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Li J, He C, Liu S, Guo Y, Zhang Y, Zhang L, Zhou X, Xu D, Luo X, Liu H, Yang X, Wang Y, Shi J, Yang B, Wang J, Wang P, Deng X, Sun C. Research progress and application strategies of sugar transport mechanisms in rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1454615. [PMID: 39233915 PMCID: PMC11371564 DOI: 10.3389/fpls.2024.1454615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024]
Abstract
In plants, carbohydrates are central products of photosynthesis. Rice is a staple that contributes to the daily calorie intake for over half of the world's population. Hence, the primary objective of rice cultivation is to maximize carbohydrate production. The "source-sink" theory is proposed as a valuable principle for guiding crop breeding. However, the "flow" research lag, especially in sugar transport, has hindered high-yield rice breeding progress. This review concentrates on the genetic and molecular foundations of sugar transport and its regulation, enhancing the fundamental understanding of sugar transport processes in plants. We illustrate that the apoplastic pathway is predominant over the symplastic pathway during phloem loading in rice. Sugar transport proteins, such as SUTs and SWEETs, are essential carriers for sugar transportation in the apoplastic pathway. Additionally, we have summarized a regulatory pathway for sugar transport genes in rice, highlighting the roles of transcription factors (OsDOF11, OsNF-YB1, OsNF-YC12, OsbZIP72, Nhd1), OsRRM (RNA Recognition Motif containing protein), and GFD1 (Grain Filling Duration 1). Recognizing that the research shortfall in this area stems from a lack of advanced research methods, we discuss cutting-edge analytical techniques such as Mass Spectrometry Imaging and single-cell RNA sequencing, which could provide profound insights into the dynamics of sugar distribution and the associated regulatory mechanisms. In summary, this comprehensive review serves as a valuable guide, directing researchers toward a deep understanding and future study of the intricate mechanisms governing sugar transport.
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Affiliation(s)
- Jun Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shihang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuting Guo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuxiu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lanjing Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dongyu Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xu Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hongying Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Wang
- College of Agricultural Science, Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Jun Shi
- Mianyang Academy of Agricultural Sciences, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, China
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
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Morffy N, Van den Broeck L, Miller C, Emenecker RJ, Bryant JA, Lee TM, Sageman-Furnas K, Wilkinson EG, Pathak S, Kotha SR, Lam A, Mahatma S, Pande V, Waoo A, Wright RC, Holehouse AS, Staller MV, Sozzani R, Strader LC. Identification of plant transcriptional activation domains. Nature 2024; 632:166-173. [PMID: 39020176 DOI: 10.1038/s41586-024-07707-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
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Affiliation(s)
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Caelan Miller
- Department of Biology, Duke University, Durham, NC, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - John A Bryant
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Tyler M Lee
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | - Sunita Pathak
- Department of Biology, Duke University, Durham, NC, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Angelica Lam
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Saloni Mahatma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Vikram Pande
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Aman Waoo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - R Clay Wright
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Max V Staller
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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Pedenla Bomzan D, Sharma A, Lemos Cruz P, Carqueijeiro I, Bellenger L, Rai A, Thippesh AK, Chinnegowda VS, Parihar D, Ducos E, Courdavault V, Nagegowda DA. ROP GTPases with a geranylgeranylation motif modulate alkaloid biosynthesis in Catharanthus roseus. PLANT PHYSIOLOGY 2024; 195:2213-2233. [PMID: 38466200 DOI: 10.1093/plphys/kiae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
Rho of Plant (ROP) GTPases function as molecular switches that control signaling processes essential for growth, development, and defense. However, their role in specialized metabolism is poorly understood. Previously, we demonstrated that inhibition of protein geranylgeranyl transferase (PGGT-I) negatively impacts the biosynthesis of monoterpene indole alkaloids (MIA) in Madagascar periwinkle (Catharanthus roseus), indicating the involvement of prenylated proteins in signaling. Here, we show through biochemical, molecular, and in planta approaches that specific geranylgeranylated ROPs modulate C. roseus MIA biosynthesis. Among the six C. roseus ROP GTPases (CrROPs), only CrROP3 and CrROP5, having a C-terminal CSIL motif, were specifically prenylated by PGGT-I. Additionally, their transcripts showed higher expression in most parts than other CrROPs. Protein-protein interaction studies revealed that CrROP3 and CrROP5, but not ΔCrROP3, ΔCrROP5, and CrROP2 lacking the CSIL motif, interacted with CrPGGT-I. Further, CrROP3 and CrROP5 exhibited nuclear localization, whereas CrROP2 was localized to the plasma membrane. In planta functional studies revealed that silencing of CrROP3 and CrROP5 negatively affected MIA biosynthesis, while their overexpression upregulated MIA formation. In contrast, silencing and overexpression of CrROP2 had no effect on MIA biosynthesis. Moreover, overexpression of ΔCrROP3 and ΔCrROP5 mutants devoid of sequence coding for the CSIL motif failed to enhance MIA biosynthesis. These results implicate that CrROP3 and CrROP5 have a positive regulatory role on MIA biosynthesis and thus shed light on how geranylgeranylated ROP GTPases mediate the modulation of specialized metabolism in C. roseus.
