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He H, Wang J, Meng Z, Dijkwel PP, Du P, Shi S, Dong Y, Li H, Xie Q. Genome-Wide Analysis of the SRPP/ REF Gene Family in Taraxacum kok-saghyz Provides Insights into Its Expression Patterns in Response to Ethylene and Methyl Jasmonate Treatments. Int J Mol Sci 2024; 25:6864. [PMID: 38999970 PMCID: PMC11241686 DOI: 10.3390/ijms25136864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Taraxacum kok-saghyz (TKS) is a model plant and a potential rubber-producing crop for the study of natural rubber (NR) biosynthesis. The precise analysis of the NR biosynthesis mechanism is an important theoretical basis for improving rubber yield. The small rubber particle protein (SRPP) and rubber elongation factor (REF) are located in the membrane of rubber particles and play crucial roles in rubber biosynthesis. However, the specific functions of the SRPP/REF gene family in the rubber biosynthesis mechanism have not been fully resolved. In this study, we performed a genome-wide identification of the 10 TkSRPP and 2 TkREF genes' family members of Russian dandelion and a comprehensive investigation on the evolution of the ethylene/methyl jasmonate-induced expression of the SRPP/REF gene family in TKS. Based on phylogenetic analysis, 12 TkSRPP/REFs proteins were divided into five subclades. Our study revealed one functional domain and 10 motifs in these proteins. The SRPP/REF protein sequences all contain typical REF structural domains and belong to the same superfamily. Members of this family are most closely related to the orthologous species T. mongolicum and share the same distribution pattern of SRPP/REF genes in T. mongolicum and L. sativa, both of which belong to the family Asteraceae. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the TkSRPP/REFs gene family. The expression levels of most TkSRPP/REF members were significantly increased in different tissues of T. kok-saghyz after induction with ethylene and methyl jasmonate. These results will provide a theoretical basis for the selection of candidate genes for the molecular breeding of T. kok-saghyz and the precise resolution of the mechanism of natural rubber production.
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Affiliation(s)
- Huan He
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Jiayin Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Zhuang Meng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Paul P Dijkwel
- School of Natural Sciences, Massey University, Tennent Drive, Palmerston North 4474, New Zealand
| | - Pingping Du
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Shandang Shi
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Yuxuan Dong
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-basin System Ecology, College of Life Sciences, Shihezi University, Shihezi 832003, China
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Tripathi A, Chauhan N, Mukhopadhyay P. Recent advances in understanding the regulation of plant secondary metabolite biosynthesis by ethylene-mediated pathways. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:543-557. [PMID: 38737326 PMCID: PMC11087406 DOI: 10.1007/s12298-024-01441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
Plants produce a large repertoire of secondary metabolites. The pathways that lead to the biosynthesis of these metabolites are majorly conserved in the plant kingdom. However, a significant portion of these metabolites are specific to certain groups or species due to variations in the downstream pathways and evolution of the enzymes. These metabolites show spatiotemporal variation in their accumulation and are of great importance to plants due to their role in development, stress response and survival. A large number of these metabolites are in huge industrial demand due to their potential use as therapeutics, aromatics and more. Ethylene, as a plant hormone is long known, and its biosynthetic process, signaling mechanism and effects on development and response pathways have been characterized in many plants. Through exogenous treatments, ethylene and its inhibitors have been used to manipulate the production of various secondary metabolites. However, the research done on a limited number of plants in the last few years has only started to uncover the mechanisms through which ethylene regulates the accumulation of these metabolites. Often in association with other hormones, ethylene participates in fine-tuning the biosynthesis of the secondary metabolites, and brings specificity in the regulation depending on the plant, organ, tissue type and the prevailing conditions. This review summarizes the related studies, interprets the outcomes, and identifies the gaps that will help to breed better varieties of the related crops and produce high-value secondary metabolites for human benefits.
