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Devi R, Goyal P, Verma B, Hussain S, Chowdhary F, Arora P, Gupta S. A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L. BMC Genomics 2024; 25:315. [PMID: 38532362 DOI: 10.1186/s12864-024-10227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Transcriptome-wide survey divulged a total of 181 ABC transporters in G. glabra which were phylogenetically classified into six subfamilies. Protein-Protein interactions revealed nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) corresponding to five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21). Significant transcript accumulation of ABCB6 (31.8 folds), -B14 (147.5 folds), -B15 (17 folds), -B25 (19.7 folds), -B26 (18.31 folds), -B31 (61.89 folds), -B40 (1273 folds) and -B42 (51 folds) was observed under the influence of auxin. Auxin transport-specific inhibitor, N-1-naphthylphthalamic acid, showed its effectiveness only at higher (10 µM) concentration where it down regulated the expression of ABCBs, PINs (PIN FORMED) and TWD1 (TWISTED DWARF 1) genes in shoot tissues, while their expression was seen to enhance in the root tissues. Further, qRT-PCR analysis under various growth conditions (in-vitro, field and growth chamber), and subjected to abiotic stresses revealed differential expression implicating role of ABCBs in stress management. Seven of the nine genes were shown to be involved in the stress physiology of the plant. GgABCB6, 15, 25 and ABCB31 were induced in multiple stresses, while GgABCB26, 40 & 42 were exclusively triggered under drought stress. No study pertaining to the ABC transporters from G. glabra is available till date. The present investigation will give an insight to auxin transportation which has been found to be associated with plant growth architecture; the knowledge will help to understand the association between auxin transportation and plant responses under the influence of various conditions.
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Affiliation(s)
- Ritu Devi
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Goyal
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Bhawna Verma
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Fariha Chowdhary
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Biotechnology Division, Jammu, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Suphla Gupta
- Plant Biotechnology Division, Jammu, India.
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Mi Y, Cao X, Zhu X, Chen W, Meng X, Wan H, Sun W, Wang S, Chen S. Characterization and co-expression analysis of ATP-binding cassette transporters provide insight into genes related to cannabinoid transport in Cannabis sativa L. Int J Biol Macromol 2023:124934. [PMID: 37224907 DOI: 10.1016/j.ijbiomac.2023.124934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
Plant ATP-binding cassette (ABC) transporters contribute the transport of diverse secondary metabolites. However, their roles in cannabinoid trafficking are still unsolved in Cannabis sativa. In this study, 113 ABC transporters were identified and characterized in C. sativa from their physicochemical properties, gene structure, and phylogenic relationship, as well as spatial gene expression patterns. Eventually, seven core transporters were proposed including one member in ABC subfamily B (CsABCB8) and six ABCG members (CsABCG4, CsABCG10, CsABCG11, CsABCG32, CsABCG37, and CsABCG41), harboring potential in participating cannabinoid transport, by combining phylogenetic and co-expression analysis from the gene and metabolite level. The candidate genes exhibited a high correlation with cannabinoid biosynthetic pathway genes and the cannabinoid content, and they were highly expressed where cannabinoids appropriately biosynthesized and accumulated. The findings underpin further research on the function of ABC transporters in C. sativa, especially in unveiling the mechanisms of cannabinoid transport to boost systematic and targeted metabolic engineering.
