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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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2
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Mai HJ, Baby D, Bauer P. Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1204723. [PMID: 37554559 PMCID: PMC10406446 DOI: 10.3389/fpls.2023.1204723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/04/2023] [Indexed: 08/10/2023]
Abstract
Cellular homeostasis of the micronutrient iron is highly regulated in plants and responsive to nutrition, stress, and developmental signals. Genes for iron management encode metal and other transporters, enzymes synthesizing chelators and reducing substances, transcription factors, and several types of regulators. In transcriptome or proteome datasets, such iron homeostasis-related genes are frequently found to be differentially regulated. A common method to detect whether a specific cellular pathway is affected in the transcriptome data set is to perform Gene Ontology (GO) enrichment analysis. Hence, the GO database is a widely used resource for annotating genes and identifying enriched biological pathways in Arabidopsis thaliana. However, iron homeostasis-related GO terms do not consistently reflect gene associations and levels of evidence in iron homeostasis. Some genes in the existing iron homeostasis GO terms lack direct evidence of involvement in iron homeostasis. In other aspects, the existing GO terms for iron homeostasis are incomplete and do not reflect the known biological functions associated with iron homeostasis. This can lead to potential errors in the automatic annotation and interpretation of GO term enrichment analyses. We suggest that applicable evidence codes be used to add missing genes and their respective ortholog/paralog groups to make the iron homeostasis-related GO terms more complete and reliable. There is a high likelihood of finding new iron homeostasis-relevant members in gene groups and families like the ZIP, ZIF, ZIFL, MTP, OPT, MATE, ABCG, PDR, HMA, and HMP. Hence, we compiled comprehensive lists of genes involved in iron homeostasis that can be used for custom enrichment analysis in transcriptomic or proteomic studies, including genes with direct experimental evidence, those regulated by central transcription factors, and missing members of small gene families or ortholog/paralog groups. As we provide gene annotation and literature alongside, the gene lists can serve multiple computational approaches. In summary, these gene lists provide a valuable resource for researchers studying iron homeostasis in A. thaliana, while they also emphasize the importance of improving the accuracy and comprehensiveness of the Gene Ontology.
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Affiliation(s)
- Hans-Jörg Mai
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Dibin Baby
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
- Heinrich Heine University, Center of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
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Yu Y, Wang Y, Yao Z, Wang Z, Xia Z, Lee J. Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications. Methods Mol Biol 2023; 2665:95-111. [PMID: 37166596 DOI: 10.1007/978-1-0716-3183-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Vital biochemical reactions including photosynthesis to respiration require iron, which should be tightly regulated. Although increasing evidence reveals the importance of epigenetic regulation in gene expression and signaling, the role of histone modifications and chromatin remodeling in plant iron homeostasis is not well understood. In this study, we surveyed publicly available ChIP-seq datasets of Arabidopsis wild-type and mutants defective in key enzymes of histone modification and chromatin remodeling and compared the deposition of epigenetic marks on loci of genes involved in iron regulation. Based on the analysis, we compiled a comprehensive list of iron homeostasis genes with differential enrichment of various histone modifications. This report will provide a resource for future studies to investigate epigenetic regulatory mechanisms of iron homeostasis in plants.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Yuxin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Zhujun Yao
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Zijun Xia
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Jiangsu, China.
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O’Rourke JA, Graham MA. Coupling VIGS with Short- and Long-Term Stress Exposure to Understand the Fiskeby III Iron Deficiency Stress Response. Int J Mol Sci 2022; 24:ijms24010647. [PMID: 36614091 PMCID: PMC9820625 DOI: 10.3390/ijms24010647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Yield loss due to abiotic stress is an increasing problem in agriculture. Soybean is a major crop for the upper Midwestern United States and calcareous soils exacerbate iron deficiency for growers, resulting in substantial yield losses. Fiskeby III is a soybean variety uniquely resistant to a variety of abiotic stresses, including iron deficiency. Previous studies identified a MATE transporter (Glyma.05G001700) associated with iron stress tolerance in Fiskeby III. To understand the function of this gene in the Fiskeby III response to iron deficiency, we coupled its silencing using virus-induced gene silencing with RNAseq analyses at two timepoints. Analyses of these data confirm a role for the MATE transporter in Fiskeby III iron stress responses. Further, they reveal that Fiskeby III induces transcriptional reprogramming within 24 h of iron deficiency stress, confirming that like other soybean varieties, Fiskeby III is able to quickly respond to stress. However, Fiskeby III utilizes novel genes and pathways in its iron deficiency response. Identifying and characterizing these genes and pathways in Fiskeby III provides novel targets for improving abiotic stress tolerance in elite soybean lines.
