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Wang S, Wang W. Interpretable prediction of mRNA abundance from promoter sequence using contextual regression models. NAR Genom Bioinform 2024; 6:lqae055. [PMID: 38807713 PMCID: PMC11131020 DOI: 10.1093/nargab/lqae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/08/2024] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
While machine learning models have been successfully applied to predicting gene expression from promoter sequences, it remains a great challenge to derive intuitive interpretation of the model and reveal DNA motif grammar such as motif cooperation and distance constraint between motif sites. Previous interpretation approaches are often time-consuming or have difficulty to learn the combinatory rules. In this work, we designed interpretable neural network models to predict the mRNA expression levels from DNA sequences. By applying the Contextual Regression framework we developed, we extracted weighted features to cluster samples into different groups, which have different gene expression levels. We performed motif analysis in each cluster and found motifs with active or repressive regulation on gene expression. By comparing the co-occurrence locations of discovered motifs, we also uncovered multiple grammars of motif combination including communities of cooperative motifs and distance constraints between motif pairs. These results revealed new insights of the regulatory architecture of promoter sequences.
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Affiliation(s)
- Song Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, USA
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Lu WJ, Zhang MS, Lu DL, Li ZW, Yang ZD, Wu L, Ni JT, Chen WD, Deng JJ, Luo XC. Sustainable valorizing high-protein feather waste utilization through solid-state fermentation by keratinase-enhanced Streptomyces sp. SCUT-3 using a novel promoter. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 174:528-538. [PMID: 38134540 DOI: 10.1016/j.wasman.2023.12.015] [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: 09/10/2023] [Revised: 11/24/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
Feather waste, a rich source of proteins, has traditionally been processed through high-temperature puffing and acid-base hydrolysis, contributing to generation of greenhouse gases and H2S. To address this issue, we employed circular economy techniques to recover the nutritional value of feather waste. Streptomyces sp. SCUT-3, an efficient proteolytic and chitinolytic bacterium, was isolated for feather degradation previously. This study aimed to valorize feather waste for feed purposes by enhancing its feather transformation ability through promoter optimization. Seven promoters were identified through omics analysis and compared to a common Streptomyces promoter ermE*p. The strongest promoter, p24880, effectively enhanced the expression of three candidate keratinases (Sep39, Sep40, and Sep53). The expression efficiency of double-, triple-p24880 and sandwich p24880-sep39-p24880 promoters were further verified. The co-overexpression strain SCUT-3-p24880-sep39-p24880-sep40 exhibited a 16.21-fold increase in keratinase activity compared to the wild-type. Using this strain, a solid-state fermentation process was established that increased the feather/water ratio (w/w) to 1:1.5, shortened the fermentation time to 2.5 days, and increased soluble peptide and free amino acid yields to 0.41 g/g and 0.14 g/g, respectively. The resulting has high protein content (90.49 %), with high in vitro digestibility (94.20 %). This method has the potential to revolutionize the feather waste processing industry.
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Affiliation(s)
- Wen-Jun Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Ming-Shu Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - De-Lin Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Zhi-Wei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Zhen-Dong Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Lei Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Jing-Tao Ni
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Wei-Dong Chen
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun-Jin Deng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China; Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Crop Germplasm Resources Conservation and Utilization, Guangzhou 510640, China.
| | - Xiao-Chun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China.
