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Bhadouriya SL, Karamchandani AN, Nayak N, Mehrotra S, Mehrotra R. Artificially designed synthetic promoter for a high level of salt induction using a cis-engineering approach. Sci Rep 2024; 14:13657. [PMID: 38871942 DOI: 10.1038/s41598-024-64537-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
This work aimed to design a synthetic salt-inducible promoter using a cis-engineering approach. The designed promoter (PS) comprises a minimal promoter sequence for basal-level expression and upstream cis-regulatory elements (CREs) from promoters of salinity-stress-induced genes. The copy number, spacer lengths, and locations of CREs were manually determined based on their occurrence within native promoters. The initial activity profile of the synthesized PS promoter in transiently transformed N. tabacum leaves shows a seven-fold, five-fold, and four-fold increase in reporter GUS activity under salt, drought, and abscisic acid stress, respectively, at the 24-h interval, compared to the constitutive CaMV35S promoter. Analysis of gus expression in stable Arabidopsis transformants showed that the PS promoter induces over a two-fold increase in expression under drought or abscisic acid stress and a five-fold increase under salt stress at 24- and 48-h intervals, compared to the CaMV35S promoter. The promoter PS exhibits higher and more sustained activity under salt, drought, and abscisic acid stress compared to the constitutive CaMV35S.
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Affiliation(s)
- Sneha Lata Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa campus, Goa, India
| | - Arti Narendra Karamchandani
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa campus, Goa, India
| | - Namitha Nayak
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa campus, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa campus, Goa, India.
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa campus, Goa, India.
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Yang Y, Chaffin TA, Shao Y, Balasubramanian VK, Markillie M, Mitchell H, Rubio‐Wilhelmi MM, Ahkami AH, Blumwald E, Neal Stewart C. Novel synthetic inducible promoters controlling gene expression during water-deficit stress with green tissue specificity in transgenic poplar. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1596-1609. [PMID: 38232002 PMCID: PMC11123411 DOI: 10.1111/pbi.14289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/16/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Synthetic promoters may be designed using short cis-regulatory elements (CREs) and core promoter sequences for specific purposes. We identified novel conserved DNA motifs from the promoter sequences of leaf palisade and vascular cell type-specific expressed genes in water-deficit stressed poplar (Populus tremula × Populus alba), collected through low-input RNA-seq analysis using laser capture microdissection. Hexamerized sequences of four conserved 20-base motifs were inserted into each synthetic promoter construct. Two of these synthetic promoters (Syn2 and Syn3) induced GFP in transformed poplar mesophyll protoplasts incubated in 0.5 M mannitol solution. To identify effect of length and sequence from a valuable 20 base motif, 5' and 3' regions from a basic sequence (GTTAACTTCAGGGCCTGTGG) of Syn3 were hexamerized to generate two shorter synthetic promoters, Syn3-10b-1 (5': GTTAACTTCA) and Syn3-10b-2 (3': GGGCCTGTGG). These promoters' activities were compared with Syn3 in plants. Syn3 and Syn3-10b-1 were specifically induced in transient agroinfiltrated Nicotiana benthamiana leaves in water cessation for 3 days. In stable transgenic poplar, Syn3 presented as a constitutive promoter but had the highest activity in leaves. Syn3-10b-1 had stronger induction in green tissues under water-deficit stress conditions than mock control. Therefore, a synthetic promoter containing the 5' sequence of Syn3 endowed both tissue-specificity and water-deficit inducibility in transgenic poplar, whereas the 3' sequence did not. Consequently, we have added two new synthetic promoters to the poplar engineering toolkit: Syn3-10b-1, a green tissue-specific and water-deficit stress-induced promoter, and Syn3, a green tissue-preferential constitutive promoter.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
| | - Timothy A. Chaffin
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | | | - Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | - Hugh Mitchell
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | | | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWAUSA
| | - Eduardo Blumwald
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - C. Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
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3
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Bull T, Khakhar A. Design principles for synthetic control systems to engineer plants. PLANT CELL REPORTS 2023; 42:1875-1889. [PMID: 37789180 DOI: 10.1007/s00299-023-03072-z] [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: 02/21/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE Synthetic control systems have led to significant advancement in the study and engineering of unicellular organisms, but it has been challenging to apply these tools to multicellular organisms like plants. The ability to predictably engineer plants will enable the development of novel traits capable of alleviating global problems, such as climate change and food insecurity. Engineering predictable multicellular phenotypes will require the development of synthetic control systems that can precisely regulate how the information encoded in genomes is translated into phenotypes. Many efficient control systems have been developed for unicellular organisms. However, it remains challenging to use such tools to study or engineer multicellular organisms. Plants are a good chassis within which to develop strategies to overcome these challenges, thanks to their capacity to withstand large-scale reprogramming without lethality. Additionally, engineered plants have great potential for solving major societal problems. Here we briefly review the progress of control system development in unicellular organisms, and how that information can be leveraged to characterize control systems in plants. Further, we discuss strategies for developing control systems designed to regulate the expression of transgenes or endogenous loci and generate dosage-dependent or discrete traits. Finally, we discuss the utility that mathematical models of biological processes have for control system deployment.
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Affiliation(s)
- Tawni Bull
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
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Aditama R, Tanjung ZA, Aprilyanto V, Sudania WM, Utomo C, Liwang T. Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density. Comput Biol Chem 2023; 106:107931. [PMID: 37481844 DOI: 10.1016/j.compbiolchem.2023.107931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
Transcription control through cis-regulatory elements (CREs) is one of important regulators of gene expression. This study aimed to identify the location of CREs in oil palm (Elaeis guineensis Jacq.) using the combination of DNA free energy and single nucleotide polymorphism (SNP) density approaches. Promoter region sequences were extracted oil palm genome spanning from 1500 nucleotides (nt) upstream to 1000 nt downstream of every annotated transcription start sites (TSS). Free energy profiles of each promoter region were calculated using PromPredict software. Raw reads from the deep sequencing of 59 oil palm origins were used to calculate SNP density of each promoter region. The result showed that the average free energy (AFE) on the upstream region of TSS is about 1.5 kcal/mol higher compared to the downstream region. Using DNA free energy method, 16,281 regions of CREs were predicted. Most of predicted CREs was located between 1 and 500 nt upstream of TSS. Anti-correlation pattern between free energy and SNP density was observed on the predicted regions of CREs. This anti-correlated pattern was also observed on an experimentally determined promoter of the oil palm metallothionein gene, EgMSP1. Considering the increasing use of promoter information on plant biotechnology, an easy and accurate promoter prediction using the combination of free energy and SNP density method could be recommended.
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Affiliation(s)
- Redi Aditama
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Zulfikar Achmad Tanjung
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Victor Aprilyanto
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Widyartini Made Sudania
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
| | - Condro Utomo
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia.
| | - Tony Liwang
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk., Bogor 16810, Indonesia
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Ahkami AH. Systems biology of root development in Populus: Review and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111818. [PMID: 37567482 DOI: 10.1016/j.plantsci.2023.111818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.
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Affiliation(s)
- Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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Cheng L, Wei S, Liu K, Zhao X, Zhang J, Zhao Y. Identification of the inducible activity in the promoter of the soybean BBI-DII gene exposed to abiotic stress or abscisic acid. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:947-957. [PMID: 37649883 PMCID: PMC10462593 DOI: 10.1007/s12298-023-01342-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/12/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
The expression of the soybean Bowman-Birk proteinase isoinhibitor DII (BBI-DII) gene and the inducible activity of its promoter were studied under salt, drought, low temperature, and abscisic acid (ABA) exposure conditions. The BBI-DII gene was induced by salt, drought, low temperature, and ABA, and the relative expression levels were 103.09-, 107.01-, 17.25- and 27.24-fold, respectively, compared with the untreated control. The putative promoter, designated BP1 (- 1255 to + 872 bp), located 5'-upstream of the BBI-DII gene was cloned. The expression of the GUS gene in pCAM-BP1 transgenic tobacco plants was highest at 5 h after treatment with salt, drought, low temperature and ABA, especially under salt and drought. Using histochemical staining and fluorescence analysis of GUS, BP1 activity under salt and drought conditions after 5 h was 1.03 and 1.07-fold, respectively, compared with that of the CaMV35S promoter. Based on a 5' deletion analysis, the segment (+ 41 to + 474 bp) was the basal region that responded to salt and drought, whereas the segment (- 820 to + 41 bp) was the area that responded to increased salt and drought activity. The BP2 (- 820 to + 872) activities were 0.98- and 1.02-fold compared with that of BP1 under salt and drought conditions and was 435 bp shorter than BP1. The salt- and drought-inducible activities of the BP2 promoter in the roots, stems, and leaves of transgenic tobacco plants were stable. Taken together, BP2 is more suitable than the BP1 promoter for the study and molecular breeding of stress-resistant soybean plants.