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Sasi JM, VijayaKumar C, Kukreja B, Budhwar R, Shukla RN, Agarwal M, Katiyar-Agarwal S. Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:985402. [PMID: 36311124 PMCID: PMC9597502 DOI: 10.3389/fpls.2022.985402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Coleoptile is the small conical, short-lived, sheath-like organ that safeguards the first leaf and shoot apex in cereals. It is also the first leaf-like organ to senesce that provides nutrition to the developing shoot and is, therefore, believed to play a crucial role in seedling establishment in rice and other grasses. Though histochemical studies have helped in understanding the pattern of cell death in senescing rice coleoptiles, genome-wide expression changes during coleoptile senescence have not yet been explored. With an aim to investigate the gene regulation underlying the coleoptile senescence (CS), we performed a combinatorial whole genome expression analysis by sequencing transcriptome and miRNAome of senescing coleoptiles. Transcriptome analysis revealed extensive reprogramming of 3439 genes belonging to several categories, the most prominent of which encoded for transporters, transcription factors (TFs), signaling components, cell wall organization enzymes, redox homeostasis, stress response and hormone metabolism. Small RNA sequencing identified 41 known and 21 novel miRNAs that were differentially expressed during CS. Comparison of gene expression and miRNA profiles generated for CS with publicly available leaf senescence (LS) datasets revealed that the two aging programs are remarkably distinct at molecular level in rice. Integration of expression data of transcriptome and miRNAome identified high confidence 140 miRNA-mRNA pairs forming 42 modules, thereby demonstrating multi-tiered regulation of CS. The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.
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Affiliation(s)
| | - Cheeni VijayaKumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Roli Budhwar
- Bionivid Technology Pvt. Limited, Bengaluru, Karnataka, India
| | | | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, India
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Li M, Si X, Liu Y, Liu Y, Cheng X, Dai Z, Yu X, Ali M, Lu G. Transcriptomic analysis of ncRNA and mRNA interactions during leaf senescence in tomato. Int J Biol Macromol 2022; 222:2556-2570. [DOI: 10.1016/j.ijbiomac.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/27/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022]
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Sasi JM, Gupta S, Singh A, Kujur A, Agarwal M, Katiyar-Agarwal S. Know when and how to die: gaining insights into the molecular regulation of leaf senescence. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1515-1534. [PMID: 36389097 PMCID: PMC9530073 DOI: 10.1007/s12298-022-01224-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.
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Affiliation(s)
- Jyothish Madambikattil Sasi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Apurva Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Alice Kujur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- USDA-ARS Plant Genetics Research Unit, The Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Centre of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324 India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007 India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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Watanabe M, Otagaki S, Matsumoto S, Shiratake K. Genome-Wide Analysis of Multidrug and Toxic Compound Extruction Transporters in Grape. FRONTIERS IN PLANT SCIENCE 2022; 13:892638. [PMID: 35909729 PMCID: PMC9330396 DOI: 10.3389/fpls.2022.892638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Grape (Vitis vinifera L.) is an important fruit crop in the world. It is used as a table grape and is also used for raisin and wine production. Grape berries accumulate secondary metabolites, such as anthocyanins, tannins, and resveratrol, which are known as functional compounds for human health. Multidrug and toxic compound extrusion transporter (MATEs) transport secondary metabolites. MATEs also transport other solutes, including organic acids, and toxic xenobiotics, depending on cation gradient and play various roles in plants. MATE comprises 300-500 amino acid residues and possesses a MATE domain and 8-12 transmembrane domains. In the present study, 59 MATE genes were identified in the grape genome, and phylogenetic analysis revealed the presence of four groups of grape MATEs (Group 1-4). Their information, such as gene structures, protein motifs, predicted subcellular localizations, and gene IDs of four genome annotations, that is, CRIBI v1, CRIBI v2, Genoscope, and Vcost v3, were annotated. The transport substrates and physiological functions of grape MATEs were estimated based on their homology with the analyzed MATEs in other plant species. Group 1 may transport toxic compounds and alkaloids, Group 2 may transport polyphenolic compounds, Group 3 may transport organic acids, and Group 4 may transport plant hormones related to signal transduction. In addition to the known anthocyanin transporters, VvMATE37 and VvMATE39, a novel anthocyanin transporter, VvMATE38 in Group 2, was suggested as a key transporter for anthocyanin accumulation in grape berry skin. VvMATE46, VvMATE47, and VvMATE49 in Group 3 may contribute to Al3+ detoxification and Fe2+/Fe3+ translocation via organic acid transport. This study provides helpful and fundamental information for grape MATE studies and resolves the confusion of gene IDs in different genome annotations.