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Chen C, Chen J, Wu G, Li L, Hu Z, Li X. A Blue Light-Responsive Strong Synthetic Promoter Based on Rational Design in Chlamydomonas reinhardtii. Int J Mol Sci 2023; 24:14596. [PMID: 37834043 PMCID: PMC10572394 DOI: 10.3390/ijms241914596] [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: 08/30/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Chlamydomonas reinhardtii (C. reinhardtii) is a single-cell green alga that can be easily genetically manipulated. With its favorable characteristics of rapid growth, low cost, non-toxicity, and the ability for post-translational protein modification, C. reinhardtii has emerged as an attractive option for the biosynthesis of various valuable products. To enhance the expression level of exogenous genes and overcome the silencing of foreign genes by C. reinhardtii, synthetic promoters such as the chimeric promoter AR have been constructed and evaluated. In this study, a synthetic promoter GA was constructed by hybridizing core fragments from the natural promoters of the acyl carrier protein gene (ACP2) and the glutamate dehydrogenase gene (GDH2). The GA promoter exhibited a significant increase (7 times) in expressing GUS, over the AR promoter as positive control. The GA promoter also displayed a strong responsiveness to blue light (BL), where the GUS expression was doubled compared to the white light (WL) condition. The ability of the GA promoter was further tested in the expression of another exogenous cadA gene, responsible for catalyzing the decarboxylation of lysine to produce cadaverine. The cadaverine yield driven by the GA promoter was increased by 1-2 times under WL and 2-3 times under BL as compared to the AR promoter. This study obtained, for the first time, a blue light-responsive GDH2 minimal fragment in C. reinhardtii, which delivered a doubling effect under BL when used alone or in hybrid. Together with the strong GA synthetic promoter, this study offered useful tools of synthetic biology to the algal biotechnology field.
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Affiliation(s)
| | | | | | | | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaozheng Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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Jia S, Liu X, Li X, Sun C, Cao X, Liu W, Guo G, Bi C. Modification of lignin composition by ectopic expressing wheat TaF5H1 led to decreased salt tolerance in transgenic Arabidopsis plants. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:153997. [PMID: 37302354 DOI: 10.1016/j.jplph.2023.153997] [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: 01/19/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 06/13/2023]
Abstract
Lignin is an important cell wall component that provides plants with mechanical support and improved tolerance to pathogen attacks. Previous studies have shown that plants rich in S-lignin content or with a higher S/G ratio always exhibit higher efficiency in the utilization of lignocellulosic biomass. Ferulate 5-hydroxylase, or coniferaldehyde 5-hydroxylase (F5H, or CAld5H), is the critical enzyme in syringyl lignin biosynthesis. Some F5Hs have been characterized in several plant species, e.g., Arabidopsis, rice, and poplar. However, information about F5Hs in wheat remains unclear. In this study, a wheat F5H gene, TaF5H1, together with its native promoter (pTaF5H1), was functionally characterized in transgenic Arabidopsis. Gus staining results showed that TaF5H1 could be expressed predominantly in the highly lignified tissues in transgenic Arabidopsis plants carrying pTaF5H1:Gus. qRT-PCR results showed that TaF5H1 was significantly inhibited by NaCl treatment. Ectopic expression of TaF5H1 driven by pTaF5H1 (i.e., pTaF5H1:TaF5H1) could increase the biomass yield, S-lignin content, and S/G ratio in transgenic Arabidopsis plants, which could also restore the traces of S-lignin in fah1-2, the Arabidopsis F5H mutant, to an even higher level than the wild type (WT), suggesting that TaF5H1 is a critical enzyme in S lignin biosynthesis, and pTaF5H1:TaF5H1 module has potential in the manipulation of S-lignin composition without any compromise on the biomass yield. However, expression of pTaF5H1:TaF5H1 also led to decreased salt tolerance compared with the WT. RNA-seq analysis showed that many stress-responsive genes and genes responsible for the biosynthesis of cell walls were differentially expressed between the seedlings harboring pTaF5H1:TaF5H1 and the WT, hinting that manipulation of the cell wall components targeting F5H may also affect the stress adaptability of the modified plants due to the interference to the cell wall integrity. In summary, this study demonstrated that the wheat pTaF5H1: TaF5H1 cassette has the potential to modulate S-lignin composition without any compromise in biomass yield in future engineering practice. Still, its negative effect on stress adaptability to transgenic plants should also be considered.
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Affiliation(s)
- Shuzhen Jia
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Xiaojun Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Xiaoyue Li
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Chen Sun
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Xiaohong Cao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Wei Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Guangyan Guo
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China.
| | - Caili Bi
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, PR China.