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Affiliation(s)
- Lishu Cheng
- College of Life Science and Agroforestry, Qiqihar University, Wenhua Street, No. 42, Qiqihar, 161006 Heilongjiang China
| | - Shuang Wei
- College of Life Science and Agroforestry, Qiqihar University, Wenhua Street, No. 42, Qiqihar, 161006 Heilongjiang China
| | - Kuocheng Liu
- College of Life Science and Agroforestry, Qiqihar University, Wenhua Street, No. 42, Qiqihar, 161006 Heilongjiang China
| | - Xu Zhao
- Jilin Province Institute of Product Quality Supervision and Inspection, Changchun, 130022 China
| | - Jun Zhang
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161005 China
| | - Yan Zhao
- College of Life Science and Agroforestry, Qiqihar University, Wenhua Street, No. 42, Qiqihar, 161006 Heilongjiang China
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Jha UC, Nayyar H, Chattopadhyay A, Beena R, Lone AA, Naik YD, Thudi M, Prasad PVV, Gupta S, Dixit GP, Siddique KHM. Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration. FRONTIERS IN PLANT SCIENCE 2023; 14:1183505. [PMID: 37229109 PMCID: PMC10204772 DOI: 10.3389/fpls.2023.1183505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, Pulse Research Station, S.D. Agricultural University SK Nagar, SK Nagar, Gujarat, India
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University (KAU), Thiruvananthapuram, Kerala, India
| | - Ajaz A. Lone
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)-Kashmir, Srinagar, India
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Girish Prasad Dixit
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Kadambot H. M. Siddique
- The University of Western Australia (UWA) Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Li X, Niu G, Fan Y, Liu W, Wu Q, Yu C, Wang J, Xiao Y, Hou L, Jin D, Chen S, Hu R, Yang Y, Pei Y. Synthetic dual hormone-responsive promoters enable engineering of plants with broad-spectrum resistance. PLANT COMMUNICATIONS 2023:100596. [PMID: 36998212 PMCID: PMC10363552 DOI: 10.1016/j.xplc.2023.100596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/17/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In plant immunity, the mutually antagonistic hormones salicylic acid (SA) and jasmonic acid (JA) are implicated in resistance to biotrophic and necrotrophic pathogens, respectively. Promoters that can respond to both SA and JA signals are urgently needed to engineer plants with enhanced resistance to a broad spectrum of pathogens. However, few natural pathogen-inducible promoters are available for this purpose. To address this problem, we have developed a strategy to synthesize dual SA- and JA-responsive promoters by combining SA- and JA-responsive cis elements based on the interaction between their cognate trans-acting factors. The resulting promoters respond rapidly and strongly to both SA and Methyl Jasmonate (MeJA), as well as different types of phytopathogens. When such a synthetic promoter was used to control expression of an antimicrobial peptide, transgenic plants displayed enhanced resistance to a diverse range of biotrophic, necrotrophic, and hemi-biotrophic pathogens. A dual-inducible promoter responsive to the antagonistic signals auxin and cytokinin was generated in a similar manner, confirming that our strategy can be used for the design of other biotically or abiotically inducible systems.
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Affiliation(s)
- Xianbi Li
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Guoqing Niu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yanhua Fan
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Wenying Liu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Qian Wu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Chen Yu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Jian Wang
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yuehua Xiao
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Lei Hou
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Dan Jin
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Song Chen
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Rongyu Hu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yumei Yang
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yan Pei
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Beibei, Chongqing 400716, China; Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China.
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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: 12] [Impact Index Per Article: 12.0] [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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Zhao Y, Wei L, Wen S, Li H. Overexpression of the Liriodendron tulipifera BOP2 Gene ( LtuBOP2) Affects Leaf Margin Development in Transgenic Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24043262. [PMID: 36834696 PMCID: PMC9961763 DOI: 10.3390/ijms24043262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
BLADE-ON-PETIOLE 2 (BOP2) plays a pivotal role in leaf morphogenesis. Liriodendron tulipifera is a suitable model for exploring the molecular mechanisms underlying leaf serration formation, which are largely unknown. Here, we isolated the full-length LtuBOP2 gene and its promoter from L. tulipifera and characterized its function in leaf morphogenesis through multidimensional approaches. The spatiotemporal expression pattern of LtuBOP2 indicated the high expression of LtuBOP2 in stems and leaf buds. We constructed LtuBOP2 promoter, fused the promoter sequences to the β-glucuronidase (GUS) gene, and then transformed them into Arabidopsis thaliana. Histochemical GUS staining results indicated that GUS activity was higher in petioles and the main vein. LtuBOP2 overexpression in A. thaliana caused moderate serration in the leaf tip, owing to the increased number of abnormal lamina epidermal cells and defective vascular tissue, thus indicating a novel role of BOP2. The ectopic expression of LtuBOP2 in A. thaliana promoted the expression of the lateral organ boundary gene ASYMMETRIC LEAVES2 (AS2) and inhibited JAGGED (JAG) and CUP-SHAPED COTYLEDON2 (CUC2) expression to establish leaf proximal-distal polarity. Moreover, LtuBOP2 participated in leaf serration formation by promoting the antagonistic relationship between KNOX I and hormones during leaf margin development. Our findings revealed the role of LtuBOP2 in the proximal-distal polarity formation and development of leaf margin morphology, providing new insights into the regulatory mechanisms of the leaf formation development of L. tulipifera.
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Affiliation(s)
- Yanqing Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Lingmin Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Shaoying Wen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-025-8542-8731
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12
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Sherpa T, Jha DK, Kumari K, Chanwala J, Dey N. Synthetic sub-genomic transcript promoter from Horseradish Latent Virus (HRLV). PLANTA 2023; 257:40. [PMID: 36653682 DOI: 10.1007/s00425-023-04066-7] [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: 11/29/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
We characterized an efficient chimeric sub-genomic transcript promoter from Horseradish Latent Virus, FHS4, active in both dicot and monocot plants, and it could be a potential tool for plant biotechnology. Plant pararetroviruses are a rich source of novel plant promoters widely used for biotechnological applications. Here, we comprehensively characterized a unique sub-genomic transcript (Sgt) promoter of Horseradish Latent Virus (HRLV) and identified a fragment (HS4; - 340 to + 10; 351 bp) that showed the highest expression of reporter genes in both transient and transgenic assays as evidenced by biochemical, histochemical GUS reporter assay and transcript analysis of uidA gene by qRT-PCR. Phylogenetic analysis showed that the HSgt promoter was closely related to the sub-genomic promoter of the Cauliflower Mosaic Virus (CaMV19S). We found that the as-1 element and W-box played an important role in the transcriptional activity of the HS4 promoter. Furthermore, the HS4 promoter was also induced by salicylic acid. Alongside, we enhanced the activity of the HS4 promoter by coupling the enhancer region from Figwort Mosaic Virus (FMV) promoter to the upstream region of it. This hybrid promoter FHS4 was around 1.1 times stronger than the most commonly used promoter, 35S (Cauliflower Mosaic Virus full-length transcript promoter), and was efficient in driving reporter genes in both dicot and monocot plants. Subsequently, transgenic tobacco plants expressing an anti-microbial peptide BrLTP2.1 (Brassica rapa lipid transport protein 2.1), under the control of the FHS4 promoter, were developed. The in vitro anti-fungal assay revealed that the plant-derived BrLTP2.1 protein driven by an FHS4 promoter manifested increased resistance against an important plant fungal pathogen, Alternaria alternata. Finally, we concluded that the FHS4 promoter can be used as an alternative to the 35S promoter and has a high potential to become an efficient tool in plant biotechnology.
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Affiliation(s)
- Tsheten Sherpa
- Division of Plant Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Deepak Kumar Jha
- Division of Plant Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Khushbu Kumari
- Division of Plant Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Jeky Chanwala
- Division of Plant Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Nrisingha Dey
- Division of Plant Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
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13
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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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14
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Saeed S, Usman B, Shim SH, Khan SU, Nizamuddin S, Saeed S, Shoaib Y, Jeon JS, Jung KH. CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111435. [PMID: 36031021 DOI: 10.1016/j.plantsci.2022.111435] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.
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Affiliation(s)
- Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Babar Usman
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Su-Hyeon Shim
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Shahid Ullah Khan
- Department of Biochemistry, Women Medical and Dental College, Khyber Medical University KPK, Pakistan
| | - Sabzoi Nizamuddin
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Sundus Saeed
- School of Engineering, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Yasira Shoaib
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
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15
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Yang Y, Shao Y, Chaffin TA, Lee JH, Poindexter MR, Ahkami AH, Blumwald E, Stewart CN. Performance of abiotic stress-inducible synthetic promoters in genetically engineered hybrid poplar ( Populus tremula × Populus alba). FRONTIERS IN PLANT SCIENCE 2022; 13:1011939. [PMID: 36330242 PMCID: PMC9623294 DOI: 10.3389/fpls.2022.1011939] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 05/27/2023]
Abstract
Abiotic stresses can cause significant damage to plants. For sustainable bioenergy crop production, it is critical to generate resistant crops to such stress. Engineering promoters to control the precise expression of stress resistance genes is a very effective way to address the problem. Here we developed stably transformed Populus tremula × Populus alba hybrid poplar (INRA 717-1B4) containing one-of-six synthetic drought stress-inducible promoters (SDs; SD9-1, SD9-2, SD9-3, SD13-1, SD18-1, and SD18-3) identified previously by transient transformation assays. We screened green fluorescent protein (GFP) induction in poplar under osmotic stress conditions. Of six transgenic lines containing synthetic promoter, three lines (SD18-1, 9-2, and 9-3) had significant GFP expression in both salt and osmotic stress treatments. Each synthetic promoter employed heptamerized repeats of specific and short cis-regulatory elements (7 repeats of 7-8 bases). To verify whether the repeats of longer sequences can improve osmotic stress responsiveness, a transgenic poplar containing the synthetic promoter of the heptamerized entire SD9 motif (20 bases, containing all partial SD9 motifs) was generated and measured for GFP induction under osmotic stress. The heptamerized entire SD9 motif did not result in higher GFP expression than the shorter promoters consisting of heptamerized SD9-1, 9-2, and 9-3 (partial SD9) motifs. This result indicates that shorter synthetic promoters (~50 bp) can be used for versatile control of gene expression in transgenic poplar. These synthetic promoters will be useful tools to engineer stress-resilient bioenergy tree crops in the future.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Yuanhua Shao
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Timothy A. Chaffin
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Jun Hyung Lee
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Magen R. Poindexter
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - C. Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
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16
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Moreno-Giménez E, Selma S, Calvache C, Orzáez D. GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants. ACS Synth Biol 2022; 11:3037-3048. [PMID: 36044643 PMCID: PMC9486966 DOI: 10.1021/acssynbio.2c00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 01/24/2023]
Abstract
Programmable transcriptional factors based on the CRISPR architecture are becoming commonly used in plants for endogenous gene regulation. In plants, a potent CRISPR tool for gene induction is the so-called dCasEV2.1 activation system, which has shown remarkable genome-wide specificity combined with a strong activation capacity. To explore the ability of dCasEV2.1 to act as a transactivator for orthogonal synthetic promoters, a collection of DNA parts was created (GB_SynP) for combinatorial synthetic promoter building. The collection includes (i) minimal promoter parts with the TATA box and 5'UTR regions, (ii) proximal parts containing single or multiple copies of the target sequence for the gRNA, thus functioning as regulatory cis boxes, and (iii) sequence-randomized distal parts that ensure the adequate length of the resulting promoter. A total of 35 promoters were assembled using the GB_SynP collection, showing in all cases minimal background and predictable activation levels depending on the proximal parts used. GB_SynP was also employed in a combinatorial expression analysis of an autoluminescence pathway in Nicotiana benthamiana, showing the value of this tool in extracting important biological information such as the determination of the limiting steps in an enzymatic pathway.