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Affiliation(s)
- Yaolei Mi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Xue Cao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Xuewen Zhu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China
| | - Sifan Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100070, China; Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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Nie Z, Kang G, Yan D, Qin H, Yang L, Zeng R. Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:504-520. [PMID: 36524729 PMCID: PMC10107253 DOI: 10.1111/tpj.16063] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/01/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Tapping panel dryness (TPD) is a century-old problem that has plagued the natural rubber production of Hevea brasiliensis. TPD may result from self-protective mechanisms of H. brasiliensis in response to stresses such as excessive hormone stimulation and mechanical wounding (bark tapping). It has been hypothesized that TPD impairs rubber biosynthesis; however, the underlying mechanisms remain poorly understood. In the present study, we firstly verified that TPD-affected rubber trees exhibited lower rubber biosynthesis activity and greater rubber molecular weight compared to healthy rubber trees. We then demonstrated that HbFPS1, a key gene of rubber biosynthesis, and its expression products were downregulated in the latex of TPD-affected rubber trees, as revealed by transcriptome sequencing and iTRAQ-based proteome analysis. We further discovered that the farnesyl diphosphate synthase HbFPS1 could be recruited to small rubber particles by HbSRPP1 through protein-protein interactions to catalyze farnesyl diphosphate (FPP) synthesis and facilitate rubber biosynthesis initiation. FPP content in the latex of TPD-affected rubber trees was significantly decreased with the downregulation of HbFPS1, ultimately resulting in abnormal development of rubber particles, decreased rubber biosynthesis activity, and increased rubber molecular weight. Upstream regulator assays indicated that a novel regulator, MYB2-like, may be an important regulator of downregulation of HbFPS1 in the latex of TPD-affected rubber trees. Our findings not only provide new directions for studying the molecular events involved in rubber biosynthesis and TPD syndrome and contribute to rubber management strategies, but also broaden our knowledge of plant isoprenoid metabolism and its regulatory networks.
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Affiliation(s)
- Zhiyi Nie
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Guijuan Kang
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Dong Yan
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Huaide Qin
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Lifu Yang
- Institute of Scientific and Technical InformationChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Rizhong Zeng
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
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Lima LGAD, Ferreira SS, Simões MS, Cunha LXD, Fernie AR, Cesarino I. Comprehensive expression analyses of the ABCG subfamily reveal SvABCG17 as a potential transporter of lignin monomers in the model C4 grass Setaria viridis. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153900. [PMID: 36525838 DOI: 10.1016/j.jplph.2022.153900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Although several aspects of lignin metabolism have been extensively characterized, the mechanism(s) by which lignin monomers are transported across the plasma membrane remains largely unknown. Biochemical, proteomic, expression and co-expression analyses from several plant species support the involvement of active transporters, mainly those belonging to the ABC superfamily. Here, we report on the genome-wide characterization of the ABCG gene subfamily in the model C4 grass Setaria viridis and further identification of the members potentially involved in monolignol transport. A total of 48 genes encoding SvABCGs were found in the S. viridis genome, from which 21 SvABCGs were classified as full-size transporters and 27 as half-size transporters. Comprehensive analysis of the ABCG subfamily in S. viridis based on expression and co-expression analyses support a role for SvABCG17 in monolignol transport: (i) SvABCG17 is orthologous to AtABCG29, a monolignol transporter in Arabidopsis thaliana; (ii) SvABCG17 displays a similar expression profile to that of lignin biosynthetic genes in a set of different S. viridis tissues and along the elongating internode; (iii) SvABCG17 is highly co-expressed with lignin-related genes in a public transcriptomic database; (iv) SvABCG17displays particularly high expression in the top of the S. viridis elongating internode, a tissue undergoing active lignification; (v) SvABCG17 mRNA localization coincides with the histochemical pattern of lignin deposition; and (vi) the promoter of SvABCG17 is activated by secondary cell wall-associated transcription factors, especially by lignin-specific activators of the MYB family. Further studies might reveal further aspects of this potential monolignol transporter, including its real substrate specificity and whether it works redundantly with other ABC members during S. viridis lignification.
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Affiliation(s)
- Leydson Gabriel Alves de Lima
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil
| | - Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil
| | - Marcella Siqueira Simões
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil
| | - Lucas Xavier da Cunha
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, Brazil; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, 370, 05508-020, São Paulo, Brazil.
