, but with decreased activity in the condition of most treatments. Interestingly, merely D1 seedlings that contained an abscisic acid responsive cis-element (ABRE-element) had an extremely powerful GUS activity under the treatment of ABA, which implies that fragment spanning nucleotides of -1235 to -896 bp might be a crucial component for the responses of ABA. Eight different types of potential transcriptional regulators of IbGI were isolated by Y1H, including TGA2.2, SPLT1 and GADPH, suggesting the complex interaction mode of protein-DNA on the IbGI promoter. Taken together, these present results help to better understand the transcriptional regulation mechanism of the IbGI gene, and provides an insight into the IbGI promoter, which can be considered as an alternation for breeding transgenic plants.
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Affiliation(s)
- Wei Tang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Xiaoxiao Wang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Meng Kou
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Hui Yan
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Runfei Gao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Chen Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Weihan Song
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China.
| | - Qiang Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou, 221131, PR China.
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El-Sappah AH, Elbaiomy RG, Elrys AS, Wang Y, Zhu Y, Huang Q, Yan K, Xianming Z, Abbas M, El-Tarabily KA, Li J. Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. Front Genet 2021; 12:713224. [PMID: 34603378 PMCID: PMC8482800 DOI: 10.3389/fgene.2021.713224] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.
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Affiliation(s)
- Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yumin Zhu
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qiulan Huang
- College of Tea Science, Yibin University, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Zhao Xianming
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates.,Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
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Viana VE, Carlos da Maia L, Busanello C, Pegoraro C, Costa de Oliveira A. When rice gets the chills: comparative transcriptome profiling at germination shows WRKY transcription factor responses. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23 Suppl 1:100-112. [PMID: 33773005 DOI: 10.1111/plb.13262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Rice is vital for food security. Due to its tropical origin, rice suffers from cold temperatures that affect its entire life cycle. Key genes have been identified involved in cold tolerance. WRKYs are generally downstream of the MAPK cascade and can act together with VQ proteins to regulate stress-responsive genes. Chilling treatment was applied at germination to two rice genotypes (tolerant and sensitive). Shoots at S3 stage were collected for RNA-seq to identify OsWRKY, OsMAPKs and OsVQs expression. Relationships among MAPKs, WRKYs and VQs were predicted through correlation analysis. OsWRKY transcriptional regulation was predicted by in silico analysis of cis-regulatory elements. A total of 39 OsWRKYs were differentially expressed. OsWRKY21, OsWRK24 and OsWRKY69 are potential positive regulators, while OsWRKY10, OsWRK47, OsWRKY62, OsWRKY72 and OsWRKY77 are potential negative regulators, of chilling tolerance. 12 OsMAPKs were differentially expressed. OsMAPKs were downregulated and negatively correlated with the upregulated OsWRKYs in the tolerant genotype. 19 OsVQs were differentially expressed, three and six OsVQs were positively correlated with OsWRKYs in the tolerant and sensitive genotypes, respectively. Seven differentially expressed OsWRKYs have cold-responsive elements in their promoters and five upregulated OsWRKYs in the tolerant genotype contained the W-box motif. Chilling causes changes in OsWRKY, OsMAPK and OsVQ gene expression at germination. OsWRKYs may not act downstream of the MAPK cascade to coordinate chilling tolerance, but OsWRKYs may act with VQs to regulate chilling tolerance. Candidate OsWRKYs are correlated and have a W-box in the promoter, suggesting an auto-regulation mechanism.
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Affiliation(s)
- V E Viana
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - L Carlos da Maia
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - C Busanello
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - C Pegoraro
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - A Costa de Oliveira
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
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Ali E, Saand MA, Khan AR, Shah JM, Feng S, Ming C, Sun P. Genome-wide identification and expression analysis of detoxification efflux carriers (DTX) genes family under abiotic stresses in flax. PHYSIOLOGIA PLANTARUM 2021; 171:483-501. [PMID: 32270877 DOI: 10.1111/ppl.13105] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 05/19/2023]
Abstract
The detoxification efflux carriers (DTX)/multidrug and toxic compound extrusion (MATE) transporters encompass an ancient gene family of secondary transporters involved in the process of plant detoxification. A genome-wide analysis of these transporters was carried out in order to better understand the transport of secondary metabolites in flaxseed genome (Linum usitassimum). A total of 73 genes coding for DTX/MATE transporters were identified. Gene structure, protein domain and motif organization were found to be notably conserved over the distinct phylogenetic groups, showing the evolutionary significant role of each class. Gene ontology (GO) annotation revealed a link to transporter activities, response to stimulus and localizations. The presence of various hormone and stress-responsive cis-regulatory elements in promoter regions could be directly correlated with the alteration of their transcripts. Tertiary structure showed conservation for pore size and constrains in the pore, which indicate their involvement in the exclusion of toxic substances from the cell. MicroRNA target analysis revealed that LuDTXs genes were targeted by different classes of miRNA families. Twelve LuDTX genes were chosen for further quantitative real-time polymerase chain reaction analysis in response to cold, salinity and cadmium stress at 0, 6, 12 and 24 hours after treatment. Altogether, the identified members of the DTX gene family, their expression profile, phylogenetic and miRNAs analysis might provide opportunities for future functional validation of this important gene family in flax.