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Affiliation(s)
- Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anuj Sharma
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pamela Lemos Cruz
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Léo Bellenger
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Avanish Rai
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
| | - Akshay Kumar Thippesh
- Department of Biotechnology and Crop Improvement, College of Horticulture, UHS Bagalkot, Mysuru 571130, India
| | - Venkatesha S Chinnegowda
- Department of Biotechnology and Crop Improvement, College of Horticulture, UHS Bagalkot, Mysuru 571130, India
| | - Durgesh Parihar
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Eric Ducos
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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4
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Tian C, Li J, Wu Y, Wang G, Zhang Y, Zhang X, Sun Y, Wang Y. An integrative database and its application for plant synthetic biology research. PLANT COMMUNICATIONS 2024; 5:100827. [PMID: 38297840 PMCID: PMC11121754 DOI: 10.1016/j.xplc.2024.100827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants. Limited by few well-characterized bioparts for plant chassis, the development of plant synthetic biology lags behind that of its microbial counterpart. Here, we constructed a web-based Plant Synthetic BioDatabase (PSBD), which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals. Online bioinformatics tools including local BLAST, chem similarity, phylogenetic analysis, and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta. We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quantitative regulation in tobacco leaves. More powerful synthetic devices were then assembled to amplify the transcriptional signals, enabling enhanced expression of flavivirus non-structure 1 proteins in plants. The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.
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Affiliation(s)
- Chenfei Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jianhua Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuhan Wu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Guangyi Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yixin Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Xiaowei Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuwei Sun
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Yong Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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5
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Qi X, Gao H, Lv R, Mao W, Zhu J, Liu C, Mao L, Li X, Xie C. CRISPR/dCas-mediated gene activation toolkit development and its application for parthenogenesis induction in maize. PLANT COMMUNICATIONS 2023; 4:100449. [PMID: 36089769 PMCID: PMC10030315 DOI: 10.1016/j.xplc.2022.100449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/15/2022] [Accepted: 09/09/2022] [Indexed: 05/04/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems can be engineered as programmable transcription factors to either activate (CRISPRa) or inhibit transcription. Apomixis is extremely valuable for the seed industry in breeding clonal seeds with pure genetic backgrounds. We report here a CRISPR/dCas9-based toolkit equipped with dCas9-VP64 and MS2-p65-HSF1 effectors that may specifically target genes with high activation capability. We explored the application of in vivo CRISPRa targeting of maize BABY BOOM2 (ZmBBM2), acting as a fertilization checkpoint, as a means to engineer parthenogenesis. We detected ZmBBM2 transcripts only in egg cells but not in other maternal gametic cells. Activation of ZmBBM2 in egg cells in vivo caused maternal cell-autonomous parthenogenesis to produce haploid seeds. Our work provides a highly specific gene-activation CRISPRa technology for target cells and verifies its application for parthenogenesis induction in maize.
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Affiliation(s)
- Xiantao Qi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China; Hainan Yazhou Bay Seed Lab, Hainan Province 572024 China
| | - Huimin Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China
| | - Renyao Lv
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China
| | - Wenbo Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China
| | - Jinjie Zhu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China; Hainan Yazhou Bay Seed Lab, Hainan Province 572024 China
| | - Changling Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China
| | - Long Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China; Hainan Yazhou Bay Seed Lab, Hainan Province 572024 China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081 China; Hainan Yazhou Bay Seed Lab, Hainan Province 572024 China.