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Dietz J, Jacobsen F, Zhuge H, Daya N, Bigot A, Zhang W, Ehrhardt A, Vorgerd M, Ehrke-Schulz E. Muscle Specific Promotors for Gene Therapy - A Comparative Study in Proliferating and Differentiated Cells. J Neuromuscul Dis 2023:JND221574. [PMID: 37270809 DOI: 10.3233/jnd-221574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
BACKGROUND Depending on the therapy approach and disease background, the heterogeneity of muscular tissues complicates the development of targeted gene therapy, where either expression in all muscle types or restriction to only one muscle type is warranted. Muscle specificity can be achieved using promotors mediating tissue specific and sustained physiological expression in the desired muscle types but limited activity in non-targeted tissue. Several muscle specific promotors have been described, but direct comparisons between them are lacking. OBJECTIVE Here we present a direct comparison of muscle specific Desmin-, MHCK7, microRNA206- and Calpain3 promotor. METHODS To directly compare these muscle specific promotors we utilized transfection of reporter plasmids using an in vitro model based on electrical pulse stimulation (EPS) to provoke sarcomere formation in 2D cell culture for quantification of promotor activities in far differentiated mouse and human myotubes. RESULTS We found that Desmin- and MHCK7 promotors showed stronger reporter gene expression levels in proliferating and differentiated myogenic cell lines than miR206 and CAPN3 promotor. However, Desmin and MHCK7 promotor promoted gene expression also cardiac cells whereas miR206 and CAPN3 promotor expression was restricted to skeletal muscle. CONCLUSIONS Our results provides direct comparison of muscle specific promotors with regard to expression strengths and specificity as this is important feature to avoid undesired transgene expression in non-target muscle cells for a desired therapy approach.
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Affiliation(s)
- Julienne Dietz
- Department of Human Medicine, Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Witten, Germany
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, Bochum, Germany
| | - Frank Jacobsen
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, Bochum, Germany
| | - Heidi Zhuge
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, Bochum, Germany
| | - Nassam Daya
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, Bochum, Germany
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Wenli Zhang
- Department of Human Medicine, Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Anja Ehrhardt
- Department of Human Medicine, Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Matthias Vorgerd
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, Bochum, Germany
| | - Eric Ehrke-Schulz
- Department of Human Medicine, Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Witten, Germany
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6
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Jameel A, Ketehouli T, Wang Y, Wang F, Li X, Li H. Detection and validation of cis-regulatory motifs in osmotic stress-inducible synthetic gene switches via computational and experimental approaches. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1043-1054. [PMID: 35940614 DOI: 10.1071/fp21314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Synthetic cis -regulatory modules can improve our understanding of gene regulatory networks. We applied an ensemble approach for de novo cis motif discovery among the promoters of 181 drought inducible differentially expressed soybean (Glycine max L.) genes. A total of 43 cis motifs were identified in promoter regions of all gene sets using the binding site estimation suite of tools (BEST). Comparative analysis of these motifs revealed similarities with known cis -elements found in PLACE database and led to the discovery of cis -regulatory motifs that were not yet implicated in drought response. Compiled with the proposed synthetic promoter design rationale, three synthetic assemblies were constructed by concatenating multiple copies of drought-inducible cis motifs in a specific order with inter-motif spacing using random bases and placed upstream of 35s minimal core promoter. Each synthetic module substituted 35S promoter in pBI121 and pCAMBIA3301 to drive glucuronidase expression in soybean hairy roots and Arabidopsis thaliana L. Chimeric soybean seedlings and 3-week-old transgenic Arabidopsis plants were treated with simulated with different levels of osmotic stress. Histochemical staining of transgenic soybean hairy roots and Arabidopsis displayed drought-inducible GUS activity of synthetic promoters. Fluorometric assay and expression analysis revealed that SP2 is the better manual combination of cis -elements for stress-inducible expression. qRT-PCR results further demonstrated that designed synthetic promoters are not tissue-specific and thus active in different parts upon treatment with osmotic stress in Arabidopsis plants. This study provides tools for transcriptional upgradation of valuable crops against drought stress and adds to the current knowledge of synthetic biology.