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Affiliation(s)
- Alka Tripathi
- Plant Biotechnology division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015 India
| | - Nisha Chauhan
- Plant Biotechnology division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh 201002 India
| | - Pradipto Mukhopadhyay
- Plant Biotechnology division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh 201002 India
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Qiu YM, Guo J, Jiang WZ, Ding JH, Song RF, Zhang JL, Huang X, Yuan HM. HbBIN2 Functions in Plant Cold Stress Resistance through Modulation of HbICE1 Transcriptional Activity and ROS Homeostasis in Hevea brasiliensis. Int J Mol Sci 2023; 24:15778. [PMID: 37958762 PMCID: PMC10649430 DOI: 10.3390/ijms242115778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Cold stress poses significant limitations on the growth, latex yield, and ecological distribution of rubber trees (Hevea brasiliensis). The GSK3-like kinase plays a significant role in helping plants adapt to different biotic and abiotic stresses. However, the functions of GSK3-like kinase BR-INSENSITIVE 2 (BIN2) in Hevea brasiliensis remain elusive. Here, we identified HbBIN2s of Hevea brasiliensis and deciphered their roles in cold stress resistance. The transcript levels of HbBIN2s are upregulated by cold stress. In addition, HbBIN2s are present in both the nucleus and cytoplasm and have the ability to interact with the INDUCER OF CBF EXPRESSION1(HbICE1) transcription factor, a central component in cold signaling. HbBIN2 overexpression in Arabidopsis displays decreased tolerance to chilling stress with a lower survival rate and proline content but a higher level of electrolyte leakage (EL) and malondialdehyde (MDA) than wild type under cold stress. Meanwhile, HbBIN2 transgenic Arabidopsis treated with cold stress exhibits a significant increase in the accumulation of reactive oxygen species (ROS) and a decrease in the activity of antioxidant enzymes. Further investigation reveals that HbBIN2 inhibits the transcriptional activity of HbICE1, thereby attenuating the expression of C-REPEAT BINDING FACTOR (HbCBF1). Consistent with this, overexpression of HbBIN2 represses the expression of CBF pathway cold-regulated genes under cold stress. In conclusion, our findings indicate that HbBIN2 functions as a suppressor of cold stress resistance by modulating HbICE1 transcriptional activity and ROS homeostasis.
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Affiliation(s)
| | | | | | | | | | | | - Xi Huang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (Y.-M.Q.); (J.G.); (W.-Z.J.); (J.-H.D.); (R.-F.S.); (J.-L.Z.)
| | - Hong-Mei Yuan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (Y.-M.Q.); (J.G.); (W.-Z.J.); (J.-H.D.); (R.-F.S.); (J.-L.Z.)
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Niu YF, Li GH, Zheng C, Liu ZY, Liu J. Insights to the superoxide dismutase genes and its roles in Hevea brasiliensis under abiotic stress. 3 Biotech 2022; 12:274. [PMID: 36110566 PMCID: PMC9468202 DOI: 10.1007/s13205-022-03328-7] [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: 12/15/2021] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
The superoxide dismutase (SOD) protein significantly influences the development and growth of plants and their reaction to abiotic stresses. However, little is known about the characteristics of rubber tree SOD genes and their expression changes under abiotic stresses. The present study recognized 11 SOD genes in the rubber tree genome, including 7 Cu/ZnSODs, 2 MnSODs, and 2 FeSODs. Except for HbFSD1, SODs were scattered on five chromosomes. The phylogenetic analysis of SOD proteins in rubber trees and a few other plants demonstrated that the SOD proteins contained three major subgroups. Moreover, the genes belonging to the same clade contained similar gene structures, which confirmed their classification further. The extension of the SOD gene family in the rubber tree was mainly induced by the segmental duplication events. The cis-acting components analysis showed that HbSODs were utilized in many biological procedures. The transcriptomics data indicated that the phosphorylation of the C-terminal domain of RNA polymerase II might control the cold response genes through the CBF pathway and activate the SOD system to respond to cold stress. The qRT-PCR results showed that the expression of HbCSD1 was significantly downregulated under drought and salt stresses, which might dominate the adaption capability to different stresses. Additionally, salt promoted the expression levels of HbMSD1 and HbMSD2, exhibiting their indispensable role in the salinity reaction. The study results will provide a theoretical basis for deep research on HbSODs in rubber trees. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03328-7.