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6
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Brophy JAN, Magallon KJ, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR. Synthetic genetic circuits as a means of reprogramming plant roots. Science 2022; 377:747-751. [PMID: 35951698 DOI: 10.1126/science.abo4326] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The shape of a plant's root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.
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Affiliation(s)
- Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA
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7
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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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8
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Dhungana SR, Braun DM. Sugar transporters in grasses: Function and modulation in source and storage tissues. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153541. [PMID: 34634553 DOI: 10.1016/j.jplph.2021.153541] [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: 07/03/2021] [Revised: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Carbohydrate partitioning, the process of transporting carbohydrates from photosynthetic (source) tissues, such as leaves, to non-photosynthetic (sink) tissues, such as stems, roots, and reproductive structures, is vital not only for the growth and development of plants but also for withstanding biotic and abiotic stress. In many plants, sucrose is the primary form of carbohydrate loaded into the phloem for long-distance transport and unloaded into the sink tissues for utilization or storage. We highlight recent findings about 1) phloem loading in grasses, 2) the principal families of sugar transporters involved in sucrose transport, and 3) novel mechanisms by which the activities of sugar transporters are modulated. We discuss exciting discoveries from eudicot species that provide valuable insights regarding the regulation of these sugar transporters, which may be translatable to monocot species. As we better understand the intricate pathways that control the activities of various sugar transporters, we can utilize this knowledge for developing improved crop varieties.
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Affiliation(s)
- Singha R Dhungana
- Divisions of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri-Columbia, USA
| | - David M Braun
- Divisions of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri-Columbia, USA; Plant Science and Technology, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri-Columbia, USA.
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9
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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10
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Kim P, Xue CY, Song HD, Gao Y, Feng L, Li Y, Xuan YH. Tissue-specific activation of DOF11 promotes rice resistance to sheath blight disease and increases grain weight via activation of SWEET14. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:409-411. [PMID: 33047500 PMCID: PMC7955873 DOI: 10.1111/pbi.13489] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 05/03/2023]
Affiliation(s)
- Pyol Kim
- Key Laboratory of Saline‐alkali Vegetation Ecology RestorationMinistry of Education (Northeast Forestry University)HarbinChina
| | - Cai Yun Xue
- College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Hyon Dok Song
- Key Laboratory of Saline‐alkali Vegetation Ecology RestorationMinistry of Education (Northeast Forestry University)HarbinChina
| | - Yue Gao
- College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Lu Feng
- College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Yuhua Li
- Key Laboratory of Saline‐alkali Vegetation Ecology RestorationMinistry of Education (Northeast Forestry University)HarbinChina
| | - Yuan Hu Xuan
- College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
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11
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Erfatpour M, Pauls KP. A R2R3-MYB gene-based marker for the non-darkening seed coat trait in pinto and cranberry beans (Phaseolus vulgaris L.) derived from 'Wit-rood boontje'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1977-1994. [PMID: 32112124 PMCID: PMC7237406 DOI: 10.1007/s00122-020-03571-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/21/2020] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE The gene Phvul.010G130600 which codes for a MYB was shown to be tightly associated with seed coat darkening in Phaseolus vulgaris and a single nucleotide deletion in the allele in Wit-rood disrupts a transcription activation region that likely prevents its functioning in this non-darkening genotype. The beige and white background colors of the seed coats of conventional pinto and cranberry beans turn brown through a process known as postharvest darkening (PHD). Seed coat PHD is attributed to proanthocyanidin accumulation and its subsequent oxidation in the seed coat. The J gene is an uncharacterized classical genetic locus known to be responsible for PHD in common bean (P. vulgaris) and individuals that are homozygous for its recessive allele have a non-darkening (ND) seed coat phenotype. A previous study identified a major colorimetrically determined QTL for seed coat color on chromosome 10 that was associated with the ND trait. The objectives of this study were to identify a gene associated with seed coat postharvest darkening in common bean and understand its function in promoting seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL associated with the ND trait revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in non-darkening recombinant inbred lines derived from crosses between ND 'Wit-rood boontje' and a regular darkening pinto genotype. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) with a R2R3-MYB-type transcription factor MtPAR, which has been shown to regulate proanthocyanidin biosynthesis in Medicago truncatula seed coat tissue. The deletion in the 'Wit-rood boontje' allele of Phvul.010G130600 likely causes a translational frame shift that disrupts the function of a transcriptional activation domain contained in the C-terminus of the R2R3-MYB. A gene-based dominant marker was developed for the dominant allele of Phvul.010G130600 which can be used for marker-assisted selection of ND beans.