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Affiliation(s)
- Aysha Jameel
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Toi Ketehouli
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Yifan Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Fawei Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Xiaowei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Haiyan Li
- College of Tropical Crops, Hainan University, 570228, Haikou, China
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Huang Z, Xu Q, Fang X, Wu Z. Expression Activity of Artificial Promoters for Disease Resistance in Transgenic Eucalyptus urophylla. Genes (Basel) 2022; 13:genes13101813. [PMID: 36292698 PMCID: PMC9602378 DOI: 10.3390/genes13101813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
The transcriptional properties of artificial promoters are closely related to the type and arrangement position of cis-elements. GWSF (374-bp) was an effective SPIP with four cis-element dimers. There were four pathogen-inducible cis-elements in the GWSF promoter (GST1-boxes, W-boxes, S-boxes, and F-boxes) and a minimal cauliflower mosaic virus 35S promoter. V-element dimers were inserted into the upstream (VGWSF), midstream (GWVSF), and downstream (GWSFV) regions of the original GWSF promoter sequence to examine their affect on the position. The expression activity of promoters was analyzed and estimated using the histochemical staining of leaf discs of eucalyptus with transient expression, an image digitization method to extract the color features, and the induction treatment by a plant pathogenic microorganism/inducer and qPCR assays. The histochemical staining results of the adventitious buds indicated that the promoters had been successfully integrated into the E. urophylla genome and that they drove the expression of the gus gene. There was a noticeable difference in the intensity of color between the adventitious buds on the same callus block, as well as the intensity of color within the same adventitious bud. According to the established two-factor model of blue value, there was a greater difference between the levels of the genotype factor than the promoter factor in eucalyptus leaf discs. Further, the basal and inducible transcriptional levels of the three improved promoters were investigated by qPCR. With the basal transcriptional level of the GWSF promoter normalized to one, the relative basal levels of VGWSF, GWVSF, and GWSFV were 1.40, 1.45, and 4.15, respectively. The qPCR results were consistent with the staining results of GUS histochemical staining. The three improved promoters all had the properties of being induced by salicylic acid, Ralstonia solanacearum, and Phytophthora capsici. The three improved promoters demonstrated a significantly higher TMV induction activity: their induction activity from high to low was GWSFV > GWVSF > VGWSF. The findings will be beneficial to the construction and optimization of artificial promoters for transgenic plants.
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Affiliation(s)
- Zhenchi Huang
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China
| | - Qingchun Xu
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China
| | - Xiaolan Fang
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China
| | - Zhihua Wu
- Research Institute of Fast-Growing Trees, Chinese Academy of Forestry, Zhanjiang 524022, China
- Correspondence: ; Tel./Fax: +86-0759-3382-262 or +86-0759-3380-674
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Zhang T, Xiang Y, Geng L, Jiang W, Cheng S, Zhao Y. A Non-Canonical MITE in the WOX11 Promoter Is Associated with Robust Crown Root development in Rice. PLANT & CELL PHYSIOLOGY 2022; 63:1052-1062. [PMID: 35727725 DOI: 10.1093/pcp/pcac075] [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: 10/27/2021] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The formation of tissues and organs in multicellular organisms is tightly controlled by transcriptional programs determined by temporal and spatial patterns of gene expression. As an important regulator of rice crown root development, WOX11 is essential for crown root formation and its transcript level is positively correlated with crown root biomass. However, how WOX11 is regulated during crown root primordium emergence and outgrowth still remains unknown. In this study, variations of the WOX11 genomic sequence were analyzed, and the highest genetic diversity was found within its promoter, which contained a non-canonical miniature inverted-repeat transposable element (ncMITE) sequence. Analysis of the WOX11 promoter-driven reporter gene GUS (β-glucuronidase) transgenic plants pWOX11(ncMITE+):GUS and pWOX11(ncMITE-):GUS uncovered higher GUS expression levels in crown roots of pWOX11(ncMITE+):GUS plants. Furthermore, pWOX11(ncMITE+):WOX11-FLAG in wox11 background could complement the crown root number and length compared to those of the wild type, while pWOX11(ncMITE-):WOX11-FLAG could not. These results suggested that the ncMITE was positively associated with WOX11 transcripts in rice crown roots. In addition, DNA methylation nearby the ncMITE region attenuated the activation effect of the ncMITE on WOX11 expression, which might also be the cause conferred to the root-specific expression of WOX11. This work provides novel insight into WOX11 expression regulation and reveals a promising target for genetic improvement of root architecture in rice.