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Affiliation(s)
- Essa Ali
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
| | - Mumtaz Ali Saand
- Department of Botany, Shah Abdul Latif University, Sindh, 66020, Pakistan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, China
| | - Ali Raza Khan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | | | - Simin Feng
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
| | - Cai Ming
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
| | - Peilong Sun
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
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Lang Y, Liu Z. Basic Helix-Loop-Helix (bHLH) transcription factor family in Yellow horn (Xanthoceras sorbifolia Bunge): Genome-wide characterization, chromosome location, phylogeny, structures and expression patterns. Int J Biol Macromol 2020; 160:711-723. [DOI: 10.1016/j.ijbiomac.2020.05.253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/27/2022]
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11
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Ali E, Raza MA, Cai M, Hussain N, Shahzad AN, Hussain M, Ali M, Bukhari SAH, Sun P. Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). PLoS One 2020; 15:e0236454. [PMID: 32702710 PMCID: PMC7377914 DOI: 10.1371/journal.pone.0236454] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/05/2020] [Indexed: 12/21/2022] Open
Abstract
Flax (Linum usitatissimum) is a member of family linaceae with annual growth habit. It is included among those crops which were domesticated very early and has been used in development related studies as a model plant. In plants, Calmodulin-binding transcription activators (CAMTAs) comprise a unique set of Calmodulin-binding proteins. To elucidate the transport mechanism of secondary metabolites in flax, a genome-based study on these transporters was performed. The current investigation identified nine CAMTAs proteins, classified into three categories during phylogenetic analysis. Each group had significant evolutionary role as illustrated by the conservation of gene structures, protein domains and motif organizations over the distinctive phylogenetic classes. GO annotation suggested a link to sequence-specific DNA and protein binding, response to low temperature and transcription regulation by RNA polymerase II. The existence of different hormonal and stress responsive cis-regulatory elements in promotor region may directly correlate with the variation of their transcripts. MicroRNA target analysis revealed that various groups of miRNA families targeted the LuCAMTAs genes. Identification of CAMTA genes, miRNA studies and phylogenetic analysis may open avenues to uncover the underlying functional mechanism of this important family of genes in flax.
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Affiliation(s)
- Essa Ali
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Mohammad Ammar Raza
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Ming Cai
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Nazim Hussain
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Mubshar Hussain
- Department of Agronomy, Bahauddin Zakariya University, Multan, Pakistan
| | - Murtaza Ali
- Department of Basic Science & Humanities, University of Engineering and Technology, Mardan, Pakistan
| | | | - Peilong Sun
- Department of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
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12
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Muñoz-Amatriaín M, Hernandez J, Herb D, Baenziger PS, Bochard AM, Capettini F, Casas A, Cuesta-Marcos A, Einfeldt C, Fisk S, Genty A, Helgerson L, Herz M, Hu G, Igartua E, Karsai I, Nakamura T, Sato K, Smith K, Stockinger E, Thomas W, Hayes P. Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit. FRONTIERS IN PLANT SCIENCE 2020; 11:585927. [PMID: 33469459 PMCID: PMC7814503 DOI: 10.3389/fpls.2020.585927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/01/2020] [Indexed: 05/13/2023]
Abstract
One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
- *Correspondence: María Muñoz-Amatriaín,
| | - Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
- Javier Hernandez,
| | - Dustin Herb
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Ana Casas
- Consejo Superior de Investigaciones Científicas (CSIC), Aula Dei Experimental Station, Zaragoza, Spain
| | | | | | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Amelie Genty
- Secobra Recherches, Centre de Bois Henry, Maule, France
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Markus Herz
- Bavarian State Research Center for Agriculture, Institute for Crop Science, Freising, Germany
| | - Gongshe Hu
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aberdeen, ID, United States
| | - Ernesto Igartua
- Consejo Superior de Investigaciones Científicas (CSIC), Aula Dei Experimental Station, Zaragoza, Spain
| | - Ildiko Karsai
- Department of Molecular Breeding, Center for Agricultural Research, Martonvásár, Hungary
| | - Toshiki Nakamura
- Division of Field Crops and Horticulture Research Tohoku Agricultural Research Center National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kevin Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Eric Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, United States
| | - William Thomas
- The James Hutton Institute (JHI), Invergowrie, United Kingdom
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.). Genes (Basel) 2019; 10:genes10110914. [PMID: 31717469 PMCID: PMC6895899 DOI: 10.3390/genes10110914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 11/16/2022] Open
Abstract
Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24 h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.