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Affiliation(s)
- M Erfatpour
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - K P Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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12
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Common Functions of Disordered Proteins across Evolutionary Distant Organisms. Int J Mol Sci 2020; 21:ijms21062105. [PMID: 32204351 PMCID: PMC7139818 DOI: 10.3390/ijms21062105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
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13
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Tai Y, Hou X, Liu C, Sun J, Guo C, Su L, Jiang W, Ling C, Wang C, Wang H, Pan G, Si X, Yuan Y. Phytochemical and comparative transcriptome analyses reveal different regulatory mechanisms in the terpenoid biosynthesis pathways between Matricaria recutita L. and Chamaemelum nobile L. BMC Genomics 2020; 21:169. [PMID: 32070270 PMCID: PMC7029581 DOI: 10.1186/s12864-020-6579-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/13/2020] [Indexed: 01/20/2023] Open
Abstract
Background Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabolites – especially the essential oils present in flowers are also different, especially the terpenoids. The aim of this project was to preliminarily identify regulatory mechanisms in the terpenoid biosynthetic pathways that differ between German and Roman chamomile by performing comparative transcriptomic and metabolomic analyses. Results We determined the content of essential oils in disk florets and ray florets in these two chamomile species, and found that the terpenoid content in flowers of German chamomile is greater than that of Roman chamomile. In addition, a comparative RNA-seq analysis of German and Roman chamomile showed that 54% of genes shared > 75% sequence identity between the two species. In particular, more highly expressed DEGs (differentially expressed genes) and TF (transcription factor) genes, different regulation of CYPs (cytochrome P450 enzymes), and rapid evolution of downstream genes in the terpenoid biosynthetic pathway of German chamomile could be the main reasons to explain the differences in the types and levels of terpenoid compounds in these two species. In addition, a phylogenetic tree constructed from single copy genes showed that German chamomile and Roman chamomile are closely related to Chrysanthemum nankingense. Conclusion This work provides the first insights into terpenoid biosynthesis in two species of chamomile. The candidate unigenes related to terpenoid biosynthesis will be important in molecular breeding approaches to modulate the essential oil composition of Matricaria recutita and Chamaemelum nobile.
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Affiliation(s)
- Yuling Tai
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaojuan Hou
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiameng Sun
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Chunxiao Guo
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Ling Su
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Jiang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Chengcheng Ling
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Chengxiang Wang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Huanhuan Wang
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Guifang Pan
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Xiongyuan Si
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Yuan
- School of Life Science, Anhui Agricultural University, Hefei, 230036, China.
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14
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Augustijn D, van Tol N, van der Zaal BJ, de Groot HJM, Alia A. High-resolution magic angle spinning NMR studies for metabolic characterization of Arabidopsis thaliana mutants with enhanced growth characteristics. PLoS One 2018; 13:e0209695. [PMID: 30596736 PMCID: PMC6312362 DOI: 10.1371/journal.pone.0209695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023] Open
Abstract
Developing smart crops which yield more biomass to meet the increasing demand for plant biomass has been an active area of research in last few decades. We investigated metabolic alterations in two Arabidopsis thaliana mutants with enhanced growth characteristics that were previously obtained from a collection of plant lines expressing artificial transcription factors. The metabolic profiles were obtained directly from intact Arabidopsis leaves using high-resolution magic angle spinning (HR-MAS) NMR. Multivariate analysis showed significant alteration of metabolite levels between the mutants and the wild-type Col-0. Interestingly, most of the metabolites that were reduced in the faster-growing mutants are generally involved in the defence against stress. These results suggest a growth-defence trade-off in the phenotypically engineered mutants. Our results further corroborate the idea that plant growth can be enhanced by suppressing defence pathways.