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Affiliation(s)
- Ting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
- College of Bioengineering, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Wei Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Saifeng Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
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Genome-Wide Identification and Expression Analysis of RR-Type MYB-Related Transcription Factors in Tomato (Solanum lycopersicum L.). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Evidence have indicated that RR-type MYB-related transcription factors (TFs) are functionally diverse in regulating floral development, fruit development, leaf senescence, ABA response, and drought and salt responses. Several RR-type MYB-related TFs in Arabidopsis, Antirrhinum and rice are identified and characterized. However, the complete RR-type MYB-related family in tomato has not been studied to date. Here, a genome-wide identification of tomato RR-type MYB-related TFs (SlMYBR) was performed by bioinformatics analysis, and their expression patterns were analyzed. A total of thirteen SlMYBR genes, which were mainly distributed in the head or tail of the chromosome, were identified from tomato and were divided into three groups. Group II was all MYBR genes from eudicots without genes from monocots. For Group I and Group III, the phylogenetic tree was in accord with the evolutionary relationship of these species. SlMYBR proteins were unstable proteins and located in the nucleus. The promoters of SlMYBR contained multiple important cis-acting elements related to abiotic stress or hormone responses. SlMYBR genes had various temporal and spatial expression patterns. Experiments of spraying exogenous hormone demonstrated that the expression of most genes containing hormone response elements was changed, indicating that the expression patterns were associated with the amount of cis-acting elements. The comprehensive investigation of tomato SlMYBR genes in the present study helps to clearly understand the evolution of RR-type MYB-related TFs and provides a useful reference for the further functional study of SlMYBR genes in tomato.
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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12
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Huang D, Kosentka PZ, Liu W. Synthetic biology approaches in regulation of targeted gene expression. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102036. [PMID: 33930839 DOI: 10.1016/j.pbi.2021.102036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 05/15/2023]
Abstract
Synthetic biology approaches are highly sought-after to facilitate the regulation of targeted gene expression in plants for functional genomics research and crop trait improvement. To date, synthetic regulation of gene expression predominantly focuses at the transcription level via engineering of synthetic promoters and transcription factors, while pioneering examples have started to emerge for synthetic regulation of gene expression at the levels of mRNA stability, translation, and protein degradation. This review discusses recent advances in plant synthetic biology for the regulation of gene expression at multiple levels, and highlights their future directions.
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Affiliation(s)
- Debao Huang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Pawel Z Kosentka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA.
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13
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Khadanga B, Chanwala J, Sandeep IS, Dey N. Synthetic Promoters from Strawberry Vein Banding Virus (SVBV) and Dahlia Mosaic Virus (DaMV). Mol Biotechnol 2021; 63:792-806. [PMID: 34037929 DOI: 10.1007/s12033-021-00344-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/19/2021] [Indexed: 11/27/2022]
Abstract
We have constructed two intra-molecularly shuffled promoters, namely S100 and D100. The S100 recombinant promoter (621 bp) was generated by ligation of 250 bp long upstream activation sequence (UAS) of Strawberry vein banding virus (SV10UAS; - 352 to - 102 relative to TSS) with its 371 bp long TATA containing core promoter domain (SV10CP; - 352 to + 19). Likewise, 726 bp long D100 promoter was constructed by fusion of 170 bp long UAS of Dahlia mosaic virus (DaMV14UAS; - 203 to - 33) with its 556 bp long core promoter domain (DaMV4CP; - 474 to + 82). S100 and D100 promoters showed 1.8 and 2.2 times stronger activities than that of the CaMV35S promoter. The activity of the promoters is comparable to that of the CaMV35S2 promoter. Transcript analysis employing qRT-PCR and histochemical assays supported the above findings. Abscisic acid and salicylic acid induce the activity of the D100 promoter. Leaf protein obtained from Nicotiana tabacum plant expressing NSD2 gene (Nigella sativa L. defensin 2) driven by the D100 promoter showed antifungal activity against Alternaria alternata and Phoma exigua var. exigua and antibacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus. Strong S100 and D100 promoters have potential to become efficient candidates for plant metabolic engineering and molecular pharming.