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14
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Mir ZA, Ali S, Shivaraj SM, Bhat JA, Singh A, Yadav P, Rawat S, Paplao PK, Grover A. Genome-wide identification and characterization of Chitinase gene family in Brassica juncea and Camelina sativa in response to Alternaria brassicae. Genomics 2019; 112:749-763. [PMID: 31095998 DOI: 10.1016/j.ygeno.2019.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 10/26/2022]
Abstract
Chitinases belong to the group of Pathogenesis-related (PR) proteins that provides protection against fungal pathogens. This study presents the, genome-wide identification and characterization of chitinase gene family in two important oilseed crops B. juncea and C. sativa belonging to family Brassicaceae. We have identified 47 and 79 chitinase genes in the genomes of B. juncea and C. sativa, respectively. Phylogenetic analysis of chitinases in both the species revealed four distinct sub-groups, representing different classes of chitinases (I-V). Microscopic and biochemical study reveals the role of reactive oxygen species (ROS) scavenging enzymes in disease resistance of B. juncea and C. sativa. Furthermore, qRT-PCR analysis showed that expression of chitinases in both B. juncea and C. sativa was significantly induced after Alternaria brassicae infection. However, the fold change in chitinase gene expression was considerably higher in C. sativa compared to B. juncea, which further proves their role in C. sativa disease resistance to A. brassicae. This study provides comprehensive analysis on chitinase gene family in B. juncea and C. sativa and in future may serve as a potential candidate for improving disease resistance in B. juncea through transgenic approach.
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Affiliation(s)
- Zahoor Ahmad Mir
- National Research Centre on Plant Biotechnology, NRCPB, New Delhi, India; Amity Institute of Biotechnology, Amity University Noida, India
| | - Sajad Ali
- National Research Centre on Plant Biotechnology, NRCPB, New Delhi, India; Centre of Research for Development, University of Kashmir, Srinagar, India
| | | | - Javaid Akhter Bhat
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Noida, India
| | - Prashant Yadav
- National Research Centre on Plant Biotechnology, NRCPB, New Delhi, India
| | - Sandhya Rawat
- National Research Centre on Plant Biotechnology, NRCPB, New Delhi, India
| | | | - Anita Grover
- National Research Centre on Plant Biotechnology, NRCPB, New Delhi, India.
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15
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Genome-Wide Analysis of Multidrug and Toxic Compound Extrusion ( MATE) Family in Gossypium raimondii and Gossypium arboreum and Its Expression Analysis Under Salt, Cadmium, and Drought Stress. G3-GENES GENOMES GENETICS 2018; 8:2483-2500. [PMID: 29794162 PMCID: PMC6027885 DOI: 10.1534/g3.118.200232] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The extrusion of toxins and substances at a cellular level is a vital life process in plants under abiotic stress. The multidrug and toxic compound extrusion (MATE) gene family plays a large role in the exportation of toxins and other substrates. We carried out a genome-wide analysis of MATE gene families in Gossypium raimondii and Gossypium arboreum and assessed their expression levels under salt, cadmium and drought stresses. We identified 70 and 68 MATE genes in G. raimondii and G. arboreum, respectively. The majority of the genes were predicted to be localized within the plasma membrane, with some distributed in other cell parts. Based on phylogenetic analysis, the genes were subdivided into three subfamilies, designated as M1, M2 and M3. Closely related members shared similar gene structures, and thus were highly conserved in nature and have mainly evolved through purifying selection. The genes were distributed in all chromosomes. Twenty-nine gene duplication events were detected, with segmental being the dominant type. GO annotation revealed a link to salt, drought and cadmium stresses. The genes exhibited differential expression, with GrMATE18, GrMATE34, GaMATE41 and GaMATE51 significantly upregulated under drought, salt and cadmium stress, and these could possibly be the candidate genes. Our results provide the first data on the genome-wide and functional characterization of MATE genes in diploid cotton, and are important for breeders of more stress-tolerant cotton genotypes.