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Affiliation(s)
- Elena Moreno-Giménez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Sara Selma
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Camilo Calvache
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Diego Orzáez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
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17
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Sultana MS, Mazarei M, Millwood RJ, Liu W, Hewezi T, Stewart CN. Functional analysis of soybean cyst nematode-inducible synthetic promoters and their regulation by biotic and abiotic stimuli in transgenic soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2022; 13:988048. [PMID: 36160998 PMCID: PMC9501883 DOI: 10.3389/fpls.2022.988048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
We previously identified cis-regulatory motifs in the soybean (Glycine max) genome during interaction between soybean and soybean cyst nematode (SCN), Heterodera glycines. The regulatory motifs were used to develop synthetic promoters, and their inducibility in response to SCN infection was shown in transgenic soybean hairy roots. Here, we studied the functionality of two SCN-inducible synthetic promoters; 4 × M1.1 (TAAAATAAAGTTCTTTAATT) and 4 × M2.3 (ATATAATTAAGT) each fused to the -46 CaMV35S core sequence in transgenic soybean. Histochemical GUS analyses of transgenic soybean plants containing the individual synthetic promoter::GUS construct revealed that under unstressed condition, no GUS activity is present in leaves and roots. While upon nematode infection, the synthetic promoters direct GUS expression to roots predominantly in the nematode feeding structures induced by the SCN and by the root-knot nematode (RKN), Meloidogyne incognita. There were no differences in GUS activity in leaves between nematode-infected and non-infected plants. Furthermore, we examined the specificity of the synthetic promoters in response to various biotic (insect: fall armyworm, Spodoptera frugiperda; and bacteria: Pseudomonas syringe pv. glycinea, P. syringe pv. tomato, and P. marginalis) stresses. Additionally, we examined the specificity to various abiotic (dehydration, salt, cold, wounding) as well as to the signal molecules salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) in the transgenic plants. Our wide-range analyses provide insights into the potential applications of synthetic promoter engineering for conditional expression of transgenes leading to transgenic crop development for resistance improvement in plant.
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Affiliation(s)
- Mst Shamira Sultana
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Reginald J. Millwood
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
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18
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Fragoso RR, Arraes FBM, Lourenço-Tessutti IT, Miranda VJ, Basso MF, Ferreira AVJ, Viana AAB, Lins CBJ, Lins PC, Moura SM, Batista JAN, Silva MCM, Engler G, Morgante CV, Lisei-de-Sa ME, Vasques RM, de Almeida-Engler J, Grossi-de-Sa MF. Functional characterization of the pUceS8.3 promoter and its potential use for ectopic gene overexpression. PLANTA 2022; 256:69. [PMID: 36066773 DOI: 10.1007/s00425-022-03980-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
The pUceS8.3 is a constitutive gene promoter with potential for ectopic and strong genes overexpression or active biomolecules in plant tissues attacked by pests, including nematode-induced giant cells or galls. Soybean (Glycine max) is one of the most important agricultural commodities worldwide and a major protein and oil source. Herein, we identified the soybean ubiquitin-conjugating (E2) enzyme gene (GmUBC4; Glyma.18G216000), which is significantly upregulated in response to Anticarsia gemmatalis attack and Meloidogyne incognita-induced galls during plant parasitism by plant nematode. The GmUBC4 promoter sequence and its different modules were functionally characterized in silico and in planta using transgenic Arabidopsis thaliana and G. max lines. Its full-length transcriptional regulatory region (promoter and 5´-UTR sequences, named pUceS8.3 promoter) was able to drive higher levels of uidA (β-glucuronidase) gene expression in different tissues of transgenic A. thaliana lines compared to its three shortened modules and the p35SdAMV promoter. Notably, higher β-glucuronidase (GUS) enzymatic activity was shown in M. incognita-induced giant cells when the full pUceS8.3 promoter drove the expression of this reporter gene. Furthermore, nematode-specific dsRNA molecules were successfully overexpressed under the control of the pUceS8.3 promoter in transgenic soybean lines. The RNAi gene construct used here was designed to post-transcriptionally downregulate the previously characterized pre-mRNA splicing factor genes from Heterodera glycines and M. incognita. A total of six transgenic soybean lines containing RNAi gene construct were selected for molecular characterization after infection with M. incognita pre-parasitic second-stage (ppJ2) nematodes. A strong reduction in the egg number produced by M. incognita after parasitism was observed in those transgenic soybean lines, ranging from 71 to 92% compared to wild-type control plants. The present data demonstrated that pUceS8.3 is a gene promoter capable of effectively driving dsRNA overexpression in nematode-induced giant cells of transgenic soybean lines and can be successfully applied as an important biotechnological asset to generate transgenic crops with improved resistance to root-knot nematodes as well as other pests.
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Affiliation(s)
- Rodrigo Rocha Fragoso
- Embrapa Savannah, Planaltina, DF, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Fabricio Barbosa Monteiro Arraes
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Vívian Jesus Miranda
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Marcos Fernando Basso
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | | | | | - Camila Barrozo Jesus Lins
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Philippe Castro Lins
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Stéfanie Menezes Moura
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - João Aguiar Nogueira Batista
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Federal University of Minas Gerais, Belo Horizonte-MG, Brazil
| | - Maria Cristina Mattar Silva
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Gilbert Engler
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
| | - Carolina Vianna Morgante
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Embrapa Semiarid, Petrolina-PE, Brazil
| | - Maria Eugênia Lisei-de-Sa
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Minas Gerais Agricultural Research Company (EPAMIG), Uberaba-MG, Brazil
| | - Raquel Medeiros Vasques
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Janice de Almeida-Engler
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil.
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil.
- Catholic University of Brasilia, Brasília-DF, Brazil.
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19
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Kim HM, Park SH, Park SY, Ma SH, Do JH, Kim AY, Jeon MJ, Shim JS, Joung YH. Identification of essential element determining fruit-specific transcriptional activity in the tomato HISTIDINE DECARBOXYLASE A gene promoter. PLANT CELL REPORTS 2022; 41:1721-1731. [PMID: 35739429 DOI: 10.1007/s00299-022-02886-7] [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: 11/08/2021] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
In SlHDC-A promoter, SlHDC-A core-ES is an essential region for fruit-specific expression and interacts with GATA, HSF and AP1. Triplication of essential region was proposed as a minimal fruit-specific promoter. In plant biotechnology, fruit-specific promoter is an important tool for the improvement and utilization of tomato fruit. To expand our understanding on fruit-specific expression, it is necessary to determine the promoter region involved in fruit-specific transcriptional activity and transcriptional regulations of the promoter. In previous study, we isolated a fruit-specific SlHDC-A core promoter specifically expressed during tomato ripening stages. In this study, we identified SlHDC-A promoter region (SlHDC-A core-ES) that is essential for fruit-specific expression of the SlHDC-A. To understand the molecular mechanisms of fruit-specific expression of the SlHDC-A promoter, we first identified the putative transcription factor binding elements in the SlHDC-A core promoter region and corresponding putative transcription factors which are highly expressed during fruit maturation. Yeast one hybrid analysis confirmed that GATA, HSF, and AP1 interact with the SlHDC-A core-ES promoter region. Further transactivation analysis revealed that expression of the three transcription factors significantly activated expression of a reporter gene driven by SlHDC-A core-ES promoter. These results suggest that GATA, HSF, and AP1 are involved in the fruit-specific expression of SlHDC-A promoter. Furthermore, the synthetic promoter composed of three tandem repeats of SlHDC-A core-ES showed relatively higher activity than the constitutive 35S promoter in the transgenic tomato fruits at the orange stage. Taken together, we propose a new synthetic promoter that is specifically expressed during fruit ripening stage.
