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Xu Y, Gan ES, Ito T. Misexpression Approaches for the Manipulation of Flower Development. Methods Mol Biol 2023; 2686:429-451. [PMID: 37540372 DOI: 10.1007/978-1-0716-3299-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The generation of dominant gain-of-function mutants through activation tagging is a forward genetic approach that can be applied to study the mechanisms of flower development, complementing the screening of loss-of-function mutants. In addition, the functions of genes of interest can be further analyzed through reverse genetics. A commonly used method is gene overexpression, where ectopic expression can result in an opposite phenotype to that caused by a loss-of-function mutation. When overexpression is detrimental, the misexpression of a gene using tissue-specific promoters can be useful to study spatial-specific function. As flower development is a multistep process, it can be advantageous to control gene expression, or its protein product activity, in a temporal and/or spatial manner. This has been made possible through several inducible promoter systems as well as inducible proteins by constructing chimeric fusions between the ligand-binding domain of the glucocorticoid receptor (GR) and the protein of interest. The recently introduced CRISPR-Cas9-based platform provides a new way of bioengineering transcriptional regulators in plants. By fusing a catalytically inactive dCas9 with functional activation or repression domains, the CRISPR-Cas9 module can achieve transcriptional activation or repression of endogenous genes. All these methods allow us to genetically manipulate gene expression during flower development. In this chapter, we describe methods to produce the expression constructs, method of screening, and more general applications of the techniques.
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Affiliation(s)
- Yifeng Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Eng-Seng Gan
- Republic Polytechnic, School of Applied Science (SAS), Singapore, Singapore
| | - Toshiro Ito
- Nara Institute of Science and Technology, Biological Sciences, Plant Stem Cell Regulation and Floral Patterning Laboratory, Ikoma, Nara, Japan.
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2
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Zhang S, Xu T, Ren Y, Song L, Liu Z, Kang X, Li Y. The NAC transcription factor family in Eucommia ulmoides: Genome-wide identification, characterization, and network analysis in relation to the rubber biosynthetic genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1030298. [PMID: 37077635 PMCID: PMC10106570 DOI: 10.3389/fpls.2023.1030298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/13/2023] [Indexed: 05/03/2023]
Abstract
The NAC transcription factor family is a large plant gene family, participating in plant growth and development, secondary metabolite synthesis, biotic and abiotic stresses responses, and hormone signaling. Eucommia ulmoides is a widely planted economic tree species in China that can produce trans-polyisoprene: Eucommia rubber (Eu-rubber). However, genome-wide identification of the NAC gene family has not been reported in E. ulmoides. In this study, 71 NAC proteins were identified based on genomic database of E. ulmoides. Phylogenetic analysis showed that the EuNAC proteins were distributed in 17 subgroups based on homology with NAC proteins in Arabidopsis, including the E. ulmoides-specific subgroup Eu_NAC. Gene structure analysis suggested that the number of exons varied from 1 to 7, and multitudinous EuNAC genes contained two or three exons. Chromosomal location analysis revealed that the EuNAC genes were unevenly distributed on 16 chromosomes. Three pairs of genes of tandem duplicates genes and 12 segmental duplications were detected, which indicated that segmental duplications may provide the primary driving force of expansion of EuNAC. Prediction of cis-regulatory elements indicated that the EuNAC genes were involved in development, light response, stress response and hormone response. For the gene expression analysis, the expression levels of EuNAC genes in various tissues were quite different. To explore the effect of EuNAC genes on Eu-rubber biosynthesis, a co-expression regulatory network between Eu-rubber biosynthesis genes and EuNAC genes was constructed, which indicated that six EuNAC genes may play an important role in the regulation of Eu-rubber biosynthesis. In addition, this six EuNAC genes expression profiles in E. ulmoides different tissues were consistent with the trend in Eu-rubber content. Quantitative real-time PCR analysis showed that EuNAC genes were responsive to different hormone treatment. These results will provide a useful reference for further studies addressing the functional characteristics of the NAC genes and its potential role in Eu-rubber biosynthesis.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Tingting Xu
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Yongyu Ren
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Lianjun Song
- Weixian Eucommia National Forest Tree Germplasm Repository, Weixian Forestry Cultivation Base of Superior Species, Hebei, China
| | - Zhao Liu
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li,
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Coates RJ, Young MT, Scofield S. Optimising expression and extraction of recombinant proteins in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1074531. [PMID: 36570881 PMCID: PMC9773421 DOI: 10.3389/fpls.2022.1074531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are of paramount importance for research, industrial and medical use. Numerous expression chassis are available for recombinant protein production, and while bacterial and mammalian cell cultures are the most widely used, recent developments have positioned transgenic plant chassis as viable and often preferential options. Plant chassis are easily maintained at low cost, are hugely scalable, and capable of producing large quantities of protein bearing complex post-translational modification. Several protein targets, including antibodies and vaccines against human disease, have been successfully produced in plants, highlighting the significant potential of plant chassis. The aim of this review is to act as a guide to producing recombinant protein in plants, discussing recent progress in the field and summarising the factors that must be considered when utilising plants as recombinant protein expression systems, with a focus on optimising recombinant protein expression at the genetic level, and the subsequent extraction and purification of target proteins, which can lead to substantial improvements in protein stability, yield and purity.