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Affiliation(s)
- Badrinath Khadanga
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Jeky Chanwala
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - I Sriram Sandeep
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
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14
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Zhao C, Yaschenko A, Alonso JM, Stepanova AN. Leveraging synthetic biology approaches in plant hormone research. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101998. [PMID: 33476945 DOI: 10.1016/j.pbi.2020.101998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/20/2020] [Accepted: 12/25/2020] [Indexed: 05/18/2023]
Abstract
The study of plant hormones is critical to understanding development, physiology and interactions of plants with their environment. Synthetic biology holds promise to provide a new perspective and shed fresh light on the molecular mechanisms of plant hormone action and propel the design of novel biotechnologies. With the recent adoption of synthetic biology in plant sciences, exciting first examples of successful tool development and their applications in the area of plant hormone research are emerging, paving the way for new cadres to enter this promising field of science.
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Affiliation(s)
- Chengsong Zhao
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna Yaschenko
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
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15
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Noman M, Aysha J, Ketehouli T, Yang J, Du L, Wang F, Li H. Calmodulin binding transcription activators: An interplay between calcium signalling and plant stress tolerance. JOURNAL OF PLANT PHYSIOLOGY 2021; 256:153327. [PMID: 33302232 DOI: 10.1016/j.jplph.2020.153327] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 05/18/2023]
Abstract
In plants, next to the secondary messengers lies an array of signal relaying molecules among which Calmodulins convey the unequivocal alarms of calcium influxes to Calmodulin-Binding Transcription Activators (CAMTA). Upon reception, CAMTA transcription factors decode the calcium signatures by transcribing the genes corresponding to the specific stimulus, thus have direct/indirect engagement in the complex signalling crosstalk. CAMTA transcription factors make an important contribution to the genome of all eukaryotes, including plants, from Brassica napus (18) to Carica papaya (2), the number of CAMTA genes varies across the plant species, however they exhibit a similar evolutionarily conserved domain organization including a DNA-Binding Domain (CG-1), a Transcription Factor Immunoglobulin Binding Domain (TIG), a Calmodulin-Binding Domain (CaMBD/IQ) and several Ankyrin repeats. The regulatory region of CAMTA genes possess multiple stress-responsive cis motifs including ABRE, SARE, G-box, W-box, AuXRE, DRE and others. CAMTA TFs in Arabidopsis have been studied extensively, however in other plants (with a few exceptions), the evidence merely bases upon expression analyses. CAMTAs are reported to orchestrate biotic as well as abiotic stresses including those occurring due to water and temperature fluctuations as well as heavy metals, light and salinity. Through CG-1 domain, CAMTA TFs bind the CG-box in the promoter of their target genes and modulate their expression under adverse conditions. Here we present a glimpse of how calcium signatures are coded and decoded and translated into necessary responses. In addition, we have emphasized on exploitation of the multiple-stress responsive nature of CAMTAs in engineering plants with desired traits.
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Affiliation(s)
- Muhammad Noman
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun, Jilin Province 130118, PR China.
| | - Jameel Aysha
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun, Jilin Province 130118, PR China
| | - Toi Ketehouli
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun, Jilin Province 130118, PR China
| | - Jing Yang
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun, Jilin Province 130118, PR China
| | - Linna Du
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun, Jilin Province 130118, PR China
| | - Fawei Wang
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun, Jilin Province 130118, PR China
| | - Haiyan Li
- College of Tropical Crops, Hainan University, 570228, Haikou, China.