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Nogia P, Pati PK. Plant Secondary Metabolite Transporters: Diversity, Functionality, and Their Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:758202. [PMID: 34777438 PMCID: PMC8580416 DOI: 10.3389/fpls.2021.758202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 05/04/2023]
Abstract
Secondary metabolites (SMs) play crucial roles in the vital functioning of plants such as growth, development, defense, and survival via their transportation and accumulation at the required site. However, unlike primary metabolites, the transport mechanisms of SMs are not yet well explored. There exists a huge gap between the abundant presence of SM transporters, their identification, and functional characterization. A better understanding of plant SM transporters will surely be a step forward to fulfill the steeply increasing demand for bioactive compounds for the formulation of herbal medicines. Thus, the engineering of transporters by modulating their expression is emerging as the most viable option to achieve the long-term goal of systemic metabolic engineering for enhanced metabolite production at minimum cost. In this review article, we are updating the understanding of recent advancements in the field of plant SM transporters, particularly those discovered in the past two decades. Herein, we provide notable insights about various types of fully or partially characterized transporters from the ABC, MATE, PUP, and NPF families including their diverse functionalities, structural information, potential approaches for their identification and characterization, several regulatory parameters, and their modulation. A novel perspective to the concept of "Transporter Engineering" has also been unveiled by highlighting its potential applications particularly in plant stress (biotic and abiotic) tolerance, SM accumulation, and removal of anti-nutritional compounds, which will be of great value for the crop improvement program. The present study creates a roadmap for easy identification and a better understanding of various transporters, which can be utilized as suitable targets for transporter engineering in future research.
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Affiliation(s)
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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6
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Nakano Y, Mitsuda N, Ide K, Mori T, Mira FR, Rosmalawati S, Watanabe N, Suzuki K. Transcriptome analysis of Pará rubber tree (H. brasiliensis) seedlings under ethylene stimulation. BMC PLANT BIOLOGY 2021; 21:420. [PMID: 34517831 PMCID: PMC8436496 DOI: 10.1186/s12870-021-03196-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Natural rubber (cis-1,4-polyioprene, NR) is an indispensable industrial raw material obtained from the Pará rubber tree (H. brasiliensis). Natural rubber cannot be replaced by synthetic rubber compounds because of the superior resilience, elasticity, abrasion resistance, efficient heat dispersion, and impact resistance of NR. In NR production, latex is harvested by periodical tapping of the trunk bark. Ethylene enhances and prolongs latex flow and latex regeneration. Ethephon, which is an ethylene-releasing compound, applied to the trunk before tapping usually results in a 1.5- to 2-fold increase in latex yield. However, intense mechanical damage to bark tissues by excessive tapping and/or over-stimulation with ethephon induces severe oxidative stress in laticifer cells, which often causes tapping panel dryness (TPD) syndrome. To enhance NR production without causing TPD, an improved understanding of the molecular mechanism of the ethylene response in the Pará rubber tree is required. Therefore, we investigated gene expression in response to ethephon treatment using Pará rubber tree seedlings as a model system. RESULTS After ethephon treatment, 3270 genes showed significant differences in expression compared with the mock treatment. Genes associated with carotenoids, flavonoids, and abscisic acid biosynthesis were significantly upregulated by ethephon treatment, which might contribute to an increase in latex flow. Genes associated with secondary cell wall formation were downregulated, which might be because of the reduced sugar supply. Given that sucrose is an important molecule for NR production, a trade-off may arise between NR production and cell wall formation for plant growth and for wound healing at the tapping panel. CONCLUSIONS Dynamic changes in gene expression occur specifically in response to ethephon treatment. Certain genes identified may potentially contribute to latex production or TPD suppression. These data provide valuable information to understand the mechanism of ethylene stimulation, and will contribute to improved management practices and/or molecular breeding to attain higher yields of latex from Pará rubber trees.
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Affiliation(s)
- Yoshimi Nakano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Kohei Ide
- Bridgestone Corporation, Kodaira, Tokyo, 187-8531, Japan
| | - Teppei Mori
- Bridgestone Corporation, Kodaira, Tokyo, 187-8531, Japan
| | - Farida Rosana Mira
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology, Build. 630, Puspiptek area, Serpong, Tangerang, Selatan, 15314, Indonesia
| | - Syofi Rosmalawati
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology, Build. 630, Puspiptek area, Serpong, Tangerang, Selatan, 15314, Indonesia
| | - Norie Watanabe
- Bridgestone Corporation, Kodaira, Tokyo, 187-8531, Japan
| | - Kaoru Suzuki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 169-8555, Japan.
