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Nayak N, Mehrotra S, Karamchandani AN, Santelia D, Mehrotra R. Recent advances in designing synthetic plant regulatory modules. FRONTIERS IN PLANT SCIENCE 2025; 16:1567659. [PMID: 40241826 PMCID: PMC11999978 DOI: 10.3389/fpls.2025.1567659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Accepted: 03/17/2025] [Indexed: 04/18/2025]
Abstract
Introducing novel functions in plants through synthetic multigene circuits requires strict transcriptional regulation. Currently, the use of natural regulatory modules in synthetic circuits is hindered by our limited knowledge of complex plant regulatory mechanisms, the paucity of characterized promoters, and the possibility of crosstalk with endogenous circuits. Synthetic regulatory modules can overcome these limitations. This article introduces an integrative de novo approach for designing plant synthetic promoters by utilizing the available online tools and databases. The recent achievements in designing and validating synthetic plant promoters, enhancers, transcription factors, and the challenges of establishing synthetic circuits in plants are also discussed.
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Affiliation(s)
- Namitha Nayak
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa, India
| | | | - Diana Santelia
- Institute of Integrative Biology, ETH Zürich Universitätstrasse, Zürich, Switzerland
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences Pilani, Goa, India
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Wu B, Luo H, Chen Z, Amin B, Yang M, Li Z, Wu S, Salmen SH, Alharbi SA, Fang Z. Rice Promoter Editing: An Efficient Genetic Improvement Strategy. RICE (NEW YORK, N.Y.) 2024; 17:55. [PMID: 39212859 PMCID: PMC11364747 DOI: 10.1186/s12284-024-00735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Gene expression levels in rice (Oryza sativa L.) and other plant species are determined by the promoters, which directly control phenotypic characteristics. As essential components of genes, promoters regulate the intensity, location, and timing of gene expression. They contain numerous regulatory elements and serve as binding sites for proteins that modulate transcription, including transcription factors and RNA polymerases. Genome editing can alter promoter sequences, thereby precisely modifying the expression patterns of specific genes, and ultimately affecting the morphology, quality, and resistance of rice. This paper summarizes research on rice promoter editing conducted in recent years, focusing on improvements in yield, heading date, quality, and disease resistance. It is expected to inform the application of promoter editing and encourage further research and development in crop genetic improvement with promote.
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Affiliation(s)
- Bowen Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Hangfei Luo
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhongbo Chen
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Bakht Amin
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Manyu Yang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Zhenghan Li
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Shuai Wu
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China
| | - Saleh H Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Zhongming Fang
- Institute of Rice Industry Technology Research, Key Laboratory of Functional Agriculture of Guizhou Provincial, Department of Education, Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province, College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China.
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
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Han J, Welch T, Voß U, Vernoux T, Bhosale R, Bishopp A. The first intron of ARF7 is required for expression in root tips. iScience 2024; 27:109936. [PMID: 38832021 PMCID: PMC11145351 DOI: 10.1016/j.isci.2024.109936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/03/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024] Open
Abstract
Auxin regulates plant growth and development through the transcription factors of the AUXIN RESPONSE FACTOR (ARF) gene family. ARF7 is one of five activators that bind DNA and elicit downstream transcriptional responses. In roots, ARF7 regulates growth, gravitropism and redundantly with ARF19, lateral root organogenesis. In this study we analyzed ARF7 cis-regulation, using different non-coding sequences of the ARF7 locus to drive GFP. We show that constructs containing the first intron led to increased signal in the root tip. Although bioinformatics analyses predicted several transcription factor binding sites in the first intron, we were unable to significantly alter expression of GFP in the root by mutating these. We instead observed the intronic sequences needed to be present within the transcribed sequences to drive expression in the root meristem. These data support a mechanism by which intron-mediated enhancement regulates the tissue specific expression of ARF7 in the root meristem.
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Affiliation(s)
- Jingyi Han
- School of Biosciences, University of Nottingham, Loughborough, UK
- Department of Biosciences, Durham University, Durham, UK
| | - Thomas Welch
- School of Biosciences, University of Nottingham, Loughborough, UK
| | - Ute Voß
- School of Biosciences, University of Nottingham, Loughborough, UK
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Rahul Bhosale
- School of Biosciences, University of Nottingham, Loughborough, UK
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, UK
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Vollen K, Zhao C, Alonso JM, Stepanova AN. Sourcing DNA parts for synthetic biology applications in plants. Curr Opin Biotechnol 2024; 87:103140. [PMID: 38723389 DOI: 10.1016/j.copbio.2024.103140] [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: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024]
Abstract
Transgenic approaches are now standard in plant biology research aiming to characterize gene function or improve crops. Recent advances in DNA synthesis and assembly make constructing transgenes a routine task. What remains nontrivial is the selection of the DNA parts and optimization of the transgene design. Early career researchers and seasoned molecular biologists alike often face difficult decisions on what promoter or terminator to use, what tag to include, and where to place it. This review aims to inform about the current approaches being employed to identify and characterize DNA parts with the desired functionalities and give general advice on basic construct design. Furthermore, we hope to share the excitement about new experimental and computational tools being developed in this field.