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16
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Ben-Romdhane W, Ben-Saad R, Meynard D, Zouari N, Mahjoub A, Fki L, Guiderdoni E, Al-Doss A, Hassairi A. Overexpression of AlTMP2 gene from the halophyte grass Aeluropus littoralis in transgenic tobacco enhances tolerance to different abiotic stresses by improving membrane stability and deregulating some stress-related genes. PROTOPLASMA 2018; 255:1161-1177. [PMID: 29450758 DOI: 10.1007/s00709-018-1223-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/05/2018] [Indexed: 06/08/2023]
Abstract
Herein, we report isolation of the AlTMP2 gene from the halophytic C4 grass Aeluropus littoralis. The subcellular localization suggested that AlTMP2 is a plasma membrane protein. In A. littoralis exposed to salt and osmotic stresses, the AlTMP2 gene was induced early and at a high rate, but was upregulated relatively later in response to abscisic acid and cold treatments. Expression of AlTMP2 in tobacco conferred improved tolerance against salinity, osmotic, H2O2, heat, and freezing stresses at the germination and seedling stages. Under control conditions, no growth or yield penalty were mentioned in transgenic plants due to the constitutive expression of AlTMP2. Interestingly, under greenhouse conditions, the seed yield of transgenic plants was significantly higher than that of non-transgenic (NT) plants grown under salt or drought stress. Furthermore, AlTMP2 plants had less electrolyte leakage, higher membrane stability, and lower Na+ and higher K+ accumulation than NT plants. Finally, six stress-related genes were shown to be deregulated in AlTMP2 plants relative to NT plants under both control and stress conditions. Collectively, these results indicate that AlTMP2 confers abiotic stress tolerance by improving ion homeostasis and membrane integrity, and by deregulating certain stress-related genes.
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Affiliation(s)
- Walid Ben-Romdhane
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia
| | - Rania Ben-Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia
| | - Donaldo Meynard
- CIRAD-UMR AGAP (Centre de coopération Internationale en Recherche Agronomique pour le Développement), Avenue Agropolis, 34398, Montpellier Cedex 5, France
| | - Nabil Zouari
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia
| | - Ali Mahjoub
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia
| | - Lotfi Fki
- Laboratory of Plant Biotechnology Applied to Crop Improvement, Faculty of Sciences of Sfax, University of Sfax, B.P 802, 3038, Sfax, Tunisia
| | - Emmanuel Guiderdoni
- CIRAD-UMR AGAP (Centre de coopération Internationale en Recherche Agronomique pour le Développement), Avenue Agropolis, 34398, Montpellier Cedex 5, France
| | - Abdullah Al-Doss
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Afif Hassairi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, B.P 1177, 3018, Sfax, Tunisia.
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17
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Watanabe Y, Kadono T, Kira N, Suzuki K, Iwata O, Ohnishi K, Yamaguchi H, Adachi M. Development of endogenous promoters that drive high-level expression of introduced genes in the model diatom Phaeodactylum tricornutum. Mar Genomics 2018; 42:41-48. [PMID: 30509379 DOI: 10.1016/j.margen.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
The marine diatom Phaeodactylum tricornutum is attractive for basic and applied diatom research. We isolated putative endogenous gene promoters derived from genes that are highly expressed in P. tricornutum: the fucoxanthin chlorophyll a/c-binding protein (FCP) C gene, the vacuolar ATP synthase 16-kDa proteolipid subunit (V-ATPase C) gene, the clumping factor A gene and the solute carrier family 34 member 2 gene. Five putative promoter regions were isolated, linked to an antibiotic resistance gene (Sh ble) and transformed into P. tricornutum. Using quantitative RT-PCR, the promoter activities in the transformants were analyzed and compared to that of the diatom endogenous gene promoter, the FCP A gene promoter which has been used for the transformation of P. tricornutum. Among the five isolated potential promoters, the activity of the V-ATPase C gene promoter was approximately 2.73 times higher than that of the FCP A gene promoter. The V-ATPase C gene promoter drove the expression of Sh ble mRNA transcripts under both light and dark conditions at the stationary phase. These results suggest that the V-ATPase C gene promoter is a novel tool for the genetic engineering of P. tricornutum.
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Affiliation(s)
- Yumi Watanabe
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Nozomu Kira
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Kengo Suzuki
- Euglena Co., Ltd., 22F, Morinaga Plaza Building, Shiba-5-33-1, Minato-ku, Tokyo 108-0019, Japan
| | - Osamu Iwata
- Euglena Co., Ltd., 22F, Morinaga Plaza Building, Shiba-5-33-1, Minato-ku, Tokyo 108-0019, Japan
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Otsu-200, Nankoku, Kochi 783-8502, Japan
| | - Haruo Yamaguchi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan.