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Affiliation(s)
| | - Niels van Tol
- Institute of Biology Leiden, Leiden University, BE, Leiden, The Netherlands
| | | | - Huub J. M. de Groot
- Leiden Institute of Chemistry, Leiden University, RA Leiden, The Netherlands
| | - A. Alia
- Leiden Institute of Chemistry, Leiden University, RA Leiden, The Netherlands
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
- * E-mail:
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15
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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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16
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Sablok G, Hayward RJ, Davey PA, Santos RP, Schliep M, Larkum A, Pernice M, Dolferus R, Ralph PJ. SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants. Sci Rep 2018; 8:2749. [PMID: 29426939 PMCID: PMC5807536 DOI: 10.1038/s41598-017-18782-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/11/2017] [Indexed: 12/04/2022] Open
Abstract
Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php.
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Affiliation(s)
- Gaurav Sablok
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia.
| | - Regan J Hayward
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Peter A Davey
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Rosiane P Santos
- Laboratório de Recursos Genéticos, Universidade Federal de São João Del-Rei, Campus CTAN, São João Del Rei, Minas Gerais, 36307-352, Brazil
| | - Martin Schliep
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Anthony Larkum
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Rudy Dolferus
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Peter J Ralph
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia.
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17
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Lowder LG, Zhou J, Zhang Y, Malzahn A, Zhong Z, Hsieh TF, Voytas DF, Zhang Y, Qi Y. Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems. MOLECULAR PLANT 2018; 11:245-256. [PMID: 29197638 DOI: 10.1016/j.molp.2017.11.010] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 05/22/2023]
Abstract
User-friendly tools for robust transcriptional activation of endogenous genes are highly demanded in plants. We previously showed that a dCas9-VP64 system consisting of the deactivated CRISPR-associated protein 9 (dCas9) fused with four tandem repeats of the transcriptional activator VP16 (VP64) could be used for transcriptional activation of endogenous genes in plants. In this study, we developed a second generation of vector systems for enhanced transcriptional activation in plants. We tested multiple strategies for dCas9-based transcriptional activation, and found that simultaneous recruitment of VP64 by dCas9 and a modified guide RNA scaffold gRNA2.0 (designated CRISPR-Act2.0) yielded stronger transcriptional activation than the dCas9-VP64 system. Moreover, we developed a multiplex transcription activator-like effector activation (mTALE-Act) system for simultaneous activation of up to four genes in plants. Our results suggest that mTALE-Act is even more effective than CRISPR-Act2.0 in most cases tested. In addition, we explored tissue-specific gene activation using positive feedback loops. Interestingly, our study revealed that certain endogenous genes are more amenable than others to transcriptional activation, and tightly regulated genes may cause target gene silencing when perturbed by activation probes. Hence, these new tools could be used to investigate gene regulatory networks and their control mechanisms. Assembly of multiplex CRISPR-Act2.0 and mTALE-Act systems are both based on streamlined and PCR-independent Golden Gate and Gateway cloning strategies, which will facilitate transcriptional activation applications in both dicots and monocots.
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Affiliation(s)
- Levi G Lowder
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jianping Zhou
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology and Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yiping Qi
- Department of Biology, East Carolina University, Greenville, NC 27858, USA; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
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18
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Li Z, Zhang D, Xiong X, Yan B, Xie W, Sheen J, Li JF. A potent Cas9-derived gene activator for plant and mammalian cells. NATURE PLANTS 2017; 3:930-936. [PMID: 29158545 PMCID: PMC5894343 DOI: 10.1038/s41477-017-0046-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/11/2017] [Indexed: 05/19/2023]
Abstract
Overexpression of complementary DNA represents the most commonly used gain-of-function approach for interrogating gene functions and for manipulating biological traits. However, this approach is challenging and inefficient for multigene expression due to increased labour for cloning, limited vector capacity, requirement of multiple promoters and terminators, and variable transgene expression levels. Synthetic transcriptional activators provide a promising alternative strategy for gene activation by tethering an autonomous transcription activation domain (TAD) to an intended gene promoter at the endogenous genomic locus through a programmable DNA-binding module. Among the known custom DNA-binding modules, the nuclease-dead Streptococcus pyogenes Cas9 (dCas9) protein, which recognizes a specific DNA target through base pairing between a synthetic guide RNA and DNA, outperforms zinc-finger proteins and transcription activator-like effectors, both of which target through protein-DNA interactions 1 . Recently, three potent dCas9-based transcriptional activation systems, namely VPR, SAM and SunTag, have been developed for animal cells 2-6 . However, an efficient dCas9-based transcriptional activation platform is still lacking for plant cells 7-9 . Here, we developed a new potent dCas9-TAD, named dCas9-TV, through plant cell-based screens. dCas9-TV confers far stronger transcriptional activation of single or multiple target genes than the routinely used dCas9-VP64 activator in both plant and mammalian cells.