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Affiliation(s)
- Hyun Min Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Se Hee Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seo Young Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Sang Hoon Ma
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ju Hui Do
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ah Young Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Young Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters. PLANTS 2022; 11:plants11141861. [PMID: 35890495 PMCID: PMC9318348 DOI: 10.3390/plants11141861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. These compounds have a complex biosynthetic pathway, whose first rate limiting enzyme is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). In the present study, a new 1646 bp fragment of the S. miltiorrhiza HMGR4 gene consisting of a promoter, 5′ untranslated region and part of a coding sequence was isolated and characterised in silico using bioinformatics tools. The results indicate the presence of a TATA box, tandem repeat and pyrimidine-rich sequence, and the absence of CpG islands. The sequence was rich in motifs recognised by specific transcription factors sensitive mainly to light, salicylic acid, bacterial infection and auxins; it also demonstrated many binding sites for microRNAs. Moreover, our results suggest that HMGR4 expression is possibly regulated during flowering, embryogenesis, organogenesis and the circadian rhythm. The obtained data were verified by comparison with microarray co-expression results obtained for Arabidopsis thaliana. Alignment of the isolated HMGR4 sequence with other plant HMGRs indicated the presence of many common binding sites for transcription factors, including conserved ones. Our findings provide valuable information for understanding the mechanisms that direct transcription of the S. miltiorrhiza HMGR4 gene.
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21
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de Moura SM, Freitas EO, Ribeiro TP, Paes-de-Melo B, Arraes FBM, Macedo LLP, Paixão JFR, Lourenço-Tessutti IT, Artico S, da Cunha Valença D, Silva MCM, de Oliveira AC, Alves-Ferreira M, Grossi-de-Sa MF. Discovery and functional characterization of novel cotton promoters with potential application to pest control. PLANT CELL REPORTS 2022; 41:1589-1601. [PMID: 35665839 DOI: 10.1007/s00299-022-02880-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
pGhERF105 and pGhNc-HARBI1 promoters are highly responsive to CBW infestation and exhibit strong activity in vegetative and reproductive tissues, increasing their potential application in GM crop plants for pest control. The main challenge to cotton (Gossypium hirsutum) crop productivity is the constant attack of several pests, including the cotton boll weevil (CBW, Anthonomus grandis), which uses cotton floral buds for feeding and egg-laying. The endophytic nature of the early developmental stages of CBW makes conventional pesticide-based control poorly efficient. Most biotechnological assets used for pest control are based on Bacillus thurigiensis insecticidal Cry toxins or the silencing of insect-pest essential genes using RNA-interference technology. However, suitable plant promoter sequences are required to efficiently drive insecticidal molecules to the target plant tissue. This study selected the Ethylene Responsive Factor 105 (GhERF105) and Harbinger transposase-derived nuclease (GhNc-HARBI1) genes based on available transcriptome-wide data from cotton plants infested by CBW larvae. The GhERF105 and GhNc-HARBI1 genes showed induction kinetics from 2 to 96 h under CBW's infestation in cotton floral buds, uncovering the potential application of their promoters. Therefore, the promoter regions (1,500 base pairs) were assessed and characterized using Arabidopsis thaliana transgenic plants. The pGhERF105 and pGhNc-HARBI1 promoters showed strong activity in plant vegetative (leaves and roots) and reproductive (flowers and fruits) tissues, encompassing higher GUS transcriptional activity than the viral-constitutive Cauliflower Mosaic Virus 35S promoter (pCaMV35S). Notably, pGhERF105 and pGhNc-HARBI1 promoters demonstrated more efficiency in driving reporter genes in flowers than other previously characterized cotton flower-specific promoters. Overall, the present study provides a new set of cotton promoters suitable for biotechnological application in cotton plants for pest resistance.
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Affiliation(s)
- Stéfanie Menezes de Moura
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Elinea Oliveira Freitas
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- Federal University of Brasilia (UnB), Brasília, DF, Brazil
| | - Thuanne Pires Ribeiro
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
- Federal University of Brasilia (UnB), Brasília, DF, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Fabrício B M Arraes
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
- Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Leonardo Lima Pepino Macedo
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Joaquin F R Paixão
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
| | - Isabela T Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Sinara Artico
- Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - David da Cunha Valença
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
| | - Maria Cristina Mattar Silva
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
| | - Antonio C de Oliveira
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
- Federal University of Pelotas (UFPEL), Pelotas, RS, Brazil
| | - Marcio Alves-Ferreira
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil
- Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB, Final W5 North, PO Box 02372, Brasília, DF, 70770-917, Brazil.
- National Institute of Science and Technology, INCT PlantStress Biotech, EMBRAPA, Brasília, DF, Brazil.
- Catholic University of Brasília (UCB), Brasília, DF, Brazil.
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22
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Sethi L, Sherpa T, Kumari K, Dey N. Further Characterization of MUAS35SCP and FUAS35SCP Recombinant Promoters and Their Implication in Translational Research. Mol Biotechnol 2022; 64:1356-1366. [PMID: 35641838 DOI: 10.1007/s12033-022-00513-0] [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: 12/28/2021] [Accepted: 05/11/2022] [Indexed: 11/24/2022]
Abstract
Recombinant promoters are of high value in translational research. Earlier, we developed two recombinant promoters, namely MUAS35SCP and FUAS35SCP, and their transcriptional activities were found to be stronger than that of the most widely used CaMV35S promoter in dicot plants. Presently, we are reporting constitutive expression of both GUS and GFP reporters under the control of these promoters in several monocots, including rice, wheat, and pearl millet. We observed that these promoters could express the reporter genes constitutively, and their expression abilities were almost equal to that of the CaMV35S2 promoter. Plant-derived enriched PaDef (Persea americana var. drymifolia defensin) and NsDef2 (Nigella sativa L. defensin 2) antimicrobial peptides expressed under the control of these promoters arrest the growth of devastating phytopathogens like Pseudomonas syringae, Rhodococcus fascians, and Alternaria alternata. We observed that plant-derived NsDef2 and PaDef under control of these promoters showed approximately 80-90% inhibitory activity against Pseudomonas syringae. Hence, these promoters were constitutive and universal, as they can drive the expression of transgenes in both dicot and monocot plants. Alongside, these promoters could become a valuable tool for raising genetically modified plants with in-built resistance toward phytopathogens.
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Affiliation(s)
- Lini Sethi
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.,Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Tsheten Sherpa
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.,Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Khushbu Kumari
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.,Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
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23
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Sun Y, Hu D, Xue P, Wan X. Identification of the DcHsp20 gene family in carnation (Dianthus caryophyllus) and functional characterization of DcHsp17.8 in heat tolerance. PLANTA 2022; 256:2. [PMID: 35624182 DOI: 10.1007/s00425-022-03915-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 05/09/2023]
Abstract
33 heat shock protein 20 (Hsp20) genes were identified from the carnation genome whose expression were altered by abiotic stresses. DcHsp17.8 may function to improve the heat resistance of Arabidopsis. Heat shock proteins 20 (Hsp20s) mainly function as molecular chaperones that play crucial roles in relieving abiotic stresses such as heat stress. In this study, we identified and characterized 33 DcHsp20 genes from the carnation genome that were classified into 9 subfamilies. Gene structure analysis showed that 25 DcHsp20 genes contained 1 intron whilst the remaining 8 DcHsp20 genes did not contain introns. Motif analysis found that DcHsp20 proteins were relatively conserved. Cis-regulatory elements analysis of the Hsp20 promoters revealed a number of cis-regulatory elements that regulate growth and development, hormone and stress responses. Gene expression analysis revealed that DcHsp20 genes had multiple response patterns to heat stress. The largest range of induction occurred in DcHsp17.8 after 1 h of heat stress. Under cold stress, or treatment with saline or abscisic acid, the expression of most DcHsp20 genes was inhibited. To further understand the function of DcHsp20 genes in response to heat stress, we overexpressed DcHsp17.8 in Arabidopis and the plants showed improved heat tolerance, O2- and H2O2 activities and photosynthetic capacity with reduced relative electrolyte leakage and malondialdehyde content. Gene expression analysis revealed that DcHsp17.8 modulated the expression of genes involved in antioxidant enzyme synthesis. Our data provided a solid foundation for the further detailed study of DcHsp20 genes.
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Affiliation(s)
- Yuying Sun
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China
| | - Diandian Hu
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China
| | - Pengcheng Xue
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China
| | - Xueli Wan
- College of Landscape and Forestry, Qingdao Agricultural University, No.100, Changcheng Road, Chengyang District, Qingdao, 266109, Shandong, People's Republic of China.
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Hairy CRISPR: Genome Editing in Plants Using Hairy Root Transformation. PLANTS (BASEL, SWITZERLAND) 2021; 11:51. [PMID: 35009056 PMCID: PMC8747350 DOI: 10.3390/plants11010051] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 05/27/2023]
Abstract
CRISPR/Cas-mediated genome editing is a powerful tool of plant functional genomics. Hairy root transformation is a rapid and convenient approach for obtaining transgenic roots. When combined, these techniques represent a fast and effective means of studying gene function. In this review, we outline the current state of the art reached by the combination of these approaches over seven years. Additionally, we discuss the origins of different Agrobacterium rhizogenes strains that are widely used for hairy root transformation; the components of CRISPR/Cas vectors, such as the promoters that drive Cas or gRNA expression, the types of Cas nuclease, and selectable and screenable markers; and the application of CRISPR/Cas genome editing in hairy roots. The modification of the already known vector pKSE401 with the addition of the rice translational enhancer OsMac3 and the gene encoding the fluorescent protein DsRed1 is also described.