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Liu Z, Xiong T, Zhao Y, Qiu B, Chen H, Kang X, Yang J. Genome-wide characterization and analysis of Golden 2-Like transcription factors related to leaf chlorophyll synthesis in diploid and triploid Eucalyptus urophylla. FRONTIERS IN PLANT SCIENCE 2022; 13:952877. [PMID: 35968152 PMCID: PMC9366356 DOI: 10.3389/fpls.2022.952877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 05/02/2023]
Abstract
Golden 2-Like (GLK) transcription factors play a crucial role in chloroplast development and chlorophyll synthesis in many plant taxa. To date, no systematic analysis of GLK transcription factors in tree species has been conducted. In this study, 40 EgrGLK genes in the Eucalyptus grandis genome were identified and divided into seven groups based on the gene structure and motif composition. The EgrGLK genes were mapped to 11 chromosomes and the distribution of genes on chromosome was uneven. Phylogenetic analysis of GLK proteins between E. grandis and other species provided information for the high evolutionary conservation of GLK genes among different species. Prediction of cis-regulatory elements indicated that the EgrGLK genes were involved in development, light response, and hormone response. Based on the finding that the content of chlorophyll in mature leaves was the highest, and leaf chlorophyll content of triploid Eucalyptus urophylla was higher than that of the diploid control, EgrGLK expression pattern in leaves of triploid and diploid E. urophylla was examined by means of transcriptome analysis. Differential expression of EgrGLK genes in leaves of E. urophylla of different ploidies was consistent with the trend in chlorophyll content. To further explore the relationship between EgrGLK expression and chlorophyll synthesis, co-expression networks were generated, which indicated that EgrGLK genes may have a positive regulatory relationship with chlorophyll synthesis. In addition, three EgrGLK genes that may play an important role in chlorophyll synthesis were identified in the co-expression networks. And the prediction of miRNAs targeting EgrGLK genes showed that miRNAs might play an important role in the regulation of EgrGLK gene expression. This research provides valuable information for further functional characterization of GLK genes in Eucalyptus.
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Affiliation(s)
- Zhao Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Tao Xiong
- Guangxi Dongmen Forest Farm, Chongzuo, China
| | | | - Bingfa Qiu
- Guangxi Dongmen Forest Farm, Chongzuo, China
| | - Hao Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Xiangyang Kang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
| | - Jun Yang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- *Correspondence: Jun Yang,
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Singha DL, Das D, Sarki YN, Chowdhury N, Sharma M, Maharana J, Chikkaputtaiah C. Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects. PLANTA 2021; 255:28. [PMID: 34962611 DOI: 10.1007/s00425-021-03811-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement. CRISPR/Cas is a powerful genome-editing tool with a wide range of applications for the genetic improvement of crops. However, the constitutive genome editing of vital genes is often associated with pleiotropic effects on other genes, needless metabolic burden, or interference in the cellular machinery. Tissue-specific genome editing (TSGE), on the other hand, enables researchers to study those genes in specific cells, tissues, or organs without disturbing neighboring groups of cells. Until recently, there was only limited proof of the TSGE concept, where the CRISPR-TSKO tool was successfully used in Arabidopsis, tomato, and cotton, laying a solid foundation for crop improvement. In this review, we have laid out valuable insights into the concept and application of TSGE on relatively unexplored areas such as grain trait improvement under favorable or unfavorable conditions. We also enlisted some of the prominent tissue-specific promoters and described the procedure of their isolation with several TSGE promoter expression systems in detail. Moreover, we highlighted potential negative regulatory genes that could be targeted through TSGE using tissue-specific promoters. In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement.