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Affiliation(s)
- Katie Vollen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Chengsong Zhao
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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Ren H, Tang Q, Xue T, Wang Q, Xu H, Zhang Q, Pan C. A 24-bp indel within the sheep AHR gene is associated with litter size. Anim Biotechnol 2022; 33:1533-1538. [PMID: 33947312 DOI: 10.1080/10495398.2021.1914071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aryl Hydrocarbon Receptor (AHR) is a member of the PER-ARNT-SIM (PAS) family, which could mediate various biological processes, for instance, the balance of the immune system, cell proliferation, differentiation, vascular tissue remodeling and reproduction ability regulation. A previous research showed that the AHR gene exerted important functions on the pig reproduction, implying that it could serve as a candidate gene related to animal reproductive traits. Here, the aim of this work was to identify potential insertion/deletion (indel) mutations of the AHR gene in three sheep breeds and analyze the associations between these mutations and reproductive traits. Results showed that a 24-bp indel was uncovered three genotypes (II, ID and DD) in the Australian White sheep (AuW) and Lanzhou fat-tail sheep (LZFT) population, while there were only two genotypes (ID and DD) in Luxi black-headed sheep (LXBH). Moreover, the Fisher's exact test showed that the 24-bp indel mutation was significantly associated with litter size and live litter size in AuW sheep (Fisher's p < 0.05). Therefore, the 24-bp indel of sheep AHR gene can contribute to sheep marker-assisted selection breeding and further improve the sheep reproductive performance.
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Affiliation(s)
- Hongying Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Tao Xue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.,Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry co., Ltd, Tianjin, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Wang J, Xi X, Zhao S, Wang X, Yao L, Feng J, Han R. Introns in the Naa50 gene act as strong enhancers of tissue-specific expression in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111422. [PMID: 35988583 DOI: 10.1016/j.plantsci.2022.111422] [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: 05/28/2022] [Revised: 07/30/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Naa50 is the catalytic subunit of N-terminal acetyltransferase complex E, which plays an important role in regulating plant development, endoplasmic reticulum stress and immune responses in Arabidopsis. In this study, the complete genomic sequence (but not the coding sequence) of Naa50 rescued the phenotype of Naa50 deletion mutants. Naa50 expression was noted in whole roots except for central root cap cells. The deletion of intron 1 resulted in a loss of Naa50 expression in the root meristem zone and in the epidermis, cortex and endodermis of the elongation zone and mature zone, while the deletion of intron 2 decreased Naa50 expression in the epidermis, cortex and endodermis of the root elongation zone and mature zone. The native Naa50 promoter together with introns 1 and 2 promotes the expression of Naa50 in sepal vascular bundles, filaments, pollen and stigmas; however, neither intron has positive effect on Naa50 expression in mature rosette leaves. The results of this study show that introns 1 and 2 in the Naa50 gene function as enhancers to promote the tissue-specific expression of Naa50.
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Affiliation(s)
- Jin Wang
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China
| | - Xiaoyu Xi
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China; College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China
| | - Shifeng Zhao
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China; College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China
| | - Xiaolei Wang
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China; College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China
| | - Lixia Yao
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China; College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China
| | - Jinlin Feng
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China; College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China.
| | - Rong Han
- Higher Education Key Laboratory of Plant Molecular and Environment Stress Response (Shanxi Normal University) in Shanxi Province, Taiyuan 030000, Shanxi, China; College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China.