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Affiliation(s)
- Zhenxiang Li
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dandan Zhang
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiangyu Xiong
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bingyu Yan
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Xie
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jian-Feng Li
- Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
- Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
- Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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19
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Meng Z, Gao P, Chen L, Peng J, Huang J, Wu M, Chen K, Zhou Z. Artificial Zinc-Finger Transcription Factor of A20 Suppresses Restenosis in Sprague Dawley Rats after Carotid Injury via the PPARα Pathway. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:123-131. [PMID: 28918014 PMCID: PMC5493820 DOI: 10.1016/j.omtn.2017.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 01/25/2023]
Abstract
The inhibition of inflammation and vascular smooth muscle cell (VSMC) proliferation is an ideal strategy to suppress intimal hyperplasia after percutaneous transluminal angioplasty (PTA). Evidence has indicated that overexpression of A20 suppresses neointima formation, but its low transfection efficiency limits its application. Hence, we upregulated A20 expression via transfection of rAd.ATF (recombinant adenovirus vector of artificial transcription factor) and rAd.A20 in rat carotid arteries after balloon dilatation (in vivo) and isolated VSMCs (in vitro). In vivo, we found that after rAd.ATF and rAd.A20 transfection, A20 expression was markedly increased, whereas proliferating cell nuclear antigen (PCNA) and nuclear factor κB p65 (NF-κBp65) protein levels were significantly decreased, and intimal hyperplasia and secretion of proinflammatory factors were significantly reduced when compared with empty vector and saline control groups. Most importantly, the rAd.ATF-treated group showed more significant inhibition on intimal hyperplasia and expression of PCNA than the rAd.A20-treated group. In vitro, compared with the control group, transfection of rAd.ATF and rAd.A20 significantly increased A20 expression, which upregulated the proliferator-activated receptor (PPAR) level for both mRNA and protein, and reduced migration and proliferation of VSMCs and lipopolysaccharide (LPS)-induced inflammation. Furthermore, the PPARα agonist GW6471 could partially restore the effect of A20 on VSMCs. Our findings indicate that the ATF of A20 inhibits neointimal hyperplasia and, therefore, constitutes a novel potential alternative to prevent restenosis.
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Affiliation(s)
- Zhaoyou Meng
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Pan Gao
- Department of Geratology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Lin Chen
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Jing Peng
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Jialu Huang
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Min Wu
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Kangning Chen
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Zhenhua Zhou
- Department of Neurology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China.
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20
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Paul JW, Qi Y. CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects. PLANT CELL REPORTS 2016; 35:1417-27. [PMID: 27114166 DOI: 10.1007/s00299-016-1985-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/12/2016] [Indexed: 05/20/2023]
Abstract
The increasing burden of the world population on agriculture requires the development of more robust crops. Dissecting the basic biology that underlies plant development and stress responses will inform the design of better crops. One powerful tool for studying plants at the molecular level is the RNA-programmed genome editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9. Here, some of the recent advances in CRISPR/Cas9 technology that have profound implications for improving the study of plant biology are described. These tools are also paving the way towards new horizons for biotechnologies and crop development.
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Affiliation(s)
- Joseph W Paul
- Department of Biology, Thomas Harriot College of Arts and Sciences, East Carolina University, Greenville, NC, 27858, USA
| | - Yiping Qi
- Department of Biology, Thomas Harriot College of Arts and Sciences, East Carolina University, Greenville, NC, 27858, USA.