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Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Guo-Hua Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Zi-Yan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
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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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Guo X, Zhao B, Zhou X, Lu D, Wang Y, Chen Y, Xiao D. Analysis of the molecular basis of Saccharomyces cerevisiae mutant with high nucleic acid content by comparative transcriptomics. Food Res Int 2021; 142:110188. [PMID: 33773664 DOI: 10.1016/j.foodres.2021.110188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/13/2021] [Accepted: 01/24/2021] [Indexed: 10/22/2022]
Abstract
Ribonucleic acid (RNA) and its degradation products are important functional components widely used in the food industry. Transcription analysis was used to explore the genetic mechanism underlying nucleic acid synthesis in the chemical mutant Saccharomyces cerevisiae strain BY23-195 with high nucleic acid content. Results showed that ribosome biogenesis, meiosis, RNA transport, mitogen-activated protein kinase (MAPK) signaling pathway, tryptophan metabolism, carbon metabolism, and longevity regulating pathway are closely related to the high nucleic acid metabolism of S. cerevisiae. Fourteen most promising genes were selected to evaluate the effect of single-gene deletion or overexpression on the RNA synthesis of S. cerevisiae. Compared with the RNA content of the parent strain BY23, that of mutant strains BY23-HXT1, BY23-ΔGSP2 and BY23-ΔCTT1 increased by 8.19%, 11.60% and 14.00%, respectively. The possible reason why HXT1, GSP2, and CTT1 affect RNA content is by regulating cell fitness. This work was the first to report that regulating the transcription of HXT1, GSP2, and CTT1 could increase the RNA content of S. cerevisiae. This work also provides valuable knowledge on the genetic mechanism of high nucleic acid synthesis in S. cerevisiae and new strategies for increasing its RNA content.
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Affiliation(s)
- Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457 Tianjin, China.
| | - Bin Zhao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Xinran Zhou
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Dongxia Lu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Yaping Wang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457 Tianjin, China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin 300547, China; Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, 300457 Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457 Tianjin, China
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Identification and Characterization of Glycoproteins and Their Responsive Patterns upon Ethylene Stimulation in the Rubber Latex. Int J Mol Sci 2020; 21:ijms21155282. [PMID: 32722428 PMCID: PMC7432319 DOI: 10.3390/ijms21155282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural rubber is an important industrial material, which is obtained from the only commercially cultivated rubber tree, Hevea brasiliensis. In rubber latex production, ethylene has been extensively used as a stimulant. Recent research showed that post-translational modifications (PTMs) of latex proteins, such as phosphorylation, glycosylation and ubiquitination, are crucial in natural rubber biosynthesis. In this study, comparative proteomics was performed to identify the glycosylated proteins in rubber latex treated with ethylene for different days. Combined with Pro-Q Glycoprotein gel staining and mass spectrometry techniques, we provided the first visual profiling of glycoproteomics of rubber latex and finally identified 144 glycosylated protein species, including 65 differentially accumulated proteins (DAPs) after treating with ethylene for three and/or five days. Gene Ontology (GO) functional annotation showed that these ethylene-responsive glycoproteins are mainly involved in cell parts, membrane components and metabolism. Pathway analysis demonstrated that these glycosylated rubber latex proteins are mainly involved in carbohydrate metabolism, energy metabolism, degradation function and cellular processes in rubber latex metabolism. Protein-protein interaction analysis revealed that these DAPs are mainly centered on acetyl-CoA acetyltransferase and hydroxymethylglutaryl-CoA synthase (HMGS) in the mevalonate pathway for natural rubber biosynthesis. In our glycoproteomics, three protein isoforms of HMGS2 were identified from rubber latex, and only one HMGS2 isoform was sharply increased in rubber latex by ethylene treatment for five days. Furthermore, the HbHMGS2 gene was over-expressed in a model rubber-producing grass Taraxacum Kok-saghyz and rubber content in the roots of transgenic rubber grass was significantly increased over that in the wild type plant, indicating HMGS2 is the key component for natural rubber production.