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Affiliation(s)
- Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
| | - Elena L. Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
| | - Elizaveta D. Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
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25
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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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26
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Yang Y, Lee JH, Poindexter MR, Shao Y, Liu W, Lenaghan SC, Ahkami AH, Blumwald E, Stewart CN. Rational design and testing of abiotic stress-inducible synthetic promoters from poplar cis-regulatory elements. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1354-1369. [PMID: 33471413 PMCID: PMC8313130 DOI: 10.1111/pbi.13550] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/31/2020] [Accepted: 01/09/2021] [Indexed: 05/27/2023]
Abstract
Abiotic stress resistance traits may be especially crucial for sustainable production of bioenergy tree crops. Here, we show the performance of a set of rationally designed osmotic-related and salt stress-inducible synthetic promoters for use in hybrid poplar. De novo motif-detecting algorithms yielded 30 water-deficit (SD) and 34 salt stress (SS) candidate DNA motifs from relevant poplar transcriptomes. We selected three conserved water-deficit stress motifs (SD18, SD13 and SD9) found in 16 co-expressed gene promoters, and we discovered a well-conserved motif for salt response (SS16). We characterized several native poplar stress-inducible promoters to enable comparisons with our synthetic promoters. Fifteen synthetic promoters were designed using various SD and SS subdomains, in which heptameric repeats of five-to-eight subdomain bases were fused to a common core promoter downstream, which, in turn, drove a green fluorescent protein (GFP) gene for reporter assays. These 15 synthetic promoters were screened by transient expression assays in poplar leaf mesophyll protoplasts and agroinfiltrated Nicotiana benthamiana leaves under osmotic stress conditions. Twelve synthetic promoters were induced in transient expression assays with a GFP readout. Of these, five promoters (SD18-1, SD9-2, SS16-1, SS16-2 and SS16-3) endowed higher inducibility under osmotic stress conditions than native promoters. These five synthetic promoters were stably transformed into Arabidopsis thaliana to study inducibility in whole plants. Herein, SD18-1 and SD9-2 were induced by water-deficit stress, whereas SS16-1, SS16-2 and SS16-3 were induced by salt stress. The synthetic biology design pipeline resulted in five synthetic promoters that outperformed endogenous promoters in transgenic plants.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Magen R. Poindexter
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Wusheng Liu
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNCUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL)Pacific Northwest National Laboratory (PNNL)RichlandWAUSA
| | | | - Charles Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
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27
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Anjanappa RB, Gruissem W. Current progress and challenges in crop genetic transformation. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153411. [PMID: 33872932 DOI: 10.1016/j.jplph.2021.153411] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 05/14/2023]
Abstract
Plant transformation remains the most sought-after technology for functional genomics and crop genetic improvement, especially for introducing specific new traits and to modify or recombine already existing traits. Along with many other agricultural technologies, the global production of genetically engineered crops has steadily grown since they were first introduced 25 years ago. Since the first transfer of DNA into plant cells using Agrobacterium tumefaciens, different transformation methods have enabled rapid advances in molecular breeding approaches to bring crop varieties with novel traits to the market that would be difficult or not possible to achieve with conventional breeding methods. Today, transformation to produce genetically engineered crops is the fastest and most widely adopted technology in agriculture. The rapidly increasing number of sequenced plant genomes and information from functional genomics data to understand gene function, together with novel gene cloning and tissue culture methods, is further accelerating crop improvement and trait development. These advances are welcome and needed to make crops more resilient to climate change and to secure their yield for feeding the increasing human population. Despite the success, transformation remains a bottleneck because many plant species and crop genotypes are recalcitrant to established tissue culture and regeneration conditions, or they show poor transformability. Improvements are possible using morphogenetic transcriptional regulators, but their broader applicability remains to be tested. Advances in genome editing techniques and direct, non-tissue culture-based transformation methods offer alternative approaches to enhance varietal development in other recalcitrant crops. Here, we review recent developments in plant transformation and regeneration, and discuss opportunities for new breeding technologies in agriculture.
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Affiliation(s)
- Ravi B Anjanappa
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland; Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung City 402, Taiwan.
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28
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Sethi L, Deb D, Khadanga B, Dey N. Synthetic promoters from blueberry red ringspot virus (BRRV). PLANTA 2021; 253:121. [PMID: 33993348 DOI: 10.1007/s00425-021-03624-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION We analyzed the synthetic full-length transcript promoter of Blueberry red ringspot virus (BRRV) and developed two chimeric promoters (MBR3 and FBR3). Transcriptional activities of these chimeric promoters were found equivalent to that of the CaMV35S2 promoter. Chimeric promoters driven plant-derived PaDef protein showed high antimicrobial activities against several pathogens. Blueberry red ringspot virus (BRRV) is a pararetrovirus under the genus, Soymovirus belongs to the Caulimoviridae family. We have made a synthetic version of the BRRV-Flt promoter and analyzed its activity in detail. A 372 bp promoter fragment BR3 (- 212 to + 160) showed the strongest transcriptional activity compared with other fragments in both transient and transgenic assays; its activity was found near equivalent to that of the CaMV35S promoter. We constructed two chimeric promoters; MBR3 and FBR3 by fusing the UASs (Upstream activation sequences) of Mirabilis mosaic virus (MUAS; - 297 to - 38; 335 bp) and Figwort mosaic virus (FUAS; - 249 to - 54; 303 bp) respectively to the core promoter domain of BR3 (BR3; - 212 to + 160; 372 bp). The activities of MBR3 and FBR3 promoters were found equivalent to that of the activity of the CaMV35S2 promoter and approximately 4.0 (four) times stronger than that of the CaMV35S promoter. Histochemical and fluorometric GUS assays confirmed the above observation. The transcriptional efficacies of these recombinant promoters were tested by evaluating the antibacterial and antifungal activities of recombinant plant-derived antimicrobial peptide Persea americana var. drymifolia defensin (PaDef) driven under these promoters. Bioassays showed promising antifungal activities of the plant made PaDef against Alternaria alternata and antibacterial property against Gram-positive (S. aureus and R. fascians) and Gram-negative bacteria (E. coli and P. aeruginosa). Based upon the above results, MBR3 and FBR3 could be useful promoters for plant genetic engineering and can become useful substitutes for the widely used CaMV35S2 promoter in plant biology.
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Affiliation(s)
- Lini Sethi
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Debasish Deb
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Badrinath Khadanga
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
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Vlahoviček-Kahlina K, Jurić S, Marijan M, Mutaliyeva B, Khalus SV, Prosyanik AV, Vinceković M. Synthesis, Characterization, and Encapsulation of Novel Plant Growth Regulators (PGRs) in Biopolymer Matrices. Int J Mol Sci 2021; 22:1847. [PMID: 33673329 PMCID: PMC7918939 DOI: 10.3390/ijms22041847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Novel plant growth regulators (PGRs) based on the derivatives of dehydroamino acids 2,3-dehydroaspartic acid dimethyl ester (PGR1), Z-isomer of the potassium salt of 2-amino-3-methoxycarbonylacrylic acid (PGR2) and 1-methyl-3-methylamino-maleimide (PGR3) have been synthesized and their growth-regulating properties investigated. Laboratory testing revealed their plant growth-regulating activity. PGR1 showing the most stimulating activity on all laboratory tested cultures were used in field experiments. Results showed that PGR1 is a highly effective environmentally friendly plant growth regulator with effects on different crops. Biopolymeric microcapsule formulations (chitosan/alginate microcapsule loaded with PGR) suitable for application in agriculture were prepared and characterized. Physicochemical properties and release profiles of PGRs from microcapsule formulations depend on the molecular interactions between microcapsule constituents including mainly electrostatic interactions and hydrogen bonds. The differences in the microcapsule formulations structure did not affect the mechanism of PGRs release which was identified as diffusion through microcapsules. The obtained results opened a perspective for the future use of microcapsule formulations as new promising agroformulations with a sustained and target release for plant growth regulation.
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Affiliation(s)
- Kristina Vlahoviček-Kahlina
- Department of Chemistry, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (K.V.-K.); (S.J.); (M.M.)
| | - Slaven Jurić
- Department of Chemistry, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (K.V.-K.); (S.J.); (M.M.)
| | - Marijan Marijan
- Department of Chemistry, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (K.V.-K.); (S.J.); (M.M.)
| | - Botagoz Mutaliyeva
- Biotechnology Department, M. Auezov South-Kazakhstan University, Tauke-Khan, 160000 Shymkent, Kazakhstan;
| | - Svetlana V. Khalus
- Ukrainian State University of Chemical Technology, Gagarina, 49000 Dnipro, Ukraine; (S.V.K.); (A.V.P.)
| | - Alexander V. Prosyanik
- Ukrainian State University of Chemical Technology, Gagarina, 49000 Dnipro, Ukraine; (S.V.K.); (A.V.P.)
| | - Marko Vinceković
- Department of Chemistry, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (K.V.-K.); (S.J.); (M.M.)
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Gupta D, Dey N, Leelavathi S, Ranjan R. Development of efficient synthetic promoters derived from pararetrovirus suitable for translational research. PLANTA 2021; 253:42. [PMID: 33475866 DOI: 10.1007/s00425-021-03565-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION In this study, useful hybrid promoters were developed for efficient ectopic gene expression in monocot and dicot plants, and they hold strong prominence in both transgenic research and biotech industries. This study deals with developing novel synthetic promoters derived from Rice Tungro Bacilliform Virus (RTBV) and Mirabilis Mosaic Virus (MMV). Despite numerous availability, there is a severe scarcity of promoters universally suitable for monocot and dicot plants. Here, eight chimeric promoter constructs were synthesized as gBlocks gene fragments through domain swapping and hybridization by incorporating important domains of previously characterized RTBV and MMV promoters. The developed promoter constructs were assessed for transient GUS expression in tobacco protoplast (Xanthi Brad) and agro-infiltrated tobacco, petunia, rice and pearl millet. Protoplast expression analysis showed that two promoter constructs, namely pUPMA-RP1-MP1GUS and pUPMA-RP4-MP1GUS exhibited 3.56 and 2.5 times higher activities than that of the CaMV35S promoter. We had observed the similar type of expression patterns of these promoters in agroinfiltration-based transient studies. RP1-MP1 and RP4-MP1 promoters exhibited 1.87- and 1.68-fold increase expression in transgenic tobacco plants; while, a 1.95-fold increase was found in RP1-MP1 transgenic rice plants when compared their activities with CaMV35S promoter. Furthermore, on evaluating these promoter constructs for their expression in the bacterial system, pUPMA-RP1-MP1GFP was found to have the highest GFP expression. Moreover, the promoter construct was also evaluated for its capacity to express the HMP3 gene. Biobeads of encapsulated bacterial cells expressing HMP3 gene under control of the pUPMA-RP4-MP1 promoter were found to reduce 72.9% copper and 29.2% zinc concentration from wastewater. Our results had demonstrated that the developed promoter constructs could be used for translational research in dicot, monocot plants and bacterial systems for efficient gene expression.