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Affiliation(s)
- Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Yogita N Sarki
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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6
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Du F, Mo Y, Israeli A, Wang Q, Yifhar T, Ori N, Jiao Y. Leaflet initiation and blade expansion are separable in compound leaf development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1073-1087. [PMID: 32889762 DOI: 10.1111/tpj.14982] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/12/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Compound leaves are composed of multiple separate blade units termed leaflets. In tomato (Solanum lycopersicum) compound leaves, auxin promotes both leaflet initiation and blade expansion. However, it is unclear how these two developmental processes interact. With highly variable complexity, tomato compound leaves provide an ideal system to address this question. In this study, we obtained and analyzed mutants of the WUSCHEL-RELATED HOMEOBOX (WOX) family gene SlLAM1 from tomato, whose orthologs in tobacco (Nicotiana sylvestris) and other species are indispensable for blade expansion. We show that SlLAM1 is expressed in the middle and marginal domains of leaves, and is required for blade expansion in leaflets. We demonstrate that sllam1 mutants cause a delay of leaflet initiation and slightly alter the arrangement of first-order leaflets, whereas the overall leaflet number is comparable to that of wild-type leaves. Analysis of the genetic interactions between SlLAM1 and key auxin signaling components revealed an epistatic effect of SlLAM1 in determining the final leaf form. Finally, we show that SlLAM1 is also required for floral organ growth and affects the fertility of gametophytes. Our data suggest that SlLAM1 promotes blade expansion in multiple leaf types, and leaflet initiation can be largely uncoupled from blade expansion during compound leaf morphogenesis.
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Affiliation(s)
- Fei Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yajin Mo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Alon Israeli
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Qingqing Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tamar Yifhar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot, 76100, Israel
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Functional characterization of wheat myo-inositol oxygenase promoter under different abiotic stress conditions in Arabidopsis thaliana. Biotechnol Lett 2020; 42:2035-2047. [PMID: 32681381 DOI: 10.1007/s10529-020-02967-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/12/2020] [Indexed: 01/08/2023]
Abstract
The production of wheat is severely affected by abiotic stresses such as cold, drought, salinity, and high temperature. Although constitutive promoters are frequently used to regulate the expression of alien genes, these may lead to undesirable side-effects in transgenic plants. Therefore, identification and characterization of an inducible promoter that can express transgene only when exposed to stresses are of great importance in the genetic engineering of crop plants. Previous studies have indicated the abiotic stress-responsive behavior of myo-inositol oxygenase (MIOX) gene in different plants. Here, we isolated the MIOX gene promoter from wheat (TaMIOX). The in-silico analysis revealed the presence of various abiotic stress-responsive cis-elements in the promoter region. The TaMIOX promoter was fused with the UidA reporter gene and transformed into Arabidopsis thaliana. The T3 single-copy homozygous lines were analyzed for GUS activity using histochemical and fluorometric assays. Transcript expression of TaMIOX::UidA was significantly up-regulated by heat (five fold), cold (seven fold), and drought (five fold) stresses as compared to transgenic plants grown without stress-induced conditions. The CaMV35S::UidA plants showed very high GUS activity even in normal conditions. In contrast, the TaMIOX::UidA plants showed prominent GUS activity only in stress treatments (cold, heat, and drought), which suggests the inducible behavior of the TaMIOX promoter. The substrate myo-inositol feeding assay of TaMIOX::UidA plants showed lesser GUS activity as compared to plants treated in abiotic stress conditions. Results support that the TaMIOX promoter could be used as a potential candidate for conditional expression of the transgene in abiotic stress conditions.