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Wang Q, Xu G, Zhai J, Yuan H, Huang X. Identification of the targets of HbEIN3/EILs in genomic wide in Hevea brasiliensis. Biosci Biotechnol Biochem 2019; 83:1270-1283. [PMID: 30915888 DOI: 10.1080/09168451.2019.1597619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
EIN3/EILs are key regulators in ET signaling pathway. In this work, 4 members of EIN3/EILs of Hevea brasiliensis (HbEIN3/EILs) showed interaction with two F box proteins, HbEBF1 and HbEBF2. HbEIN3 located in nucleus and exhibited strong transcriptional activity. HbEIN3 was induced by ET treatment in C-serum, but not in B-serum of latex. HbEIN3/EILs bound to G-box cis-element. To globally search the potential targets of HbEIN3/EILs, genomic sequences of H. brasiliensis was re-annotated and an HCES (Hevea Cis-Elements Scanning) program was developed ( www.h-brasiliensis.com ). HCES scanning results showed that ET- and JA- responsive cis-elements distribute overlapping in gene promoters. 3146 genes containing G-box in promoters are potential targets of HbEIN3, including 41 genes involved in biosynthesis and drainage of latex, of which 7 rate-limiting genes of latex production were regulated by both ET and JA, suggesting that ET and JA signaling pathways coordinated the latex biosynthesis and drainage in H. brasiliensis. Abbreviations: ABRE: ABA responsive elements; bHLH: basic helix-loop-helix; COG: Orthologous Groups; DRE: dehydration response element; ERE: ethylene responsive element; ET: Ethylene; GO: Gene Ontology; HCES: Hevea Cis-Elements Scanning; JA: jasmonates; JRE: Jasmonate-responsive element; KEGG: Kyoto Encyclopedia of Genes and Genomes; NR: non-redundant database; PLACE: Plant Cis-acting Regulatory DNA Elements; qRT-PCR: quantitative real-time RT-PCR.
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Affiliation(s)
- Qichao Wang
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
| | - Gang Xu
- b School of Life Sciences , Tsinghua University , Beijing , China
| | - Jinling Zhai
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
| | - Hongmei Yuan
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
| | - Xi Huang
- a Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources , Hainan University , Haikou , P. R. China
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Men X, Wang F, Chen GQ, Zhang HB, Xian M. Biosynthesis of Natural Rubber: Current State and Perspectives. Int J Mol Sci 2018; 20:E50. [PMID: 30583567 PMCID: PMC6337083 DOI: 10.3390/ijms20010050] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Natural rubber is a kind of indispensable biopolymers with great use and strategic importance in human society. However, its production relies almost exclusively on rubber-producing plants Hevea brasiliensis, which have high requirements for growth conditions, and the mechanism of natural rubber biosynthesis remains largely unknown. In the past two decades, details of the rubber chain polymerization and proteins involved in natural rubber biosynthesis have been investigated intensively. Meanwhile, omics and other advanced biotechnologies bring new insight into rubber production and development of new rubber-producing plants. This review summarizes the achievements of the past two decades in understanding the biosynthesis of natural rubber, especially the massive information obtained from the omics analyses. Possibilities of natural rubber biosynthesis in vitro or in genetically engineered microorganisms are also discussed.
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Affiliation(s)
- Xiao Men
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Fan Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guo-Qiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Hai-Bo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
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Deng X, Guo D, Yang S, Shi M, Chao J, Li H, Peng S, Tian W. Jasmonate signalling in the regulation of rubber biosynthesis in laticifer cells of rubber tree, Hevea brasiliensis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3559-3571. [PMID: 29726901 DOI: 10.1093/jxb/ery169] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/27/2018] [Indexed: 05/27/2023]
Abstract
Rubber trees are the world's major source of natural rubber. Rubber-containing latex is obtained from the laticifer cells of the rubber tree (Hevea brasiliensis) via regular tapping. Rubber biosynthesis is a typical isoprenoid metabolic process in the laticifer cells; however, little is known about the positive feedback regulation caused by the loss of latex that occurs through tapping. In this study, we demonstrate the crucial role of jasmonate signalling in this feedback regulation. The endogenous levels of jasmonate, the expression levels of rubber biosynthesis-related genes, and the efficiency of in vitro rubber biosynthesis were found to be significantly higher in laticifer cells of regularly tapped trees than those of virgin (i.e. untapped) trees. Application of methyl jasmonate had similar effects to latex harvesting in up-regulating the rubber biosynthesis-related genes and enhancing rubber biosynthesis. The specific jasmonate signalling module in laticifer cells was identified as COI1-JAZ3-MYC2. Its activation was associated with enhanced rubber biosynthesis via up-regulation of the expression of a farnesyl pyrophosphate synthase gene and a small rubber particle protein gene. The increase in the corresponding proteins, especially that of farnesyl pyrophosphate synthase, probably contributes to the increased efficiency of rubber biosynthesis. To our knowledge, this is the first study to reveal a jasmonate signalling pathway in the regulation of rubber biosynthesis in laticifer cells. The identification of the specific jasmonate signalling module in the laticifer cells of the rubber tree may provide a basis for genetic improvement of rubber yield potential.