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Zhang W, Liao L, Xu J, Han Y, Li L. Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh). BMC Genomics 2021; 22:632. [PMID: 34461821 PMCID: PMC8406601 DOI: 10.1186/s12864-021-07943-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As an important group of the multidrug efflux transporter family, the multidrug and toxic compound extrusion (MATE) family has a wide range of functions and is distributed in all kingdoms of living organisms. However, only two MATE genes in apple have been analyzed and genome-wide comprehensive analysis of MATE family is needed. RESULTS In this study, a total of 66 MATE (MdMATE) candidates encoding putative MATE transporters were identified in the apple genome. These MdMATE genes were classified into four groups by phylogenetic analysis with MATE genes in Arabidopsis. Synteny analysis reveals that whole genome duplication (WGD) and segmental duplication events played a major role in the expansion of MATE gene family in apple. MdMATE genes show diverse expression patterns in different tissues/organs and developmental stages. Analysis of cis-regulatory elements in MdMATE promoter regions indicates that the function of MdMATE genes is mainly related to stress response. Besides, the changes of gene expression levels upon different pathogen infections reveal that MdMATE genes are involved in biotic stress response. CONCLUSIONS In this work, we systematically identified MdMATE genes in apple genome using a set of bioinformatics approaches. Our comprehensive analysis provided valuable resources for improving disease resistance in apple and further functional characterization of MATE genes in other species.
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Affiliation(s)
- Weihan Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Jinsheng Xu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Li Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Du Z, Su Q, Wu Z, Huang Z, Bao J, Li J, Tu H, Zeng C, Fu J, He H. Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa). BMC Ecol Evol 2021; 21:141. [PMID: 34243710 PMCID: PMC8268253 DOI: 10.1186/s12862-021-01873-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023] Open
Abstract
Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.
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Affiliation(s)
- Zhixuan Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qitao Su
- School of Life Sciences, Jinggangshan University, Ji'an, 343009, China
| | - Zheng Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhou Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianzhong Bao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianbin Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hang Tu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chuihai Zeng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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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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12
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Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum. PLANTS 2020; 9:plants9111448. [PMID: 33120967 PMCID: PMC7716203 DOI: 10.3390/plants9111448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022]
Abstract
Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and the detoxification of toxins. Little is known about the MATE gene family in the Solanaceae, which includes species that produce a broad range of specialized metabolites. Here, we identified and analyzed the complement of MATE genes in pepper (Capsicum annuum) and potato (Solanum tuberosum). We classified all MATE genes into five groups based on their phylogenetic relationships and their gene and protein structures. Moreover, we discovered that tandem duplication contributed significantly to the expansion of the pepper MATE family, while both tandem and segmental duplications contributed to the expansion of the potato MATE family, indicating that MATEs took distinct evolutionary paths in these two Solanaceous species. Analysis of ω values showed that all potato and pepper MATE genes experienced purifying selection during evolution. In addition, collinearity analysis showed that MATE genes were highly conserved between pepper and potato. Analysis of cis-elements in MATE promoters and MATE expression patterns revealed that MATE proteins likely function in many stages of plant development, especially during fruit ripening, and when exposed to multiple stresses, consistent with the existence of functional differentiation between duplicated MATE genes. Together, our results lay the foundation for further characterization of pepper and potato MATE gene family members.
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Pham HD, Pólya S, Müller B, Szenthe K, Sági-Kazár M, Bánkúti B, Bánáti F, Sárvári É, Fodor F, Tamás L, Philippar K, Solti Á. The developmental and iron nutritional pattern of PIC1 and NiCo does not support their interdependent and exclusive collaboration in chloroplast iron transport in Brassica napus. PLANTA 2020; 251:96. [PMID: 32297017 PMCID: PMC7214486 DOI: 10.1007/s00425-020-03388-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/04/2020] [Indexed: 05/05/2023]
Abstract
The accumulation of NiCo following the termination of the accumulation of iron in chloroplast suggests that NiCo is not solely involved in iron uptake processes of chloroplasts. Chloroplast iron (Fe) uptake is thought to be operated by a complex containing permease in chloroplast 1 (PIC1) and nickel-cobalt transporter (NiCo) proteins, whereas the role of other Fe homeostasis-related transporters such as multiple antibiotic resistance protein 1 (MAR1) is less characterized. Although pieces of information exist on the regulation of chloroplast Fe uptake, including the effect of plant Fe homeostasis, the whole system has not been revealed in detail yet. Thus, we aimed to follow leaf development-scale changes in the chloroplast Fe uptake components PIC1, NiCo and MAR1 under deficient, optimal and supraoptimal Fe nutrition using Brassica napus as model. Fe deficiency decreased both the photosynthetic activity and the Fe content of plastids. Supraoptimal Fe nutrition caused neither Fe accumulation in chloroplasts nor any toxic effects, thus only fully saturated the need for Fe in the leaves. In parallel with the increasing Fe supply of plants and ageing of the leaves, the expression of BnPIC1 was tendentiously repressed. Though transcript and protein amount of BnNiCo tendentiously increased during leaf development, it was even markedly upregulated in ageing leaves. The relative transcript amount of BnMAR1 increased mainly in ageing leaves facing Fe deficiency. Taken together chloroplast physiology, Fe content and transcript amount data, the exclusive participation of NiCo in the chloroplast Fe uptake is not supported. Saturation of the Fe requirement of chloroplasts seems to be linked to the delay of decomposing the photosynthetic apparatus and keeping chloroplast Fe homeostasis in a rather constant status together with a supressed Fe uptake machinery.