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Zhang L, Qin LN, Zeng ZR, Wu CZ, Gong YY, Liu LH, Cao FQ. Molecular identification of a root apical cell-specific and stress-responsive enhancer from an Arabidopsis enhancer trap line. PLANT METHODS 2019; 15:8. [PMID: 30733820 PMCID: PMC6354418 DOI: 10.1186/s13007-019-0393-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Plant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an Arabidopsis T-DNA insertional enhancer trap line J3411 expressing reporters (GFP) only in the root tip was adopted in this study to isolate a DNA fragment. RESULTS Using nested PCR, DNA sequencing and sequence homology search, the T-DNA insertion site(s) and its flanking genes were characterised in J3411 line. Subsequently, a 2000 bp plant DNA-fragment (Ertip1) upstream of the insert position of the coding T-DNA was in silico analysed, revealing certain putative promoter/enhancer cis-regulatory elements. Cloning and transformation of this DNA fragment and its truncated segments tagged with or without 35S minimal promoter (35Smini), all of which were fused with a GFP or GUS reporter, allowed to detect GFP and GUS expression mediated only by Ertip1 + 35mini (PErtip1+35Smini) specifically in the Arabidopsis root tip region. The PErtip1+35Smini activity was further tested to be strong and stable under many different growth conditions but suppressed by cold, salt, alkaline pH and higher ammonium and phosphorus. CONCLUSION This work describes a promising strategy to isolate a tissue-/cell-specific enhancer sequence from the enhancer trap lines, which are publically available. The reported synthetic promoter i.e. PErtip1+35Smini may provide a valuable and potent molecular-tool for comprehensive investigation of a gene function related to root growth and development as well as molecular engineering of root-architectural formation aiming to improve plant growth.
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Affiliation(s)
- Lei Zhang
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Li-Na Qin
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
- Zhaoyuan Agricultural Technology Extension Centre, Zhaoyuan, 265400 Shandong China
| | - Zi-Rui Zeng
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Chang-Zheng Wu
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Yuan-Yong Gong
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
- 3Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Lai-Hua Liu
- 1Key Laboratory of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193 China
| | - Feng-Qiu Cao
- 4Shanghai Centre for Plant Stress Biology of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602 China
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9
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Li W, Li C, Li S, Peng M. Long noncoding RNAs that respond to Fusarium oxysporum infection in 'Cavendish' banana (Musa acuminata). Sci Rep 2017; 7:16939. [PMID: 29209086 PMCID: PMC5717134 DOI: 10.1038/s41598-017-17179-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of genes that influence a variety of biological functions through acting as signal, decoy, guide, and scaffold molecules. In banana (Musa spp.), an important economic fruit crop, particularly in Southeast Asia, the wilt disease caused by Fusarium oxysporum f. sp. cubense (Foc), especially strain Foc TR4, is disastrous. In banana, how the biogenesis of these lncRNAs is regulated in response to pathogen infection is still largely unknown. In this study, strand-specific paired-end RNA sequencing of banana samples was performed on susceptible and resistant cultivars inoculated with Foc, with three biological replicates and at two different times after infection. Overall, 5,294 lncRNAs were predicted with high confidence through strict filtration, including long intergenic ncRNA (lincRNA) and antisense lncRNA. Differentially expressed (DE) lncRNAs were identified in response to Foc infection in the inoculated versus the mock-inoculated banana of the susceptible 'BX' and resistant 'NK' cultivars. Through KEGG, GO, and the expression levels of the DE lncRNAs, some DE lncRNAs were predicted to be involved in plant-pathogen interactions and phytohormone signal transduction. In this study, this catalog of lncRNAs and their properties will facilitate further experimental studies and functional classifications of these genes.
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Affiliation(s)
- Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Chunqiang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Shuxia Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
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10
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Brophy JAN, LaRue T, Dinneny JR. Understanding and engineering plant form. Semin Cell Dev Biol 2017; 79:68-77. [PMID: 28864344 DOI: 10.1016/j.semcdb.2017.08.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022]
Abstract
A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.