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Affiliation(s)
- Xiaomin Deng
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
| | - Dong Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shuguang Yang
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
| | - Minjing Shi
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
| | - Jinquan Chao
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
| | - Huiliang Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shiqing Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weimin Tian
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
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11
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Montoro P, Wu S, Favreau B, Herlinawati E, Labrune C, Martin-Magniette ML, Pointet S, Rio M, Leclercq J, Ismawanto S, Kuswanhadi. Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness. Sci Rep 2018; 8:8483. [PMID: 29855601 PMCID: PMC5981547 DOI: 10.1038/s41598-018-26854-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 05/21/2018] [Indexed: 02/01/2023] Open
Abstract
Tapping Panel Dryness (TPD) affects latex production in Hevea brasiliensis. This physiological syndrome involves the agglutination of rubber particles, which leads to partial or complete cessation of latex flow. Latex harvesting consists in tapping soft bark. Ethephon can be applied to stimulate latex flow and its regeneration in laticifers. Several studies have reported transcriptome changes in bark tissues. This study is the first report on deep RNA sequencing of latex to compare the effect of ethephon stimulation and TPD severity. Trees were carefully selected for paired-end sequencing using an Illumina HiSeq 2000. In all, 43 to 60 million reads were sequenced for each treatment in three biological replicates (slight TPD trees without ethephon stimulation, and slight and severe TPD trees with ethephon treatment). Differentially expressed genes were identified and annotated, giving 8,111 and 728 in response to ethephon in slight TPD trees and in ethephon-induced severe TPD trees, respectively. A biological network of responses to ethephon and TPD highlighted the major influence of metabolic processes and the response to stimulus, especially wounding and jasmonate depression in TPD-affected trees induced by ethephon stimulation.
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Affiliation(s)
- Pascal Montoro
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Shuangyang Wu
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bénédicte Favreau
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Eva Herlinawati
- Indonesian Rubber Research Institute, Sembawa Research Centre, Palembang, Indonesia
| | - Cécile Labrune
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005, Paris, France
| | - Stéphanie Pointet
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Maryannick Rio
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Julie Leclercq
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sigit Ismawanto
- Indonesian Rubber Research Institute, Sembawa Research Centre, Palembang, Indonesia
| | - Kuswanhadi
- Indonesian Rubber Research Institute, Sembawa Research Centre, Palembang, Indonesia
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12
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Liu JP, Hu J, Liu YH, Yang CP, Zhuang YF, Guo XL, Li YJ, Zhang L. Transcriptome analysis of Hevea brasiliensis in response to exogenous methyl jasmonate provides novel insights into regulation of jasmonate-elicited rubber biosynthesis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:349-358. [PMID: 29692543 PMCID: PMC5911270 DOI: 10.1007/s12298-018-0529-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/07/2018] [Accepted: 03/27/2018] [Indexed: 05/14/2023]
Abstract
The phytohomorne methyl jasmonate (MeJA) is known to trigger extensive reprogramming of gene expression leading to transcriptional activation of many secondary metabolic pathways. However, natural rubber is a commercially important secondary metabolite and little is known about the genetic and genomic basis of jasmonate-elicited rubber biosynthesis in rubber tree (Hevea brasiliensis). RNA sequencing (RNA-seq) of H. brasiliensis bark treated with 1 g lanolin paste containing 0.02% w/w MeJA for 24 h (M2) and 0.04% w/w MeJA for 24 h (M4) was performed. A total of 2950 and 2850 differentially expressed genes in M2 and M4 compared with control (C) were respectively detected. Key genes involved in 2-C-methyl-D-erythritol 4-phosphate, rubber biosynthesis, glycolysis and carbon fixation (Calvin cycle) pathway were found to be up-regulated by MeJA treatment. Particularly, the expression of 3-hydroxy-3-metylglutaryl coenzyme A reductase in MVA pathway was down-regulated by MeJA treatment, but the expression of farnesyl diphosphate synthase (FPS) and cis-prenyltransferase (CPT, or rubber transferase) in rubber biosynthesis pathway were up-regulated by MeJA treatment. Up-regulation of critical genes in JA biosynthesis in response to MeJA treatment exhibited the self-activation of JA biosynthesis. In addition, up-regulated genes of great regulatory importance in cross-talk between JA and other hormone signaling, and of transcriptional regulation were identified. The increased expression levels of FPS and CPT in rubber biosynthesis pathway possibly resulted in an increased latex production in rubber tree treated with MeJA. The present results provide insights into the mechanism by which MeJA activates the rubber biosynthesis and the transcriptome data can also serve as the foundation for future research into the molecular basis for MeJA regulation of other cellular processes.