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Zaynab M, Wang Z, Hussain A, Bahadar K, Sajid M, Sharif Y, Azam M, Sughra K, Raza MA, Khan KA, Li S. ATP-binding cassette transporters expression profiling revealed its role in the development and regulating stress response in Solanum tuberosum. Mol Biol Rep 2021; 49:5251-5264. [PMID: 34480688 DOI: 10.1007/s11033-021-06697-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
The ATP-binding cassette (ABC) transporter gene family plays a vital role in substance transportation, including secondary metabolites, and phytohormones across membranous structures. It is still uncovered in potato (Solanum tuberosum), grown worldwide as a 3rd important food crop. The current study identified a total of 54 Stabc genes in potato genome. The accumulative phylogenetic tree of Stabc with arabidopsis, divided into eight groups (ABCA to ABCH). ABCG was the most prominent group covering 90% of Stabc genes, followed by ABCB group. The number and architecture of exon-intron varied from gene to gene. In addition, the presence of stress-responsive elements in the regulatory regions depicted their role in environmental stress. Furthermore, the tissue-specific and stress-specific expression profiling of Stabc genes and their validation through real-time-qPCR analysis revealed their role in development and stress. The presented results provided useful information for further functional analysis of Stabc genes and can also use as a reference study for other important crops.
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Affiliation(s)
- Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China
| | - Zongkang Wang
- Shenzhen Batian Ecotypic Engineering Company Limited, Shenzhen, 518105, China
| | - Athar Hussain
- Genomics Lab, Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Khalida Bahadar
- National Agriculture Research Center, PARC Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
| | - Mateen Sajid
- Department of Horticulture, Ghazi University, Dera Ghazi Khan, 32200, Pakistan
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Muhammad Azam
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Kalsoom Sughra
- Department of Biochemistry & Biotechnology, Hafiz Hayat Campus University of Gujrat, Gujrat City, Pakistan
| | - Muhammad Ammar Raza
- Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia.,Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China.
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Borghi L, Kang J, de Brito Francisco R. Filling the Gap: Functional Clustering of ABC Proteins for the Investigation of Hormonal Transport in planta. FRONTIERS IN PLANT SCIENCE 2019; 10:422. [PMID: 31057565 PMCID: PMC6479136 DOI: 10.3389/fpls.2019.00422] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/20/2019] [Indexed: 05/09/2023]
Abstract
Plant hormones regulate a myriad of plant processes, from seed germination to reproduction, from complex organ development to microelement uptake. Much has been discovered on the factors regulating the activity of phytohormones, yet there are gaps in knowledge about their metabolism, signaling as well as transport. In this review we analyze the potential of the characterized phytohormonal transporters belonging to the ATP-Binding Cassette family (ABC proteins), thus to identify new candidate orthologs in model plants and species important for human health and food production. Previous attempts with phylogenetic analyses on transporters belonging to the ABC family suggested that sequence homology per se is not a powerful tool for functional characterization. However, we show here that sequence homology might indeed support functional conservation of characterized members of different classes of ABC proteins in several plant species, e.g., in the case of ABC class G transporters of strigolactones and ABC class B transporters of auxinic compounds. Also for the low-affinity, vacuolar abscisic acid (ABA) transporters belonging to the ABCC class we show that localization-, rather than functional-clustering occurs, possibly because of sequence conservation for targeting the tonoplast. The ABC proteins involved in pathogen defense are phylogenetically neighboring despite the different substrate identities, suggesting that sequence conservation might play a role in their activation/induction after pathogen attack. Last but not least, in case of the multiple lipid transporters belong to different ABC classes, we focused on ABC class D proteins, reported to transport/affect the synthesis of hormonal precursors. Based on these results, we propose that phylogenetic approaches followed by transport bioassays and in vivo investigations might accelerate the discovery of new hormonal transport routes and allow the designing of transgenic and genome editing approaches, aimed to improve our knowledge on plant development, plant-microbe symbioses, plant nutrient uptake and plant stress resistance.