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Affiliation(s)
- Dipinte Gupta
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed University), Dayalbagh, Agra, 282005, India
| | - Nrisingha Dey
- Institute of Life Science, Nalco Square, Bhubaneshwar, Odisha, 751023, India
| | - Sadhu Leelavathi
- Plant Biology: Plant Transformation Research Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rajiv Ranjan
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed University), Dayalbagh, Agra, 282005, India.
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Sethi L, Kumari K, Dey N. Engineering of Plants for Efficient Production of Therapeutics. Mol Biotechnol 2021; 63:1125-1137. [PMID: 34398446 PMCID: PMC8365136 DOI: 10.1007/s12033-021-00381-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Plants are becoming useful platforms for recombinant protein production at present time. With the advancement of efficient molecular tools of genomics, proteomics, plants are now being used as a biofactory for production of different life saving therapeutics. Plant-based biofactory is an established production system with the benefits of cost-effectiveness, high scalability, rapid production, enabling post-translational modification, and being devoid of harmful pathogens contamination. This review introduces the main challenges faced by plant expression system: post-translational modifications, protein stability, biosafety concern and regulation. It also summarizes essential factors to be considered in engineering plants, including plant expression system, promoter, post-translational modification, codon optimization, and fusion tags, protein stabilization and purification, subcellular targeting, and making vaccines in an edible way. This review will be beneficial and informative to scholars and readers in the field of plant biotechnology.
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Affiliation(s)
- Lini Sethi
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha 751023 India ,Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi) 121001 India
| | - Khushbu Kumari
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha 751023 India ,Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi) 121001 India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha 751023 India
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32
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Dickinson PJ, Kneřová J, Szecówka M, Stevenson SR, Burgess SJ, Mulvey H, Bågman AM, Gaudinier A, Brady SM, Hibberd JM. A bipartite transcription factor module controlling expression in the bundle sheath of Arabidopsis thaliana. NATURE PLANTS 2020; 6:1468-1479. [PMID: 33230313 DOI: 10.1038/s41477-020-00805-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
C4 photosynthesis evolved repeatedly from the ancestral C3 state, improving photosynthetic efficiency by ~50%. In most C4 lineages, photosynthesis is compartmented between mesophyll and bundle sheath cells, but how gene expression is restricted to these cell types is poorly understood. Using the C3 model Arabidopsis thaliana, we identified cis-elements and transcription factors driving expression in bundle sheath strands. Upstream of the bundle sheath preferentially expressed MYB76 gene, we identified a region necessary and sufficient for expression containing two cis-elements associated with the MYC and MYB families of transcription factors. MYB76 expression is reduced in mutant alleles for these transcription factors. Moreover, downregulated genes shared by both mutants are preferentially expressed in the bundle sheath. Our findings are broadly relevant for understanding the spatial patterning of gene expression, provide specific insights into mechanisms associated with the evolution of C4 photosynthesis and identify a short tuneable sequence for manipulating gene expression in the bundle sheath.
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Affiliation(s)
| | - Jana Kneřová
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Marek Szecówka
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Sean R Stevenson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven J Burgess
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hugh Mulvey
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, CA, USA
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, CA, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA, USA
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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33
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Efremova LN, Strelnikova SR, Gazizova GR, Minkina EA, Komakhin RA. A Synthetic Strong and Constitutive Promoter Derived from the Stellaria media pro-SmAMP1 and pro-SmAMP2 Promoters for Effective Transgene Expression in Plants. Genes (Basel) 2020; 11:E1407. [PMID: 33256091 PMCID: PMC7760760 DOI: 10.3390/genes11121407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 01/05/2023] Open
Abstract
Synthetic promoters are vital for genetic engineering-based strategies for crop improvement, but effective methodologies for their creation and systematic testing are lacking. We report here on the comparative analysis of the promoters pro-SmAMP1 and pro-SmAMP2 from Stellaria media ANTIMICROBIAL PEPTIDE1 (AMP1) and ANTIMICROBIAL PEPTIDE2 (AMP2). These promoters are more effective than the well-known Cauliflower mosaic virus 35S promoter. Although these promoters share about 94% identity, the pro-SmAMP1 promoter demonstrated stronger transient expression of a reporter gene in Agrobacterium infiltration of Nicotiana benthamiana leaves, while the pro-SmAMP2 promoter was more effective for the selection of transgenic tobacco (Nicotiana tabacum) cells when driving a selectable marker. Using the cap analysis of gene expression method, we detected no differences in the structure of the transcription start sites for either promoter in transgenic plants. For both promoters, we used fine-scale deletion analysis to identify 160 bp-long sequences that retain the unique properties of each promoter. With the use of chimeric promoters and directed mutagenesis, we demonstrated that the superiority of the pro-SmAMP1 promoter for Agrobacterium-mediated infiltration is caused by the proline-inducible ACTCAT cis-element strictly positioned relative to the TATA box in the core promoter. Surprisingly, the ACTCAT cis-element not only activated but also suppressed the efficiency of the pro-SmAMP1 promoter under proline stress. The absence of the ACTCAT cis-element and CAANNNNATC motif (negative regulator) in the pro-SmAMP2 promoter provided a more constitutive gene expression profile and better selection of transgenic cells on selective medium. We created a new synthetic promoter that enjoys high effectiveness both in transient expression and in selection of transgenic cells. Intact promoters with differing properties and high degrees of sequence identity may thus be used as a basis for the creation of new synthetic promoters for precise and coordinated gene expression.
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Affiliation(s)
- Larisa N. Efremova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
| | - Svetlana R. Strelnikova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
| | - Guzel R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (G.R.G.); (E.A.M.)
| | - Elena A. Minkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (G.R.G.); (E.A.M.)
| | - Roman A. Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (L.N.E.); (S.R.S.)
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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35
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McCarthy DM, Medford JI. Quantitative and Predictive Genetic Parts for Plant Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2020; 11:512526. [PMID: 33123175 PMCID: PMC7573182 DOI: 10.3389/fpls.2020.512526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Plant synthetic biology aims to harness the natural abilities of plants and to turn them to new purposes. A primary goal of plant synthetic biology is to produce predictable and programmable genetic circuits from simple regulatory elements and well-characterized genetic components. The number of available DNA parts for plants is increasing, and the methods for rapid quantitative characterization are being developed, but the field of plant synthetic biology is still in its early stages. We here describe methods used to describe the quantitative properties of genetic components needed for plant synthetic biology. Once the quantitative properties and transfer function of a variety of genetic parts are known, computers can select the optimal components to assemble into functional devices, such as toggle switches and positive feedback circuits. However, while the variety of circuits and traits that can be put into plants are limitless, doing synthetic biology in plants poses unique challenges. Plants are composed of differentiated cells and tissues, each representing potentially unique regulatory or developmental contexts to introduced synthetic genetic circuits. Further, plants have evolved to be highly sensitive to environmental influences, such as light or temperature, any of which can affect the quantitative function of individual parts or whole circuits. Measuring the function of plant components within the context of a plant cell and, ideally, in a living plant, will be essential to using these components in gene circuits with predictable function. Mathematical modeling will be needed to account for the variety of contexts a genetic part will experience in different plant tissues or environments. With such understanding in hand, it may be possible to redesign plant traits to serve human and environmental needs.
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36
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Gengenbach BB, Opdensteinen P, Buyel JF. Robot Cookies - Plant Cell Packs as an Automated High-Throughput Screening Platform Based on Transient Expression. Front Bioeng Biotechnol 2020; 8:393. [PMID: 32432097 PMCID: PMC7214789 DOI: 10.3389/fbioe.2020.00393] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022] Open
Abstract
The high-throughput screening of recombinant protein expression is advantageous during early process development because it allows the identification of optimal expression constructs and process conditions. Simple screening platforms based on microtiter plates are available for microbes and animal cells, but this was not possible for plants until the development of plant cell packs (PCPs), also known as “cookies,” which provide a versatile and scalable screening tool for recombinant protein production. PCPs are prepared from plant cell suspension cultures by removing the medium and molding the biomass. PCPs can be cast into 96-well plates for high-throughput screening, but the manual handling effort currently limits the throughput to ∼500 samples per day. We have therefore integrated the PCP method with a fully automated laboratory liquid-handling station. The “robot cookies” can be prepared and infiltrated with Agrobacterium tumefaciens by centrifugation, minimizing operator handling and reducing the likelihood of errors during repeated runs, such as those required in a design of experiments approach. The accumulation of fluorescent protein in the cytosol, apoplast, endoplasmic reticulum or plastids is easily detected using an integrated plate reader, reducing the inter-experimental variation to <5%. We also developed a detergent-based chemical lysis method for protein extraction in a 96-well format, which was adapted for automated downstream processing using miniaturized columns allowing subsequent protein analysis. The new automated method reduces the costs of the platform to <0.5 € per PCP infiltration (a saving of >50%) and facilitates a five-fold increase in throughput to >2500 samples per day.