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Affiliation(s)
- Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Jin Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Yan-Hui Liu
- Center for Genomics and Biotechnology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Cui-Ping Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Yu-Fen Zhuang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Xiu-Li Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Yi-Jian Li
- Service Center of Science and Technology, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan Province China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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13
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Zhu L, Jin X, Xie Q, Yao Q, Wang X, Li H. Calcium-Dependent Protein Kinase Family Genes Involved in Ethylene-Induced Natural Rubber Production in Different Hevea brasiliensis Cultivars. Int J Mol Sci 2018; 19:ijms19040947. [PMID: 29565813 PMCID: PMC5979512 DOI: 10.3390/ijms19040947] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/10/2018] [Accepted: 03/16/2018] [Indexed: 11/16/2022] Open
Abstract
Natural rubber latex production can be improved by ethylene stimulation in the rubber tree (Hevea brasiliensis). However, the expression levels of most functional proteins for natural rubber biosynthesis are not induced after ethylene application, indicating that post-translational modifications, especially protein phosphorylation, may play important roles in ethylene signaling in Hevea. Here, we performed a comprehensive investigation on evolution, ethylene-induced expression and protein-protein interaction of calcium-dependent protein kinases (CPKs), an important serine/threonine protein kinase family, in Hevea. Nine duplication events were determined in the 30 identified HbCPK genes. Expression profiling of HbCPKs in three rubber tree cultivars with low, medium and high ethylene sensitivity showed that HbCPK6, 17, 20, 22, 24, 28 and 30 are induced by ethylene in at least one cultivar. Evolution rate analysis suggested accelerated evolution rates in two paralogue pairs, HbCPK9/18 and HbCPK19/20. Analysis of proteomic data for rubber latex after ethylene treatment showed that seven HbCPK proteins could be detected, including six ethylene-induced ones. Protein-protein interaction analysis of the 493 different abundant proteins revealed that protein kinases, especially calcium-dependent protein kinases, possess most key nodes of the interaction network, indicating that protein kinase and protein phosphorylation play important roles in ethylene signaling in latex of Hevea. In summary, our data revealed the expression patterns of HbCPK family members and functional divergence of two HbCPK paralogue pairs, as well as the potential important roles of HbCPKs in ethylene-induced rubber production improvement in Hevea.
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Affiliation(s)
- Liping Zhu
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Xiang Jin
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou 571158, China.
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Quanliang Xie
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Qi Yao
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou 571158, China.
| | - Xuchu Wang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou 571158, China.
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
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14
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Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress response. Genes Genomics 2018; 40:1181-1197. [DOI: 10.1007/s13258-018-0681-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/28/2018] [Indexed: 01/26/2023]
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15
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Makita Y, Kawashima M, Lau NS, Othman AS, Matsui M. Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. BMC Genomics 2018; 19:922. [PMID: 29363422 PMCID: PMC5780850 DOI: 10.1186/s12864-017-4333-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. RESULTS A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. CONCLUSION The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/ .