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Skopenkova VV, Egorova TV, Bardina MV. Muscle-Specific Promoters for Gene Therapy. Acta Naturae 2021; 13:47-58. [PMID: 33959386 PMCID: PMC8084301 DOI: 10.32607/actanaturae.11063] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Many genetic diseases that are responsible for muscular disorders have been described to date. Gene replacement therapy is a state-of-the-art strategy used to treat such diseases. In this approach, the functional copy of a gene is delivered to the affected tissues using viral vectors. There is an urgent need for the design of short, regulatory sequences that would drive a high and robust expression of a therapeutic transgene in skeletal muscles, the diaphragm, and the heart, while exhibiting limited activity in non-target tissues. This review focuses on the development and improvement of muscle-specific promoters based on skeletal muscle α-actin, muscle creatine kinase, and desmin genes, as well as other genes expressed in muscles. The current approaches used to engineer synthetic muscle-specific promoters are described. Other elements of the viral vectors that contribute to tissue-specific expression are also discussed. A special feature of this review is the presence of up-to-date information on the clinical and preclinical trials of gene therapy drug candidates that utilize muscle-specific promoters.
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Affiliation(s)
- V. V. Skopenkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - T. V. Egorova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
| | - M. V. Bardina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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17
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Liu K, Yang J, Ding S, Gao Y. Daisy Chain Topology Based Mammalian Synthetic Circuits for RNA-Only Delivery. ACS Synth Biol 2020; 9:269-282. [PMID: 31895544 DOI: 10.1021/acssynbio.9b00313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Owing to superior safety, the RNA-only delivery synthetic circuit is more suitable for cell-based medicine. Modules which possess matching inputs and outputs could be strung by daisy-chaining to compose RNA-only delivery synthetic gene circuits. In this study, we engineered well-characterized biological parts to construct composable modules, each of which could receive signals from the upstream module and transmit the processed signal to the next module using standard interfaces. Capsid-cNOT7, through which logic gates could be changed by merely changing the type of it, was used as the core element for logical process. Daisy chain topology was used to build RNA-only delivery mammalian synthetic circuits which possess validated functions such as fan out, protein sensing, drug sensing, light sensing, 2-input logic gate, 3-input logic gate, and volatile memory, providing a new method to simplify the design of RNA-only delivery synthetic circuits.
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Affiliation(s)
- Kaiyu Liu
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Yi Gao
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
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18
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Jameel A, Noman M, Liu W, Ahmad N, Wang F, Li X, Li H. Tinkering Cis Motifs Jigsaw Puzzle Led to Root-Specific Drought-Inducible Novel Synthetic Promoters. Int J Mol Sci 2020; 21:E1357. [PMID: 32085397 PMCID: PMC7072871 DOI: 10.3390/ijms21041357] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
Following an in-depth transcriptomics-based approach, we first screened out and analyzed (in silico) cis motifs in a group of 63 drought-inducible genes (in soybean). Six novel synthetic promoters (SynP14-SynP19) were designed by concatenating 11 cis motifs, ABF, ABRE, ABRE-Like, CBF, E2F-VARIANT, G-box, GCC-Box, MYB1, MYB4, RAV1-A, and RAV1-B (in multiple copies and various combination) with a minimal 35s core promoter and a 222 bp synthetic intron sequence. In order to validate their drought-inducibility and root-specificity, the designed synthetic assemblies were transformed in soybean hairy roots to drive GUS gene using pCAMBIA3301. Through GUS histochemical assay (after a 72 h 6% PEG6000 treatment), we noticed higher glucuronidase activity in transgenic hairy roots harboring SynP15, SynP16, and SynP18. Further screening through GUS fluorometric assay flaunted SynP16 as the most appropriate combination of efficient drought-responsive cis motifs. Afterwards, we stably transformed SynP15, SynP16, and SynP18 in Arabidopsis and carried out GUS staining as well as fluorometric assays of the transgenic plants treated with simulated drought stress. Consistently, SynP16 retained higher transcriptional activity in Arabidopsis roots in response to drought. Thus the root-specific drought-inducible synthetic promoters designed using stimulus-specific cis motifs in a definite fashion could be exploited in developing drought tolerance in soybean and other crops as well. Moreover, the rationale of design extends our knowledge of trial-and-error based cis engineering to construct synthetic promoters for transcriptional upgradation against other stresses.
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Affiliation(s)
| | | | | | | | | | - Xiaowei Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, China; (A.J.); (M.N.); (W.L.); (N.A.)
| | - Haiyan Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, China; (A.J.); (M.N.); (W.L.); (N.A.)
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