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Affiliation(s)
- Jennifer A N Brophy
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Therese LaRue
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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11
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Conforte AJ, Guimarães-Dias F, Neves-Borges AC, Bencke-Malato M, Felix-Whipps D, Alves-Ferreira M. Isolation and characterization of a promoter responsive to salt, osmotic and dehydration stresses in soybean. Genet Mol Biol 2017; 40:226-237. [PMID: 28350037 PMCID: PMC5452143 DOI: 10.1590/1678-4685-gmb-2016-0052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 11/21/2016] [Indexed: 11/22/2022] Open
Abstract
Drought stress is the main limiting factor of soybean yield. Currently, genetic
engineering has been one important tool in the development of drought-tolerant
cultivars. A widely used strategy is the fusion of genes that confer tolerance under
the control of the CaMV35S constitutive promoter; however,
stress-responsive promoters would constitute the best alternative to the generation
of drought-tolerant crops. We characterized the promoter of α-galactosidase soybean
(GlymaGAL) gene that was previously identified as highly
up-regulated by drought stress. The β-glucuronidase (GUS) activity
of Arabidopsis transgenic plants bearing 1000- and 2000-bp fragments of the
GlymaGAL promoter fused to the uidA gene was
evaluated under air-dried, polyethylene glycol (PEG) and salt stress treatments.
After 24 h of air-dried and PEG treatments, the pGAL-2kb led to an
increase in GUS expression in leaf and root samples when compared to
the control samples. These results were corroborated by qPCR expression analysis of
the uidA gene. The pGAL-1kb showed no difference in
GUS activity between control and treated samples. The
pGAL-2kb promoter was evaluated in transgenic soybean roots,
leading to an increase in EGFP expression under air-dried treatment.
Our data indicates that pGAL-2kb could be a useful tool in
developing drought-tolerant cultivars by driving gene expression.
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Affiliation(s)
| | - Fábia Guimarães-Dias
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Anna Cristina Neves-Borges
- Department of Botany. Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | - Marta Bencke-Malato
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Durvalina Felix-Whipps
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Márcio Alves-Ferreira
- Department of Genetics. Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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12
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Comparative transcriptome analysis in different tissues of a medicinal herb, Picrorhiza kurroa pinpoints transcription factors regulating picrosides biosynthesis. Mol Biol Rep 2016; 43:1395-1409. [DOI: 10.1007/s11033-016-4073-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 09/01/2016] [Indexed: 11/25/2022]
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13
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Koramutla MK, Bhatt D, Negi M, Venkatachalam P, Jain PK, Bhattacharya R. Strength, Stability, and cis-Motifs of In silico Identified Phloem-Specific Promoters in Brassica juncea (L.). FRONTIERS IN PLANT SCIENCE 2016; 7:457. [PMID: 27148290 PMCID: PMC4834444 DOI: 10.3389/fpls.2016.00457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/24/2016] [Indexed: 05/03/2023]
Abstract
Aphids, a hemipteran group of insects pose a serious threat to many of the major crop species including Brassica oilseeds. Transgenic strategies for developing aphid-resistant plant types necessitate phloem-bound expression of the insecticidal genes. A few known phloem-specific promoters, in spite of tissue-specific activity fail to confer high level gene-expression. Here, we identified seven orthologues of phloem-specific promoters in B. juncea (Indian mustard), and experimentally validated their strength of expression in phloem exudates. Significant cis-motifs, globally occurring in phloem-specific promoters showed variable distribution frequencies in these putative phloem-specific promoters of B. juncea. In RT-qPCR based gene-expression study promoter of Glutamine synthetase 3A (GS3A) showed multifold higher activity compared to others, across the different growth stages of B. juncea plants. A statistical method employing four softwares was devised for rapidly analysing stability of the promoter-activities across the plant developmental stages. Different statistical softwares ranked these B. juncea promoters differently in terms of their stability in promoter-activity. Nevertheless, the consensus in output empirically suggested consistency in promoter-activity of the six B. juncea phloem- specific promoters including GS3A. The study identified suitable endogenous promoters for high level and consistent gene-expression in B. juncea phloem exudate. The study also demonstrated a rapid method of assessing species-specific strength and stability in expression of the endogenous promoters.