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Jung HJ, Kayum MA, Thamilarasan SK, Nath UK, Park JI, Chung MY, Hur Y, Nou IS. Molecular characterisation and expression profiling of calcineurin B-like (CBL) genes in Chinese cabbage under abiotic stresses. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:739-750. [PMID: 32480603 DOI: 10.1071/fp16437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/28/2017] [Indexed: 06/11/2023]
Abstract
Calcium signals act as a second messenger in plant responses to various abiotic stresses, which regulate a range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, belong to a unique group of calcium sensors that play a role in calcium signalling. However, their identities and functions are unknown in Chinese cabbage. In this study, 17 CBL genes were identified from the Brassica rapa L. (Chinese cabbage) database and Br135K microarray datasets. They were used to construct a phylogenetic tree with known CBL proteins of other species. Analysis of genomic distribution and evolution revealed different gene duplication in Chinese cabbage compared to Arabidopsis. The microarray expression analysis showed differential expression of BrCBL genes at various temperatures. Organ-specific expression was observed by RT-PCR, and qRT-PCR analyses revealed responsiveness of BrCBL genes to cold, drought and salt stresses. Our findings confirm that CBL genes are involved in calcium signalling and regulate responses to environmental stimuli, suggesting this family gene have crucial role to play in plant responses to abiotic stresses. The results facilitate selection of candidate genes for further functional characterisation. In addition, abiotic stress-responsive genes reported in this study might be exploited for marker-aided backcrossing of Chinese cabbage.
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Affiliation(s)
- Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Senthil Kumar Thamilarasan
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Yoonkang Hur
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
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Liu J, Li Y, Wang W, Gai J, Li Y. Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean. BMC Genomics 2016; 17:223. [PMID: 26968518 PMCID: PMC4788864 DOI: 10.1186/s12864-016-2559-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 02/29/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Multidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean. RESULTS A total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean (Glycine max), which were denominated as GmMATE1 - GmMATE117. These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive cis-elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis-element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes. CONCLUSIONS A total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The cis-elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.
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Affiliation(s)
- Juge Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wei Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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20
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Rocha PSCF. Plant abiotic stress-related RCI2/PMP3s: multigenes for multiple roles. PLANTA 2016; 243:1-12. [PMID: 26306604 DOI: 10.1007/s00425-015-2386-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/14/2015] [Indexed: 05/23/2023]
Abstract
RCI2 / PMP3 s participate in abiotic stress responses and impact the expression of other genes. Their multifunctionality is determined by differential expression and by distinct activities of their structurally different proteins. In plants, RCI2/PMP3 genes, which encode small membrane proteins of the PMP3 family, are closely associated with abiotic stress responses. Their involvement in mediating stress tolerance is supported by genetic evidence and overexpression studies. RCI2/PMP3s occur as multigenes in plant genomes and their encoded proteins belong to distinct and conserved structural groups. In addition, different isoforms appear to be targeted to the plasma membrane or to distinct endomembrane compartments in cells. Several studies have revealed that RCI2/PMP3 proteins participate in cell ion homeostasis, and in regulation of membrane stability and polarization. They also appear to potentiate plant transcriptional responses to abiotic stresses. However, their mechanisms of action remain unknown. This paper reviews the current knowledge of the multiple roles of plant RCI2/PMP3 genes resulting from their differential expression under normal and stress conditions. The structural diversity of RCI2/PMP3 proteins is analyzed and evidence supporting their functional specialization and possible activity mechanisms is examined. Finally, strategies are discussed for exploiting new and established technologies to overcome the difficulties posed by the multigene status of RCI2s and the integral membrane character of their proteins, enabling the probing of their individual functions and collective significance.
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Affiliation(s)
- Pedro S C F Rocha
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Yuan Da Er Lu, 644, Changsha, 410125, People's Republic of China.
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Deokar AA, Tar'an B. Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1802. [PMID: 27965700 PMCID: PMC5126082 DOI: 10.3389/fpls.2016.01802] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/15/2016] [Indexed: 05/18/2023]
Abstract
Aquaporins (AQPs) are essential membrane proteins that play critical role in the transport of water and many other solutes across cell membranes. In this study, a comprehensive genome-wide analysis identified 40 AQP genes in chickpea (Cicer arietinum L.). A complete overview of the chickpea AQP (CaAQP) gene family is presented, including their chromosomal locations, gene structure, phylogeny, gene duplication, conserved functional motifs, gene expression, and conserved promoter motifs. To understand AQP's evolution, a comparative analysis of chickpea AQPs with AQP orthologs from soybean, Medicago, common bean, and Arabidopsis was performed. The chickpea AQP genes were found on all of the chickpea chromosomes, except chromosome 7, with a maximum of six genes on chromosome 6, and a minimum of one gene on chromosome 5. Gene duplication analysis indicated that the expansion of chickpea AQP gene family might have been due to segmental and tandem duplications. CaAQPs were grouped into four subfamilies including 15 NOD26-like intrinsic proteins (NIPs), 13 tonoplast intrinsic proteins (TIPs), eight plasma membrane intrinsic proteins (PIPs), and four small basic intrinsic proteins (SIPs) based on sequence similarities and phylogenetic position. Gene structure analysis revealed a highly conserved exon-intron pattern within CaAQP subfamilies supporting the CaAQP family classification. Functional prediction based on conserved Ar/R selectivity filters, Froger's residues, and specificity-determining positions suggested wide differences in substrate specificity among the subfamilies of CaAQPs. Expression analysis of the AQP genes indicated that some of the genes are tissue-specific, whereas few other AQP genes showed differential expression in response to biotic and abiotic stresses. Promoter profiling of CaAQP genes for conserved cis-acting regulatory elements revealed enrichment of cis-elements involved in circadian control, light response, defense and stress responsiveness reflecting their varying pattern of gene expression and potential involvement in biotic and abiotic stress responses. The current study presents the first detailed genome-wide analysis of the AQP gene family in chickpea and provides valuable information for further functional analysis to infer the role of AQP in the adaptation of chickpea in diverse environmental conditions.