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Wu C, Lan L, Li Y, Nie Z, Zeng R. The relationship between latex metabolism gene expression with rubber yield and related traits in Hevea brasiliensis. BMC Genomics 2018; 19:897. [PMID: 30526485 PMCID: PMC6288877 DOI: 10.1186/s12864-018-5242-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 11/12/2018] [Indexed: 11/20/2022] Open
Abstract
Background Expression patterns of many laticifer-specific gens are closely correlative with rubber yield of Hevea brasiliensis (para rubber tree). To unveil the mechanisms underlying the rubber yield, transcript levels of nine major latex metabolism-related genes, i.e., HMG-CoA synthase (HMGS), HMG-CoA reductase (HMGR), diphosphomevalonate decarboxylase (PMD), farnesyl diphosphate synthase (FPS), cis-prenyltransferase (CPT), rubber elongation factor (REF), small rubber particle protein (SRPP), dihydroxyacid dehydratase (DHAD) and actin depolymerizing factor (ADF), were dertermined, and the relationship between rubber yield with their expression levels was analysed. Results Except HbHMGR1, HbPMD and HbDHAD, most of these genes were predominantly expressed in latex, and bark tapping markedly elevated the transcript abundance of the analyzed genes, with the 7th tapping producing the greatest expression levels. Both ethephon (ETH) and methyl jasmonate (MeJA) stimulation greatly induced the expression levels of the examined genes, at least at one time point, except HbDHAD, which was unresponsive to MeJA. The genes’ expression levels, as well as the rubber yields and two yield characteristics differed significantly among the different genotypes examined. Additionally, the latex and dry rubber yields increased gradually but the dry rubber content did not. Rubber yields and/or yield characteristics were significantly positively correlated with HbCPT, HbFPS, HbHMGS, HbHMGR1 and HbDHAD expression levels, negatively correlated with that of HbREF, but not significantly correlated with HbPMD, HbSRPP and HbADF expression levels. In addition, during rubber production, significantly positive correlations existed between the expression level of HbPMD and the levels of HbREF and HbHMGR1, between HbSRPP and the levels of HbHMGS and HbHMGR1, and between HbADF and HbFPS. Conclusions The up-regulation of these genes might be related to the latex production of rubber trees under the stress of bark tapping and latex metabolism. The various correlations among the genes implied that there are differences in their synergic interactions. Thus, these nine genes might be related to rubber yield and yield-related traits in H. brasiliensis, and this work increases our understanding of their complex functions and how they are expressed in both high-and medium-yield rubber tree varieties and low-yield wild rubber tree germplasm. Electronic supplementary material The online version of this article (10.1186/s12864-018-5242-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chuntai Wu
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China
| | - Li Lan
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China.,College of Agriculture, Hainan University, Haikou, 570228, China
| | - Yu Li
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China
| | - Zhiyi Nie
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China
| | - Rizhong Zeng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, 571737, People's Republic of China.