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Nyok Sean Lau
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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16
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Yang H, Wang X, Wei Y, Deng Z, Liu H, Chen J, Dai L, Xia Z, He G, Li D. Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings. BMC PLANT BIOLOGY 2018; 18:10. [PMID: 29316882 PMCID: PMC5759766 DOI: 10.1186/s12870-017-1203-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Breeding rubber tree seedling with growth heterosis is vital for natural rubber production. It is the prerequisites for effectively utilizing growth heterosis to elucidate its molecular mechanisms, but the molecular mechanisms remain poorly understood in rubber tree. To elucidate seedling growth heterosis, we conducted comparative transcriptomic analyses between the two hybrids and their parents. RESULTS By identifying and comparing differently expressed genes (DEGs), we found that the hybrids (BT 3410 and WC 11) show significantly differential expression profiles from their parents (PR 107 and RRIM 600). In BT 3410-parent triad, 1092 (49.95%) and 1094 (50.05%) DEGs indicated clear underdominance or overdominance, respectively. Whereas in WC 11-parent triad, most DEGs (78.2%, 721) showed low- or high-parent dominance; 160 (17.35%) exhibited expression patterns that are not statistically distinguishable from additivity, and 8 (0.87%) and 33 (3.58%) DEGs exhibited underdominance and overdominance, respectively. Furthermore, some biological processes are differentially regulated between two hybrids. Interestingly, the pathway in response to stimulus is significantly downregulated and metabolic pathways are more highly regulated in BT 3410. CONCLUSIONS Taken together, the genotypes, transcriptomes and biological pathways (especially, carbohydrate metabolism) are highly divergent between two hybrids, which may be associated with growth heterosis and weakness. Analyzing gene action models in hybrid-parent triads, we propose that overdominance may play important roles on growth heterosis, whereas dominance on hybrid weakness in rubber tree seedlings. These findings bring new insights into our understanding of growth heterosis of rubber tree seedling.
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Affiliation(s)
- Hong Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Xuncheng Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871 China
| | - Yongxuan Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan 570228 China
| | - Zhi Deng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Hui Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Jiangshu Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan 570228 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, Baodao Xincun, Danzhou, Hainan 571737 China
| | - Zhihui Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, Hainan 570228 China
| | - Guangming He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871 China
| | - Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737 China
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Zou Z, Xie G, Yang L. Papain-like cysteine protease encoding genes in rubber (Hevea brasiliensis): comparative genomics, phylogenetic, and transcriptional profiling analysis. PLANTA 2017; 246:999-1018. [PMID: 28752264 DOI: 10.1007/s00425-017-2739-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 05/22/2023]
Abstract
43 HbPLCPs representing nine subfamilies or 20 orthologous groups were found in rubber, where paralogs were resulted from the recent WGD and local duplication. Several senescence-associated genes were also identified. Papain-like cysteine proteases (PLCPs) comprise a large family of proteolytic enzymes involved in plant growth and development, seed germination, organ senescence, immunity, and stress response. Despite their importance and the extensive research in the model plant Arabidopsis thaliana, little information is available on rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study performed a genome-wide identification of PLCP family genes in rubber, resulting in a relatively high number of 43 members. The phylogenetic analysis assigned these genes into nine subfamilies, i.e., RD21 (6), CEP (4), XCP (4), XBCP3 (2), THI (1), SAG12 (18), RD19 (4), ALP (2), and CTB (2). Most of them were shown to have orthologs in Arabidopsis; however, several members in SAG12, CEP and XBCP3 subfamilies form new groups as observed in other core eudicots such as Manihot esculenta, Ricinus communis, Populus trichocarpa, and Vitis vinifera. Based on an expert sequence comparison, 20 orthologous groups (OGs) were proposed for core eudicots, and rubber paralogs were shown to be resulted from the recent whole-genome duplication (WGD) as well as local duplication. Transcriptional profiling showed distinct expression pattern of different members across various tissues, e.g., root, leaf, bark, laticifer, flower, and seed. By using the senescence-specific HbSAG12H1 as the indicator, the transcriptome of senescent rubber leaves was deeply sequenced and several senescence-associated PLCP genes were identified. Results obtained from this study provide valuable information for future functional analysis and utilization of PLCP genes in Hevea and other species.
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Affiliation(s)
- Zhi Zou
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China.
| | - Guishui Xie
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China
| | - Lifu Yang
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China
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18
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Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones. Int J Mol Sci 2017; 18:ijms18050958. [PMID: 28468331 PMCID: PMC5454871 DOI: 10.3390/ijms18050958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/03/2017] [Accepted: 04/21/2017] [Indexed: 01/26/2023] Open
Abstract
Rubber elongation factor (REF) and small rubber particle protein (SRPP) are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY) 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE), each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.