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Affiliation(s)
- Benjamin Bruno Gengenbach
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Patrick Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Johannes Felix Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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37
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Leydon AR, Gala HP, Guiziou S, Nemhauser JL. Engineering Synthetic Signaling in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:767-788. [PMID: 32092279 DOI: 10.1146/annurev-arplant-081519-035852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthetic signaling is a branch of synthetic biology that aims to understand native genetic regulatory mechanisms and to use these insights to engineer interventions and devices that achieve specified design parameters. Applying synthetic signaling approaches to plants offers the promise of mitigating the worst effects of climate change and providing a means to engineer crops for entirely novel environments, such as those in space travel. The ability to engineer new traits using synthetic signaling methods will require standardized libraries of biological parts and methods to assemble them; the decoupling of complex processes into simpler subsystems; and mathematical models that can accelerate the design-build-test-learn cycle. The field of plant synthetic signaling is relatively new, but it is poised for rapid advancement. Translation from the laboratory to the field is likely to be slowed, however, by the lack of constructive dialogue between researchers and other stakeholders.
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Affiliation(s)
- Alexander R Leydon
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Jennifer L Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
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38
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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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39
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Deb D, Dey N. Synthetic Salicylic acid inducible recombinant promoter for translational research. J Biotechnol 2019; 297:9-18. [PMID: 30880184 DOI: 10.1016/j.jbiotec.2019.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/01/2019] [Accepted: 03/10/2019] [Indexed: 01/24/2023]
Abstract
In the present study, we have developed an inter-molecularly shuffled caulimoviral promoter for protein over-expression by placing the Upstream Activation Sequence (UAS) of Figwort Mosaic Virus (FMV; -249 to -54) at the 5'-end of the Cassava Vein Mosaic Virus (CsVMV) promoter fragment 8 (CsVMV8; -215 to +166) to design a hybrid promoter; FUASCsV8CP. The FUASCsV8CP promoter exhibited approximately 2.1 and 2.0 times higher GUS-activities than that obtained from the CaMV35S promoter, in tobacco (Xanthi Brad) protoplasts and in Agroinfiltration assays respectively. Hereto, when FUASCsV8CP was assayed using transgenic tobacco plants (T2- generation), it showed 2.0 times stronger activity than CaMV35S promoter and almost equivalent activity to that of CaMV35S2 promoter. The promoter displayed Salicylic acid (SA) inducibility and hence can also be used for ensuring effective gene expression in plants under constitutive as well as specific inducible conditions. Furthermore, FUASCsV8CP was used to drive the expression of victoviral Vin gene (encoding Victoriocin) transiently in tobacco. The recombinant Victoriocin could be successfully detected by western blotting three days post infiltration. Also, the in vitro Agar-based killing zone assays employing plant-derived Victoriocin-His (obtained from transient expression of Vin) revealed enhanced antifungal activity of Victoriocin against hemi-biotrophic pathogen Phoma exigua Desm. var. exigua.
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Affiliation(s)
- Debasish Deb
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India.
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Genome wide analysis of W-box element in Arabidopsis thaliana reveals TGAC motif with genes down regulated by heat and salinity. Sci Rep 2019; 9:1681. [PMID: 30737427 PMCID: PMC6368537 DOI: 10.1038/s41598-019-38757-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 12/21/2018] [Indexed: 01/10/2023] Open
Abstract
To design, synthetic promoters leading to stress-specific induction of a transgene, the study of cis-regulatory elements is of great importance. Cis-regulatory elements play a major role in regulating the gene expression spatially and temporally at the transcriptional level. The present work focuses on one of the important cis-regulatory element, W-box having TGAC as a core motif which serves as a binding site for the members of the WRKY transcription factor family. In the present study, we have analyzed the occurrence frequency of TGAC core motifs for varying spacer lengths (ranging from 0 to 30 base pairs) across the Arabidopsis thaliana genome in order to determine the biological and functional significance of these conserved sequences. Further, the available microarray data was used to determine the role of TGAC motif in abiotic stresses namely salinity, osmolarity and heat. It was observed that TGAC motifs with spacer sequences like TGACCCATTTTGAC and TGACCCATGAATTTTGAC had a significant deviation in frequency and were thought to be favored for transcriptional bindings. The microarray data analysis revealed the involvement of TGAC motif mainly with genes down-regulated under abiotic stress conditions. These results were further confirmed by the transient expression studies with promoter-reporter cassettes carrying TGAC and TGAC-ACGT variant motifs with spacer lengths of 5 and 10.
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Ali S, Kim WC. A Fruitful Decade Using Synthetic Promoters in the Improvement of Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1433. [PMID: 31737027 PMCID: PMC6838210 DOI: 10.3389/fpls.2019.01433] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/16/2019] [Indexed: 05/17/2023]
Abstract
Advances in plant biotechnology provide various means to improve crop productivity and greatly contributing to sustainable agriculture. A significant advance in plant biotechnology has been the availability of novel synthetic promoters for precise spatial and temporal control of transgene expression. In this article, we review the development of various synthetic promotors and the rise of their use over the last several decades for regulating the transcription of various transgenes. Similarly, we provided a brief description of the structure and scope of synthetic promoters and the engineering of their cis-regulatory elements for different targets. Moreover, the functional characteristics of different synthetic promoters, their modes of regulating the expression of candidate genes in response to different conditions, and the resulting plant trait improvements reported in the past decade are discussed.
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Anguraj Vadivel AK, Krysiak K, Tian G, Dhaubhadel S. Genome-wide identification and localization of chalcone synthase family in soybean (Glycine max [L]Merr). BMC PLANT BIOLOGY 2018; 18:325. [PMID: 30509179 PMCID: PMC6278125 DOI: 10.1186/s12870-018-1569-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/23/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Soybean is a paleopolyploid that has undergone two whole genome duplication events. Gene duplication is a type of genomic change that can lead to novel functions of pre-existing genes. Chalcone synthase (CHS) is the plant-specific type III polyketide synthase that catalyzes the first committed step in (iso)flavonoid biosynthesis in plants. RESULTS Here we performed a genome-wide search of CHS genes in soybean, and identified 21 GmCHS loci containing 14 unique GmCHS (GmCHS1-GmCHS14) that included 5 newly identified GmCHSs (GmCHS10-GmCHS14). Furthermore, 3 copies of GmCHS3 and 2 copies of GmCHS4 were found in soybean. Analysis of gene structure of GmCHSs revealed the presence of a single intron in protein-coding regions except for GmCHS12 that contained 3 introns. Even though GmCHS genes are located on 8 different chromosomes, a large number of these genes are present on chromosome 8 where they form 3 distinct clusters. Expression analysis of GmCHS genes revealed tissue-specific expression pattern, and that some GmCHS isoforms localize in the cytoplasm and the nucleus while other isoforms are restricted to cytoplasm only. CONCLUSION Overall, we have identified 21 GmCHS loci with 14 unique GmCHS genes in the soybean genome. Their gene structures and genomic organization together with the spatio-temporal expression and protein localization suggest their importance in the production of downstream metabolites such as (iso)flavonoids and their derived phytoalexins.
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Affiliation(s)
- Arun Kumaran Anguraj Vadivel
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
- Department of Biology, University of Western Ontario, London, ON Canada
| | - Kevin Krysiak
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
| | - Gang Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
- Department of Biology, University of Western Ontario, London, ON Canada
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Pandiarajan R, Grover A. In vivo promoter engineering in plants: Are we ready? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:132-138. [PMID: 30466578 DOI: 10.1016/j.plantsci.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 05/27/2023]
Abstract
Engineering plant promoter sequence for optimal expression of a gene has been a long standing goal for plant scientists. In recent times, Sequence Specific Nucleases (SSNs) like CRISPR/Cas9 are enabling researchers to achieve this goal, in vivo in the genome. It is well known that SSNs have met with unprecedented success in rapid transgene free crop improvement largely by targeting the coding sequence. Here, we discuss the strategies being employed by plant scientists in targeting SSNs to non-coding promoter regions/Cis Regulatory Elements (CRE). We collectively refer all such endeavors as in vivo promoter engineering (IPE). We further classify the IPE efforts into CRE addition, CRE deletion/disruption, promoter swap/insertion and targeted promoter polymorphism. Till date, IPE has proven useful in altering plant architecture in tomato, developing resistance against Xanthomonas sp in rice and citrus, and engineering drought tolerance in maize. However it is quite challenging to achieve predictable changes in gene expression using IPE at this point. In future years, data generated from high throughput techniques to investigate non coding genome may immensely augment the efforts in this direction. As IPE does not involve addition of the transgene for modifying crop traits, it will be relatively more conducive to public acceptance in crop improvement programs.
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Affiliation(s)
- Ramakrishnan Pandiarajan
- Department of Plant Molecular Biology, South Campus, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, South Campus, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India.
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Abstract
Designing the expression cassettes with desired properties remains the most important consideration of gene engineering technology. One of the challenges for predictive gene expression is the modeling of synthetic gene switches to regulate one or more target genes which would directly respond to specific chemical, environmental, and physiological stimuli. Assessment of natural promoter, high-throughput sequencing, and modern biotech inventory aided in deciphering the structure of cis elements and molding the native cis elements into desired synthetic promoter. Synthetic promoters which are molded by rearrangement of cis motifs can greatly benefit plant biotechnology applications. This review gives a glimpse of the manual in vivo gene regulation through synthetic promoters. It summarizes the integrative design strategy of synthetic promoters and enumerates five approaches for constructing synthetic promoters. Insights into the pattern of cis regulatory elements in the pursuit of desirable "gene switches" to date has also been reevaluated. Joint strategies of bioinformatics modeling and randomized biochemical synthesis are addressed in an effort to construct synthetic promoters for intricate gene regulation.