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Affiliation(s)
- Murali Krishna Koramutla
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | - Deepa Bhatt
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | - Manisha Negi
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | | | - Pradeep K. Jain
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
| | - Ramcharan Bhattacharya
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute CampusNew Delhi, India
- *Correspondence: Ramcharan Bhattacharya ;
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14
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Geng L, Duan X, Liang C, Shu C, Song F, Zhang J. Mining tissue-specific contigs from peanut (Arachis hypogaea L.) for promoter cloning by deep transcriptome sequencing. PLANT & CELL PHYSIOLOGY 2014; 55:1793-801. [PMID: 25231965 DOI: 10.1093/pcp/pcu111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Peanut (Arachis hypogaea L.), one of the most important oil legumes in the world, is heavily damaged by white grubs. Tissue-specific promoters are needed to incorporate insect resistance genes into peanut by genetic transformation to control the subterranean pests. Transcriptome sequencing is the most effective way to analyze differential gene expression in this non-model species and contribute to promoter cloning. The transcriptomes of the roots, seeds and leaves of peanut were sequenced using Illumina technology. A simple digital expression profile was established based on number of transcripts per million clean tags (TPM) from different tissues. Subsequently, 584 root-specific candidate transcript assembly contigs (TACs) and 316 seed-specific candidate TACs were identified. Among these candidate TACs, 55.3% were root-specific and 64.6% were seed-specific by semi-quantitative RT-PCR analysis. Moreover, the consistency of semi-quantitative RT-PCR with the simple digital expression profile was correlated with the length and TPM value of TACs. The results of gene ontology showed that some root-specific TACs are involved in stress resistance and respond to auxin stimulus, whereas, seed-specific candidate TACs are involved in embryo development, lipid storage and long-chain fatty acid biosynthesis. One root-specific promoter was cloned and characterized. We developed a high-yield screening system in peanut by establishing a simple digital expression profile based on Illumina sequencing. The feasible and rapid method presented by this study can be used for other non-model crops to explore tissue-specific or spatially specific promoters.
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Affiliation(s)
- Lili Geng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohong Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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15
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Identification of a pollen-specific gene, SlCRK1 (RFK2) in tomato. Genes Genomics 2014. [DOI: 10.1007/s13258-013-0168-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Pujar A, Menda N, Bombarely A, Edwards JD, Strickler SR, Mueller LA. From manual curation to visualization of gene families and networks across Solanaceae plant species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat028. [PMID: 23681907 PMCID: PMC3655285 DOI: 10.1093/database/bat028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants. Database URL:http://solgenomics.net/
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Affiliation(s)
- Anuradha Pujar
- Boyce Thompson Institute for Plant Research, 533, Tower Road, Ithaca, NY 14853, USA
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17
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David-Schwartz R, Weintraub L, Vidavski R, Zemach H, Murakhovsky L, Swartzberg D, Granot D. The SlFRK4 promoter is active only during late stages of pollen and anther development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 199-200:61-70. [PMID: 23265319 DOI: 10.1016/j.plantsci.2012.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/07/2012] [Accepted: 09/24/2012] [Indexed: 05/20/2023]
Abstract
Carbohydrates are essential for male gametophyte development. However, our understanding of the mechanism by which the sugar supply is controlled in the stamen is still in its infancy. We previously reported on the stamen-specific expression of the tomato (Solanum lycopersicum) sugar metabolic gene, fructokinase 4 (SlFRK4). Here, we present the cloning and the characterization of the SlFRK4 promoter and show its differential activation during anther development. We also show that the tissue-specific expression of SlFRK4 promoter is maintained in Arabidopsis thaliana. By histochemical analyses of the GUS reporter gene and DTA toxin driven by the SlFRK4 promoter, we show that the SlFRK4 promoter is gradually activated in pollen grains throughout the later stages of anther development and upon pollen germination. In addition, we analyzed the expression profile of SlFRK4 and other sugar metabolic genes and found that SlFRK4 and the invertase LIN7 are co-expressed in mature and germinated pollen. These findings point to the existence of a specialized mechanism in which carbohydrates are provided to the male gametophyte during the later stages of its development and suggest a valuable tool for manipulating the development of male gametophytes in crop species.
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Affiliation(s)
- Rakefet David-Schwartz
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
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