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Affiliation(s)
- Hong Diep Pham
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Sára Pólya
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Brigitta Müller
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Kálmán Szenthe
- RT-Europe Nonprofit Research Ltd., Mosonmagyaróvár, Hungary
| | - Máté Sági-Kazár
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | | | - Ferenc Bánáti
- RT-Europe Nonprofit Research Ltd., Mosonmagyaróvár, Hungary
| | - Éva Sárvári
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Fodor
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - László Tamás
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Katrin Philippar
- Center for Human - and Molecular Biology, Plant Biology, Saarland University, Saarbrücken, Germany
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
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14
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Upadhyay N, Kar D, Deepak Mahajan B, Nanda S, Rahiman R, Panchakshari N, Bhagavatula L, Datta S. The multitasking abilities of MATE transporters in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4643-4656. [PMID: 31106838 DOI: 10.1093/jxb/erz246] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/14/2019] [Indexed: 05/20/2023]
Abstract
As sessile organisms, plants constantly monitor environmental cues and respond appropriately to modulate their growth and development. Membrane transporters act as gatekeepers of the cell regulating both the inflow of useful materials as well as exudation of harmful substances. Members of the multidrug and toxic compound extrusion (MATE) family of transporters are ubiquitously present in almost all forms of life including prokaryotes and eukaryotes. In bacteria, MATE proteins were originally characterized as efflux transporters conferring drug resistance. There are 58 MATE transporters in Arabidopsis thaliana, which are also known as DETOXIFICATION (DTX) proteins. In plants, these integral membrane proteins are involved in a diverse array of functions, encompassing secondary metabolite transport, xenobiotic detoxification, aluminium tolerance, and disease resistance. MATE proteins also regulate overall plant development by controlling phytohormone transport, tip growth processes, and senescence. While most of the functional characterizations of MATE proteins have been reported in Arabidopsis, recent reports suggest that their diverse roles extend to numerous other plant species. The wide array of functions exhibited by MATE proteins highlight their multitasking ability. In this review, we integrate information related to structure and functions of MATE transporters in plants. Since these transporters are central to mechanisms that allow plants to adapt to abiotic and biotic stresses, their study can potentially contribute to improving stress tolerance under changing climatic conditions.
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Affiliation(s)
- Neha Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
| | - Debojyoti Kar
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
| | - Bhagyashri Deepak Mahajan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
- Cellular Organization and Signalling, National Centre for Biological Sciences (NCBS), Bengaluru, India
| | - Sanchali Nanda
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
| | - Rini Rahiman
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Nimisha Panchakshari
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
- Department of Genetics, Ludwig Maximilians Universität, Biocenter, Germany
| | - Lavanya Bhagavatula
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
| | - Sourav Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, India
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15
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Min X, Jin X, Liu W, Wei X, Zhang Z, Ndayambaza B, Wang Y. Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L. PeerJ 2019; 7:e6302. [PMID: 30723620 PMCID: PMC6360082 DOI: 10.7717/peerj.6302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/14/2018] [Indexed: 11/20/2022] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa (Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge of the MATE transcripts family and the characterisation of specific MATE members involved in alfalfa Al stress remain unclear. In this study, 88 alfalfa MATE (MsMATE) transporters were identified at the whole transcriptome level. Phylogenetic analysis classified them into four subfamilies comprising 11 subgroups. Generally, five kinds of motifs were found in group G1, and most were located at the N-terminus, which might confer these genes with Al detoxification functions. Furthermore, 10 putative Al detoxification-related MsMATE genes were identified and the expression of five genes was significantly increased after Al treatment, indicating that these genes might play important roles in conferring Al tolerance to alfalfa. Considering the limited functional understanding of MATE transcripts in alfalfa, our findings will be valuable for the functional investigation and application of this family in alfalfa.
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Affiliation(s)
- Xueyang Min
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Xiaoyu Jin
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Xingyi Wei
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Boniface Ndayambaza
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, P. R. China.,Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, P. R. China.,Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou, P. R. China.,College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P. R. China
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