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Sazegari S, Niazi A, Ahmadi FS. A study on the regulatory network with promoter analysis for Arabidopsis DREB-genes. Bioinformation 2015; 11:101-6. [PMID: 25848171 PMCID: PMC4369686 DOI: 10.6026/97320630011101] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 02/27/2015] [Indexed: 12/31/2022] Open
Abstract
Dehydration response element binding factors (DREBs) are one of the principal plant transcription factor subfamilies that regulate the expression of many abiotic stress-inducible genes. This sub-family belongs to AP2 transcription factor family and plays a considerable role in improving abiotic stresses tolerance in plants. Therefore, it is of interest to identify critical cis-acting elements involved in abiotic stress responses. In this study, we survey promoter cis-elements for ATDREBs genes (Arabidopsis thaliana DREBs). Regulatory networks based on ATDREB candidate genes were also generated to find other genes that are functionally similar to DREBs. The study was conducted on all 20 Arabidopsis thaliana non redundant DREB genes stored in RefSeq database. Promoter analysis and regulatory network prediction was accomplished by use of Plant CARE program and GeneMANIA web tool, respectively. The results indicated that among all genes, DREB1A, DREB1C, DREB2C, DREB2G and DEAR3 have the most type of diverse motifs involved in abiotic stress responses. It is implied that co-operation of abscisic acid, ethylene, salicylic acid and methyl jasmonate signaling is crucial for the regulation of the expression of drought and cold responses through DREB transcription factors. Gene network analysis showed different co-expressed but functionally similar genes that had physical and functional interactions with candidate DREB genes.
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Affiliation(s)
- Sima Sazegari
- Department of Crop Biotechnology and Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Niazi
- Faculty member of Biotechnology Institute. Biotechnology Institute, Shiraz University, Shiraz, Iran
| | - Farajolah Shahriary Ahmadi
- Department of Crop Biotechnology and Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Transgenic barley: a prospective tool for biotechnology and agriculture. Biotechnol Adv 2013; 32:137-57. [PMID: 24084493 DOI: 10.1016/j.biotechadv.2013.09.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 11/21/2022]
Abstract
Barley (Hordeum vulgare L.) is one of the founder crops of agriculture, and today it is the fourth most important cereal grain worldwide. Barley is used as malt in brewing and distilling industry, as an additive for animal feed, and as a component of various food and bread for human consumption. Progress in stable genetic transformation of barley ensures a potential for improvement of its agronomic performance or use of barley in various biotechnological and industrial applications. Recently, barley grain has been successfully used in molecular farming as a promising bioreactor adapted for production of human therapeutic proteins or animal vaccines. In addition to development of reliable transformation technologies, an extensive amount of various barley genetic resources and tools such as sequence data, microarrays, genetic maps, and databases has been generated. Current status on barley transformation technologies including gene transfer techniques, targets, and progeny stabilization, recent trials for improvement of agricultural traits and performance of barley, especially in relation to increased biotic and abiotic stress tolerance, and potential use of barley grain as a protein production platform have been reviewed in this study. Overall, barley represents a promising tool for both agricultural and biotechnological transgenic approaches, and is considered an ancient but rediscovered crop as a model industrial platform for molecular farming.
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Integration of low temperature and light signaling during cold acclimation response in Arabidopsis. Proc Natl Acad Sci U S A 2011; 108:16475-80. [PMID: 21930922 DOI: 10.1073/pnas.1107161108] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Certain plants increase their freezing tolerance in response to low nonfreezing temperatures, an adaptive process named cold acclimation. Light has been shown to be required for full cold acclimation, although how light and cold signals integrate and cross-talk to enhance freezing tolerance still remains poorly understood. Here, we show that HY5 levels are regulated by low temperature transcriptionally, via a CBF- and ABA-independent pathway, and posttranslationally, via protein stabilization through nuclear depletion of COP1. Furthermore, we demonstrate that HY5 positively regulates cold-induced gene expression through the Z-box and other cis-acting elements, ensuring the complete development of cold acclimation. These findings uncover unexpected functions for HY5, COP1, and the Z-box in Arabidopsis response to low temperature, provide insights on how cold and light signals integrate to optimize plant survival under freezing temperatures, and reveal the complexity of the molecular mechanisms plants have evolved to respond and adapt to their fluctuating natural environment.