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Ofori PA, Mizuno A, Suzuki M, Martinoia E, Reuscher S, Aoki K, Shibata D, Otagaki S, Matsumoto S, Shiratake K. Genome-wide analysis of ATP binding cassette (ABC) transporters in tomato. PLoS One 2018; 13:e0200854. [PMID: 30048467 PMCID: PMC6062036 DOI: 10.1371/journal.pone.0200854] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
ATP binding cassette (ABC) transporters are proteins that actively mediate the transport of a wide range of molecules, such as organic acids, metal ions, phytohormones and secondary metabolites. Therefore, ABC transporters must play indispensable roles in growth and development of tomato, including fruit development. Most ABC transporters have transmembrane domains (TMDs) and belong to the ABC protein family, which includes not only ABC transporters but also soluble ABC proteins lacking TMDs. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC proteins in tomato (Solanum lycopersicum), which is a valuable horticultural crop and a model plant for studying fleshy fruits. In the tomato genome, a total of 154 genes putatively encoding ABC transporters, including 9 ABCAs, 29 ABCBs, 26 ABCCs, 2 ABCDs, 2 ABCEs, 6 ABCFs, 70 ABCGs and 10 ABCIs, were identified. Gene expression data from the eFP Browser and reverse transcription-semi-quantitative PCR analysis revealed their tissue-specific and development-specific expression profiles. This work suggests physiological roles of ABC transporters in tomato and provides fundamental information for future studies of ABC transporters not only in tomato but also in other Solanaceae species.
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Affiliation(s)
- Peter Amoako Ofori
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ayaka Mizuno
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | | | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail:
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Nie Z, Wang Y, Wu C, Li Y, Kang G, Qin H, Zeng R. Acyl-CoA-binding protein family members in laticifers are possibly involved in lipid and latex metabolism of Hevea brasiliensis (the Para rubber tree). BMC Genomics 2018; 19:5. [PMID: 29295704 PMCID: PMC5751871 DOI: 10.1186/s12864-017-4419-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/22/2017] [Indexed: 01/08/2023] Open
Abstract
Background Acyl-CoA-binding proteins (ACBPs) are mainly involved in acyl-CoA ester binding and trafficking in eukaryotic cells, and their various functions have been characterized in model plants, such as Arabidopsis thaliana (A. thaliana), Oryza sativa (rice), and other plant species. In the present study, genome-wide mining and expression analysis of ACBP genes was performed on Hevea brasiliensis (the para rubber tree), the most important latex-producing crop in the world. Results Six members of the H. brasiliensis ACBP family genes, designated HbACBP1-HbACBP6, were identified from the H. brasiliensis genome. They can be categorized into four classes with different amino acid sequences and domain structures based on the categorization of their A. thaliana counterparts. Phylogenetic analysis shows that the HbACBPs were clustered with those of other closely related species, such as Manihot esculenta, Ricinus communis, and Jatropha carcas, but were further from those of A. thaliana, a distantly related species. Expression analysis demonstrated that the HbACBP1 and HbACBP2 genes are more prominently expressed in H. brasiliensis latex, and their expression can be significantly enhanced by bark tapping (a mechanical wound) and jasmonic acid stimulation, whereas HbACBP3-HbACBP6 had almost the same expression patterns with relatively high levels in mature leaves and male flowers, but a markedly low abundance in the latex. HbACBP1 and HbACBP2 may have crucial roles in lipid and latex metabolism in laticifers, so their subcellular location was further investigated and the results indicated that HbACBP1 is a cytosol protein, whereas HbACBP2 is an endoplasmic reticulum-associated ACBP. Conclusions In this study, the H. brasiliensis ACBP family genes were identified. Phylogenetic analyses of the HbABCPs indicate that there is a high conservation and evolutionary relationship between ACBPs in land plants. The HbACBPs are organ/tissue-specifically expressed and have different expression patterns in response to stimulation by bark tapping or ethrel/jasmonic acid. HbACBP1 and HbACBP2 are two important latex ACBPs that might be involved in the lipid and latex metabolism. The results may provide valuable information for further investigations into the biological functions of HbACBPs during latex metabolism and stress responses in H. brasiliensis. Electronic supplementary material The online version of this article (10.1186/s12864-017-4419-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiyi Nie
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Yihang Wang
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.,College of Agriculture, Hainan University, Haikou, 570228, China
| | - Chuntai Wu
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Yu Li
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Guijuan Kang
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Huaide Qin
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Rizhong Zeng
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber Trees, Ministry of Agriculture of China, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.