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19
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Cao X, Guo X, Yang X, Wang H, Hua W, He Y, Kang J, Wang Z. Transcriptional Responses and Gentiopicroside Biosynthesis in Methyl Jasmonate-Treated Gentiana macrophylla Seedlings. PLoS One 2016; 11:e0166493. [PMID: 27851826 PMCID: PMC5112864 DOI: 10.1371/journal.pone.0166493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/28/2016] [Indexed: 12/24/2022] Open
Abstract
Gentiana macrophylla, a medicinal plant with significant pharmacological properties, contains the bioactive compound gentiopicroside. Methyl jasmonate (MeJA) is an effective elicitor for enhancing the production of such compounds. However, little is known about MeJA-mediated biosynthesis of gentiopicroside. We investigated this phenomenon as well as gene expression profiles to determine the molecular mechanisms for MeJA-mediated gentiopicroside biosynthesis and regulation in G. macrophylla. Our HPLC results showed that Gentiana macrophylla seedlings exposed to MeJA had significantly higher concentrations of gentiopicroside when compared with control plants. We used RNA sequencing to compare transcriptional profiles in seedlings treated for 5 d with either 0 μmol L-1 MeJA (C) or 250 μmol L-1 MeJA (M5) and detected differentially expressed genes (DEGs). In total, 77,482 unique sequences were obtained from approximately 34 million reads. Of these, 48,466 (57.46%) sequences were annotated based on BLASTs performed against public databases. We identified 5,206 DEGs between the C and M5 samples, including genes related to the α-lenolenic acid degradation pathway, JA signaling pathway, and gentiopicroside biosynthesis. Expression of numerous enzyme genes in the glycolysis pathway was significantly up-regulated. Many genes encoding transcription factors (e.g. ERF, bHLH, MYB, and WRKY) also responded to MeJA elicitation. Rapid acceleration of the glycolysis pathway that supplies precursors for IPP biosynthesis and up-regulates the expression of enzyme genes in that IPP pathway are probably most responsible for MeJA stimulation of gentiopicroside synthesis. Our qRT-PCR results showed that the expression profiles of 12 gentiopicroside biosynthesis genes were consistent with the RNA-Seq data. These results increase our understanding about how the gentiopicroside biosynthesis pathway in G. macrophylla responds to MeJA.
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Affiliation(s)
- Xiaoyan Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xiaorong Guo
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xinbing Yang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Huaiqin Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Wenping Hua
- Department of Biological Science and Technology, Shaanxi XueQian Normal University, Xi’an, China
| | - Yihan He
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jiefang Kang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
- * E-mail: (JK); (ZW)
| | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, China
- * E-mail: (JK); (ZW)
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Transcriptome Analysis of the Signalling Networks in Coronatine-Induced Secondary Laticifer Differentiation from Vascular Cambia in Rubber Trees. Sci Rep 2016; 6:36384. [PMID: 27808245 PMCID: PMC5093416 DOI: 10.1038/srep36384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/14/2016] [Indexed: 11/09/2022] Open
Abstract
The secondary laticifer in rubber tree (Hevea brasiliensis Muell. Arg.) is a specific tissue within the secondary phloem. This tissue differentiates from the vascular cambia, and its function is natural rubber biosynthesis and storage. Given that jasmonates play a pivotal role in secondary laticifer differentiation, we established an experimental system with jasmonate (JA) mimic coronatine (COR) for studying the secondary laticifer differentiation: in this system, differentiation occurs within five days of the treatment of epicormic shoots with COR. In the present study, the experimental system was used to perform transcriptome sequencing and gene expression analysis. A total of 67,873 unigenes were assembled, and 50,548 unigenes were mapped at least in one public database. Of these being annotated unigenes, 15,780 unigenes were differentially expressed early after COR treatment, and 19,824 unigenes were differentially expressed late after COR treatment. At the early stage, 8,646 unigenes were up-regulated, while 7,134 unigenes were down-regulated. At the late stage, the numbers of up- and down-regulated unigenes were 7,711 and 12,113, respectively. The annotation data and gene expression analysis of the differentially expressed unigenes suggest that JA-mediated signalling, Ca2+ signal transduction and the CLAVATA-MAPK-WOX signalling pathway may be involved in regulating secondary laticifer differentiation in rubber trees.
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