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21
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Dalton JC, Bätz U, Liu J, Curie GL, Quail PH. A Modified Reverse One-Hybrid Screen Identifies Transcriptional Activation Domains in PHYTOCHROME-INTERACTING FACTOR 3. FRONTIERS IN PLANT SCIENCE 2016; 7:881. [PMID: 27379152 PMCID: PMC4911399 DOI: 10.3389/fpls.2016.00881] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/03/2016] [Indexed: 05/27/2023]
Abstract
Transcriptional activation domains (TADs) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput manner. A plant transcriptional activator, PIF3 (phytochrome interacting factor 3), was fused to the yeast GAL4-DNA-binding Domain (BD), driving expression of the URA3 (Orotidine 5'-phosphate decarboxylase) reporter, and used for negative selection on 5-fluroorotic acid (5FOA). Randomly mutagenized variants of PIF3 were then selected for a loss or reduction in transcriptional activation activity by survival on FOA. In the process, we developed a strategy to eliminate false positives from negative selection that can be used for both reverse-1- and 2-hybrid screens. With this method we were able to identify two distinct regions in PIF3 with transcriptional activation activity, both of which are functionally conserved in PIF1, PIF4, and PIF5. Both are collectively necessary for full PIF3 transcriptional activity, but neither is sufficient to induce transcription autonomously. We also found that the TAD appear to overlap physically with other PIF3 functions, such as phyB binding activity and consequent phosphorylation. Our protocol should provide a valuable tool for identifying, analyzing and characterizing novel TADs in eukaryotic transcription factors, and thus potentially contribute to the unraveling of the mechanism underlying transcriptional activation.
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22
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Ullrich KK, Hiss M, Rensing SA. Means to optimize protein expression in transgenic plants. Curr Opin Biotechnol 2015; 32:61-67. [DOI: 10.1016/j.copbio.2014.11.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 10/29/2014] [Accepted: 11/10/2014] [Indexed: 11/24/2022]
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23
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Rastogi S, Meena S, Bhattacharya A, Ghosh S, Shukla RK, Sangwan NS, Lal RK, Gupta MM, Lavania UC, Gupta V, Nagegowda DA, Shasany AK. De novo sequencing and comparative analysis of holy and sweet basil transcriptomes. BMC Genomics 2014; 15:588. [PMID: 25015319 PMCID: PMC4125705 DOI: 10.1186/1471-2164-15-588] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/04/2014] [Indexed: 01/08/2023] Open
Abstract
Background Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing. Results The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes. Conclusion This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-588) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Dinesh A Nagegowda
- Biotechnology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, 226015 Lucknow, U,P, India.
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DePaoli HC, Borland AM, Tuskan GA, Cushman JC, Yang X. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3381-93. [PMID: 24567493 DOI: 10.1093/jxb/eru038] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To meet future food and energy security needs, which are amplified by increasing population growth and reduced natural resource availability, metabolic engineering efforts have moved from manipulating single genes/proteins to introducing multiple genes and novel pathways to improve photosynthetic efficiency in a more comprehensive manner. Biochemical carbon-concentrating mechanisms such as crassulacean acid metabolism (CAM), which improves photosynthetic, water-use, and possibly nutrient-use efficiency, represent a strategic target for synthetic biology to engineer more productive C3 crops for a warmer and drier world. One key challenge for introducing multigene traits like CAM onto a background of C3 photosynthesis is to gain a better understanding of the dynamic spatial and temporal regulatory events that underpin photosynthetic metabolism. With the aid of systems and computational biology, vast amounts of experimental data encompassing transcriptomics, proteomics, and metabolomics can be related in a network to create dynamic models. Such models can undergo simulations to discover key regulatory elements in metabolism and suggest strategic substitution or augmentation by synthetic components to improve photosynthetic performance and water-use efficiency in C3 crops. Another key challenge in the application of synthetic biology to photosynthesis research is to develop efficient systems for multigene assembly and stacking. Here, we review recent progress in computational modelling as applied to plant photosynthesis, with attention to the requirements for CAM, and recent advances in synthetic biology tool development. Lastly, we discuss possible options for multigene pathway construction in plants with an emphasis on CAM-into-C3 engineering.
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Affiliation(s)
- Henrique C DePaoli
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Anne M Borland
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA School of Biology, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Xiaohan Yang
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
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Abstract
Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.
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