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12
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Loh SC, Thottathil GP, Othman AS. Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:45-55. [PMID: 27236227 DOI: 10.1016/j.plaphy.2016.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 05/27/2023]
Abstract
The natural rubber of Para rubber tree, Hevea brasiliensis, is the main crop involved in industrial rubber production due to its superior quality. The Hevea bark is commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. The laticifer is well defined in the aspect of morphology; however, only some genes associated with its development have been reported. We successfully induced secondary laticifer in the jasmonic acid (JA)-treated and linolenic acid (LA)-treated Hevea bark but secondary laticifer is not observed in the ethephon (ET)-treated and untreated Hevea bark. In this study, we analysed 27,195 gene models using NimbleGen microarrays based on the Hevea draft genome. 491 filtered differentially expressed (FDE) transcripts that are common to both JA- and LA-treated bark samples but not ET-treated bark samples were identified. In the Eukaryotic Orthologous Group (KOG) analysis, 491 FDE transcripts belong to different functional categories that reflect the diverse processes and pathways involved in laticifer differentiation. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) and KOG analysis, the profile of the FDE transcripts suggest that JA- and LA-treated bark samples have a sufficient molecular basis for secondary laticifer differentiation, especially regarding secondary metabolites metabolism. FDE genes in this category are from the cytochrome (CYP) P450 family, ATP-binding cassette (ABC) transporter family, short-chain dehydrogenase/reductase (SDR) family, or cinnamyl alcohol dehydrogenase (CAD) family. The data includes many genes involved in cell division, cell wall synthesis, and cell differentiation. The most abundant transcript in FDE list was SDR65C, reflecting its importance in laticifer differentiation. Using the Basic Local Alignment Search Tool (BLAST) as part of annotation and functional prediction, several characterised as well as uncharacterized transcription factors and genes were found in the dataset. Hence, the further characterization of these genes is necessary to unveil their role in laticifer differentiation. This study provides a platform for the further characterization and identification of the key genes involved in secondary laticifer differentiation.
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Affiliation(s)
- Swee Cheng Loh
- Centre for Chemical Biology, Sains @ Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia.
| | - Gincy P Thottathil
- Centre for Chemical Biology, Sains @ Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Sains @ Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia.
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Nie Z, Kang G, Duan C, Li Y, Dai L, Zeng R. Profiling Ethylene-Responsive Genes Expressed in the Latex of the Mature Virgin Rubber Trees Using cDNA Microarray. PLoS One 2016; 11:e0152039. [PMID: 26985821 PMCID: PMC4795647 DOI: 10.1371/journal.pone.0152039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
Ethylene is commonly used as a latex stimulant of Hevea brasiliensis by application of ethephon (chloro-2-ethylphosphonic acid); however, the molecular mechanism by which ethylene increases latex production is not clear. To better understand the effects of ethylene stimulation on the laticiferous cells of rubber trees, a latex expressed sequence tag (EST)-based complementary DNA microarray containing 2,973 unique genes (probes) was first developed and used to analyze the gene expression changes in the latex of the mature virgin rubber trees after ethephon treatment at three different time-points: 8, 24 and 48 h. Transcript levels of 163 genes were significantly altered with fold-change values ≥ 2 or ≤ –2 (q-value < 0.05) in ethephon-treated rubber trees compared with control trees. Of the 163 genes, 92 were up-regulated and 71 down-regulated. The microarray results were further confirmed using real-time quantitative reverse transcript-PCR for 20 selected genes. The 163 ethylene-responsive genes were involved in several biological processes including organic substance metabolism, cellular metabolism, primary metabolism, biosynthetic process, cellular response to stimulus and stress. The presented data suggest that the laticifer water circulation, production and scavenging of reactive oxygen species, sugar metabolism, and assembly and depolymerization of the latex actin cytoskeleton might play important roles in ethylene-induced increase of latex production. The results may provide useful insights into understanding the molecular mechanism underlying the effect of ethylene on latex metabolism of H. brasiliensis.
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Affiliation(s)
- Zhiyi Nie
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Guijuan Kang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Cuifang Duan
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Yu Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Longjun Dai
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Rizhong Zeng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
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