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Hensel G, Himmelbach A, Chen W, Douchkov DK, Kumlehn J. Transgene expression systems in the Triticeae cereals. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:30-44. [PMID: 20739094 DOI: 10.1016/j.jplph.2010.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 07/19/2010] [Accepted: 07/21/2010] [Indexed: 05/29/2023]
Abstract
The control of transgene expression is vital both for the elucidation of gene function and for the engineering of transgenic crops. Given the dominance of the Triticeae cereals in the agricultural economy of the temperate world, the development of well-performing transgene expression systems of known functionality is of primary importance. Transgenes can be expressed either transiently or stably. Transient expression systems based on direct or virus-mediated gene transfer are particularly useful in situations where the need is to rapidly screen large numbers of genes. However, an unequivocal understanding of gene function generally requires that a transgene functions throughout the plant's life and is transmitted through the sexual cycle, since this alone allows its effect to be decoupled from the plant's response to the generally stressful gene transfer event. Temporal, spatial and quantitative control of a transgene's expression depends on its regulatory environment, which includes both its promoter and certain associated untranslated region sequences. While many transgenic approaches aim to manipulate plant phenotype via ectopic gene expression, a transgene sequence can be also configured to down-regulate the expression of its endogenous counterpart, a strategy which exploits the natural gene silencing machinery of plants. In this review, current technical opportunities for controlling transgene expression in the Triticeae species are described. Apart from protocols for transient and stable gene transfer, the choice of promoters and other untranslated regulatory elements, we also consider signal peptides, as they too govern the abundance and particularly the sub-cellular localization of transgene products.
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Affiliation(s)
- Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, Gatersleben, Germany
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Ibraheem O, Botha CEJ, Bradley G. In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. Comput Biol Chem 2010; 34:268-83. [PMID: 21036669 DOI: 10.1016/j.compbiolchem.2010.09.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 09/14/2010] [Accepted: 09/27/2010] [Indexed: 11/18/2022]
Abstract
The regulation of gene expression involves a multifarious regulatory system. Each gene contains a unique combination of cis-acting regulatory sequence elements in the 5' regulatory region that determines its temporal and spatial expression. Cis-acting regulatory elements are essential transcriptional gene regulatory units; they control many biological processes and stress responses. Thus a full understanding of the transcriptional gene regulation system will depend on successful functional analyses of cis-acting elements. Cis-acting regulatory elements present within the 5' regulatory region of the sucrose transporter gene families in rice (Oryza sativa Japonica cultivar-group) and Arabidopsis thaliana, were identified using a bioinformatics approach. The possible cis-acting regulatory elements were predicted by scanning 1.5kbp of 5' regulatory regions of the sucrose transporter genes translational start sites, using Plant CARE, PLACE and Genomatix Matinspector professional databases. Several cis-acting regulatory elements that are associated with plant development, plant hormonal regulation and stress response were identified, and were present in varying frequencies within the 1.5kbp of 5' regulatory region, among which are; A-box, RY, CAT, Pyrimidine-box, Sucrose-box, ABRE, ARF, ERE, GARE, Me-JA, ARE, DRE, GA-motif, GATA, GT-1, MYC, MYB, W-box, and I-box. This result reveals the probable cis-acting regulatory elements that possibly are involved in the expression and regulation of sucrose transporter gene families in rice and Arabidopsis thaliana during cellular development or environmental stress conditions.
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Affiliation(s)
- Omodele Ibraheem
- Plant Stress Response Group, Department of Biochemistry & Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
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Kole C, Michler CH, Abbott AG, Hall TC. Levels and Stability of Expression of Transgenes. TRANSGENIC CROP PLANTS 2010. [PMCID: PMC7122870 DOI: 10.1007/978-3-642-04809-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is well known that in a given cell, at a particular time, only a fraction of the entire genome is expressed. Expression of a gene, nuclear, or organellar starts with the onset of transcription and ends in the synthesis of the functional protein. The regulation of gene expression is a complex process that requires the coordinated activity of different proteins and nucleic acids that ultimately determine whether a gene is transcribed, and if transcribed, whether it results in the production of a protein that develops a phenotype. The same also holds true for transgenic crops, which lie at the very core of insert design. There are multiple checkpoints at which the expression of a gene can be regulated and controlled. Much of the emphasis of studies related to gene expression has been on regulation of gene transcription, and a number of methods are used to effect the control of gene expression. Controlling transgene expression for a commercially valuable trait is necessary to capture its value. Many gene functions are either lethal or produce severe deformity (resulting in loss of value) if over-expressed. Thus, expression of a transgene at a particular site or in response to a particular elicitor is always desirable.