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Azuma M, Oshima Y, Sakamoto S, Mitsuda N, Ohme-Takagi M, Otagaki S, Matsumoto S, Shiratake K. Dissecting promoter of InMYB1 gene showing petal-specific expression. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:243-248. [PMID: 31819729 PMCID: PMC6879369 DOI: 10.5511/plantbiotechnology.18.0529a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/29/2018] [Indexed: 06/10/2023]
Abstract
We had previously reported that the InMYB1 promoter, the 1023 bp upstream region of InMYB1, works petal-specifically in various dicot plants by recognizing petal identity at a cellular level. To determine the petal-specific region in the InMYB1 promoter, Arabidopsis plants harboring InMYB1_1023b::GUS (β-glucuronidase), InMYB1_713b::GUS, InMYB1_506b::GUS, InMYB1_403b::GUS, InMYB1_332b::GUS, InMYB1_200b::GUS and InMYB1_140b::GUS were produced and confirmed a shortest region, which has the petal-specific promoter activity by using histochemical GUS assay. Petal-specific GUS staining was not observed in the Arabidopsis plants transformed with InMYB1_200b::GUS and InMYB1_140b::GUS, but observed in transgenic Arabidopsis plants harboring from InMYB1_1023b::GUS to InMYB1_332b::GUS. cDNA sequence of InMYB1 shows that 120 bp upstream region of InMYB1 is 5' untranslated region, suggesting that the 332-121 bp upstream region of InMYB1 contains an important element for petal-specific gene expression. In the Arabidopsis harboring the InMYB1_332-121b×3_TATA_Ω::GUS, petal-specific GUS staining was observed and the staining was stronger than in the Arabidopsis harboring InMYB1_1023b::GUS. This result shows that the 332-121 bp region is enough and essential for the petal specificity and the InMYB1_332-121b×3_TATA_Ω could be used for the molecular breeding of floricultural crops.
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Affiliation(s)
- Mirai Azuma
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
- Department of Agricultural Bioscience, College of Bioresource Sciences, Nihon University, Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Yoshimi Oshima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Institute for Environmental Science and Technology, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
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Genome-wide analysis of purple acid phosphatase structure and expression in ten vegetable species. BMC Genomics 2018; 19:646. [PMID: 30170550 PMCID: PMC6119273 DOI: 10.1186/s12864-018-5022-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/20/2018] [Indexed: 12/04/2022] Open
Abstract
Background Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency. Herein, we identified PAP homologs in the genomes of 10 vegetable species, along with Arabidopsis thaliana and Amborella trichopoda as references, to provide fundamental knowledge for this family. Results Phylogenetic analysis of protein sequences revealed nine distinct clades, indicating that functional differentiation of extant PAPs was established prior to the emergence of early angiosperms, and conserved among homologs in each clade. Analysis of transcript abundance in different tissues (root, stem, leaf, flower, and fruit) and following phosphates (Pi) starvation treatments from published RNA-seq transcriptome datasets facilitated comprehensive evaluation of expression patterns, and some groups of tissue-specific and Pi starvation-induced PAPs were characterised. Conserved motifs identified from upstream sequences of homologs that are highly expressed in particular tissues or following starvation treatment suggests that divergence in PAP gene expression is associated with cis-acting elements in promoters. Conclusions The genome-wide analysis of PAP enzyme structure and transcriptional expression patterns advance our understanding of PAP family in vegetables genomes. Therefore, PAP homologs with known enzyme structures and expression profiles could serve as targets for plant breeding and/or genetic engineering programs to improve P acquisition and use. Electronic supplementary material The online version of this article (10.1186/s12864-018-5022-1) contains supplementary material, which is available to authorized users.
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Nuccio ML, Paul M, Bate NJ, Cohn J, Cutler SR. Where are the drought tolerant crops? An assessment of more than two decades of plant biotechnology effort in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:110-119. [PMID: 29907303 DOI: 10.1016/j.plantsci.2018.01.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 05/22/2023]
Abstract
Since the dawn of modern biotechnology public and private enterprise have pursued the development of a new breed of drought tolerant crop products. After more than 20 years of research and investment only a few such products have reached the market. This is due to several technical and market constraints. The technical challenges include the difficulty in defining tractable single-gene trait development strategies, the logistics of moving traits from initial to commercial genetic backgrounds, and the disconnect between conditions in farmer's fields and controlled environments. Market constraints include the significant difficulty, and associated costs, in obtaining access to markets around the world. Advances in the biology of plant water management, including response to water deficit reveal new opportunities to improve crop response to water deficit and new genome-based tools promise to usher in the next era of crop improvement. As biotechnology looks to improve crop productivity under drought conditions, the environmental and food security advantages will influence public perception and shift the debate toward benefits rather than risks.
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Affiliation(s)
- Michael L Nuccio
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Matthew Paul
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Nicholas J Bate
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Jonathan Cohn
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Sean R Cutler
- Plant Cell Biology and Chemistry, Botany and Plant Sciences Chemistry Genomics Building, University of California Riverside, CA, 92521, USA.
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Shrestha A, Khan A, Dey N. cis-trans Engineering: Advances and Perspectives on Customized Transcriptional Regulation in Plants. MOLECULAR PLANT 2018; 11:886-898. [PMID: 29859265 DOI: 10.1016/j.molp.2018.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 05/03/2023]
Abstract
Coordinated transcriptional control employing synthetic promoters and transcription factors (TFs) can be used to achieve customized regulation of gene expression in planta. Synthetic promoter technology has yielded a series of promoters with modified cis-regulatory elements that provide useful tools for efficient modulation of gene expression. In addition, the use of zinc fingers (ZFs), transcription activator-like effectors (TALEs), and catalytically inactive clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (dCas9) has made it feasible to engineer TFs that can produce targeted gene expression regulation; these approaches are particularly effective when artificial TFs are coupled with transcriptional activators or repressors. This review focuses on strategies used to engineer both promoters and TFs in the context of targeted transcriptional regulation. We also discuss the creation of synthetic inducible platforms, which can be used to impart stress tolerance to plants. We propose that combinatorial "cis-trans engineering" using a CRISPR-dCas9-based bipartite module could be used to regulate the expression of multiple target genes. This approach provides an attractive tool for introduction of specific qualitative traits into plants, thus enhancing their overall environmental adaptability.
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Affiliation(s)
- Ankita Shrestha
- Division of Microbial and Plant Biotechnology, Institute of Life Sciences, Department of Biotechnology, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Ahamed Khan
- Division of Microbial and Plant Biotechnology, Institute of Life Sciences, Department of Biotechnology, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Division of Microbial and Plant Biotechnology, Institute of Life Sciences, Department of Biotechnology, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India.
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Deb D, Shrestha A, Maiti IB, Dey N. Recombinant Promoter (MUASCsV8CP) Driven Totiviral Killer Protein 4 (KP4) Imparts Resistance Against Fungal Pathogens in Transgenic Tobacco. FRONTIERS IN PLANT SCIENCE 2018; 9:278. [PMID: 29556246 PMCID: PMC5844984 DOI: 10.3389/fpls.2018.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/16/2018] [Indexed: 05/19/2023]
Abstract
Development of disease-resistant plant varieties achieved by engineering anti-microbial transgenes under the control of strong promoters can suffice the inhibition of pathogen growth and simultaneously ensure enhanced crop production. For evaluating the prospect of such strong promoters, we comprehensively characterized the full-length transcript promoter of Cassava Vein Mosaic Virus (CsVMV; -565 to +166) and identified CsVMV8 (-215 to +166) as the highest expressing fragment in both transient and transgenic assays. Further, we designed a new chimeric promoter 'MUASCsV8CP' through inter-molecular hybridization among the upstream activation sequence (UAS) of Mirabilis Mosaic Virus (MMV; -297 to -38) and CsVMV8, as the core promoter (CP). The MUASCsV8CP was found to be ∼2.2 and ∼2.4 times stronger than the CsVMV8 and CaMV35S promoters, respectively, while its activity was found to be equivalent to that of the CaMV35S2 promoter. Furthermore, we generated transgenic tobacco plants expressing the totiviral 'Killer protein KP4' (KP4) under the control of the MUASCsV8CP promoter. Recombinant KP4 was found to accumulate both in the cytoplasm and apoplast of plant cells. The agar-based killing zone assays revealed enhanced resistance of plant-derived KP4 against two deuteromycetous foliar pathogenic fungi viz. Alternaria alternata and Phoma exigua var. exigua. Also, transgenic plants expressing KP4 inhibited the growth progression of these fungi and conferred significant fungal resistance in detached-leaf and whole plant assays. Taken together, we establish the potential of engineering "in-built" fungal stress-tolerance in plants by expressing KP4 under a novel chimeric caulimoviral promoter in a transgenic approach.
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Affiliation(s)
- Debasish Deb
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| | - Ankita Shrestha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| | - Indu B. Maiti
- Department of Molecular Plant Virology and Plant Genetic Engineering, KTRDC, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- *Correspondence: Nrisingha Dey, ;
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Shigenaga AM, Berens ML, Tsuda K, Argueso CT. Towards engineering of hormonal crosstalk in plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2017. [PMID: 28624670 DOI: 10.1016/j.pbi.2017.04.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant hormones regulate physiological responses in plants, including responses to pathogens and beneficial microbes. The last decades have provided a vast amount of evidence about the contribution of different plant hormones to plant immunity, and also of how they cooperate to orchestrate immunity activation, in a process known as hormone crosstalk. In this review we highlight the complexity of hormonal crosstalk in immunity and approaches currently being used to further understand this process, as well as perspectives to engineer hormone crosstalk for enhanced pathogen resistance and overall plant fitness.
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Affiliation(s)
- Alexandra M Shigenaga
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Matthias L Berens
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.
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