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Affiliation(s)
- Chittaranjan Kole
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Charles H. Michler
- NSF I/UCRC Center for Tree Genetics, Hardwood Tree Improvement and Regeneration Center at Purdue University, West Lafayette, IN 47907 USA
| | - Albert G. Abbott
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Timothy C. Hall
- Institute of Developmental & Molecular Biology Department of Biology, Texas A&M University, College Station, TX 77843 USA
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Liu S, Lee H, Kang PS, Huang X, Yim JH, Lee HK, Kim IC. Complementary DNA library construction and expressed sequence tag analysis of an Arctic moss, Aulacomnium turgidum. Polar Biol 2009. [DOI: 10.1007/s00300-009-0737-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chang WC, Wang YK, Liu PF, Tsai YF, Kong LR, Lin CK, Yang CH, Pan RL. Regulation of Ku gene promoters in Arabidopsis by hormones and stress. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:265-280. [PMID: 32688782 DOI: 10.1071/fp07249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 04/29/2008] [Indexed: 06/11/2023]
Abstract
The Ku70/Ku80 heterodimer plays a crucial role in non-homologous end-joining during DNA repair, and is also involved in multiple cellular processes such as telomere maintenance, transcription, and apoptosis. In this study, we investigate the regulation of AtKu genes in higher plants. Promoters of the AtKu70 and AtKu80 were isolated from Arabidopsis and their activities characterised using GUS reporter constructs. AtKu promoter activities were relatively higher in hypocotyls and cotyledons upon germination and in stigma and siliques as well at their early developing stages. Furthermore, AtKu promoter activities could be enhanced by gibberellic acid, auxins, and jasmonic acid, but repressed by abscisic acid, salicylic acid, heat, drought and cold, respectively. Deletion analysis demonstrates minimal lengths of ~400 bp and 600 bp upstream of transcription start site for functional promoters of AtKu70 and AtKu80, respectively. Taken together, expressions of Ku genes are regulated both by developmental programs as well as by plant hormones and environmental stresses.
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Affiliation(s)
- Wen-Chi Chang
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Yung-Kai Wang
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Pei-Feng Liu
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Yu-Fang Tsai
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Lih-Ren Kong
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chi-Kai Lin
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Chang-Hsien Yang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Rong-Long Pan
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin-Chu 30013, Taiwan
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Ernst D, Aarts M. cis Elements and Transcription Factors Regulating Gene Promoters in Response to Environmental Stress. ECOLOGICAL STUDIES 2004. [DOI: 10.1007/978-3-662-08818-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Dal Bosco C, Busconi M, Govoni C, Baldi P, Stanca AM, Crosatti C, Bassi R, Cattivelli L. cor Gene expression in barley mutants affected in chloroplast development and photosynthetic electron transport. PLANT PHYSIOLOGY 2003; 131:793-802. [PMID: 12586903 PMCID: PMC166855 DOI: 10.1104/pp.014530] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Revised: 10/17/2002] [Accepted: 11/05/2002] [Indexed: 05/18/2023]
Abstract
The expression of several barley (Hordeum vulgare) cold-regulated (cor) genes during cold acclimation was blocked in the albino mutant a(n), implying a chloroplast control on mRNAs accumulation. By using albino and xantha mutants ordered according to the step in chloroplast biogenesis affected, we show that the cold-dependent accumulation of cor14b, tmc-ap3, and blt14 mRNAs depends on plastid developmental stage. Plants acquire the ability to fully express cor genes only after the development of primary thylakoid membranes in their chloroplasts. To investigate the chloroplast-dependent mechanism involved in cor gene expression, the activity of a 643-bp cor14b promoter fragment was assayed in wild-type and albino mutant a(n) leaf explants using transient beta-glucuronidase reporter expression assay. Deletion analysis identified a 27-bp region between nucleotides -274 and -247 with respect to the transcription start point, encompassing a boundary of some element that contributes to the cold-induced expression of cor14b. However, cor14b promoter was equally active in green and in albino a(n) leaves, suggesting that chloroplast controls cor14b expression by posttranscriptional mechanisms. Barley mutants lacking either photosystem I or II reaction center complexes were then used to evaluate the effects of redox state of electron transport chain components on COR14b accumulation. In the mutants analyzed, the amount of COR14b protein, but not the steady-state level of the corresponding mRNA, was dependent on the redox state of the electron transport chain. Treatments of the vir-zb63 mutant with electron transport chain inhibitors showed that oxidized plastoquinone promotes COR14b accumulation, thus suggesting a molecular relationship between plastoquinone/plastoquinol pool and COR14b.
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Affiliation(s)
- Cristina Dal Bosco
- Istituto Sperimentale per la Cerealicoltura, Via S. Protaso 302, I-29017, Fiorenzuola d'Arda (PC), Italy
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