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Wu Y, Zhang L, Zeng XC, Shi W. Intronic Number Polymorphism in the Genes Encoding Potassium Channel Specific Venom Toxins from Scorpion. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422110126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Sedaghati B, Haddad R, Bandehpour M. Purslane (Portulaca oleracea L.) as a novel green-bioreactor for expression of human serum albumin (HSA) gene. Transgenic Res 2022; 31:369-380. [DOI: 10.1007/s11248-022-00296-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 01/04/2022] [Indexed: 11/29/2022]
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Hu Z, Shi X, Chen X, Zheng J, Zhang A, Wang H, Fu Q. Fine-mapping and identification of a candidate gene controlling seed coat color in melon (Cucumis melo L. var. chinensis Pangalo). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:803-815. [PMID: 34825925 DOI: 10.1007/s00122-021-03999-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
MELO3C019554 encoding a homeobox protein (PHD transcription factor) is a candidate gene that involved in the formation of seed coat color in melon. Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon is controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene is located at 11,860,000-15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A → T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 is related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.
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Affiliation(s)
- Zhicheng Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueyin Shi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuemiao Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huaisong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Qiushi Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Genome-wide identification, characterization and relative expression analysis of putative iron homeostasis genes: NAS, NAAT, and DMAS in hexaploid wheat and its progenitors. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Liu X, Ding Q, Wang W, Pan Y, Tan C, Qiu Y, Chen Y, Li H, Li Y, Ye N, Xu N, Wu X, Ye R, Liu J, Ma C. Targeted Deletion of the First Intron of the Wx b Allele via CRISPR/Cas9 Significantly Increases Grain Amylose Content in Rice. RICE (NEW YORK, N.Y.) 2022; 15:1. [PMID: 34982277 PMCID: PMC8727654 DOI: 10.1186/s12284-021-00548-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 12/28/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND The rice Waxy (Wx) gene plays a major role in seed amylose synthesis and consequently controls grain amylose content. Wx gene expression is highly regulated at the post-transcriptional level. In particular, the GT/TT polymorphism at the 5'splicing site of its 1st intron greatly affects this intron's splicing efficiency and defines two predominant Wx alleles, Wxa and Wxb. Wxa rice often harbours intermediate to high amylose contents, whereas Wxb rice exhibits low to intermediate amylose contents. By deleting the Wx 1st intron using CRISPR/Cas9 technology, we generate a completely novel Wx allele and further investigate how intron removal affects Wx gene expression and rice grain amylose content. RESULTS CRISPR/Cas9-mediated targeted deletion of the Wx 1st intron was performed on 4 rice inbred lines: KY131 (Wxb), X32 (Wxb), X35 (Wxa) and X55 (Wxlv). Deletion of the 1st intron occurred in 8.6-11.8% of the primary transformants of these 4 inbred lines. Compared to wild-type plants, amylose content was significantly increased from 13.0% to approximately 24.0% in KY131 and X32 mutant lines, which both carried the Wxb allele. However, no significant difference in amylose content was observed between wild-type plants and X35 and X55 mutant lines, which carried the Wxa and Wxlv alleles, respectively. Wx gene expression analysis of wild-type plants and mutants yielded results that were highly consistent with amylose content results. KY131 and X32 mutants accumulated increased levels of steady mRNA transcripts compared with wild-type plants, whereas steady mRNA levels were not altered in X35 and X55 mutants compared with wild-type plants. Grain quality, including appearance quality and eating and cooking quality, which are tightly associated with amylose content, was also assessed in wild-type and mutant plants, and data were presented and analysed. CONCLUSIONS This study presents a novel and rapid strategy to increase amylose content in inbred rice carrying a Wxb allele. Our data strongly suggest that the 1st intron of the Wx gene regulates Wx gene expression mainly at the post-transcriptional level in rice. This finding is in contrast to a previous hypothesis suggesting that it influences Wx gene transcription. In addition, removal of the first intron generates a completely novel Wx allele. Further studies on this new Wx allele will provide invaluable insights into the regulation of Wx gene expression, which will help researchers engineer new Wx alleles to facilitate the breeding of rice cultivars with better eating and cooking quality.
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Affiliation(s)
- Xingdan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Ding
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Wenshu Wang
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yanling Pan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Chao Tan
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yingbo Qiu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Ya Chen
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Hongjing Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Yinlong Li
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Naizhong Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Nian Xu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Xiao Wu
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Rongjian Ye
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China
| | - Jianfeng Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
| | - Chonglie Ma
- Life Science and Technology Center, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
- State Key Laboratory of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., LTD, Wuhan, 430206, Hubei, China.
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14
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Genome-Scale Computational Identification and Characterization of UTR Introns in Atalantia buxifolia. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accumulated evidence has shown that CDS introns (CIs) play important roles in regulating gene expression. However, research on UTR introns (UIs) is limited. In this study, UIs (including 5′UTR and 3′UTR introns (5UIs and 3UIs)) were identified from the Atalantia buxifolia genome. The length and nucleotide distribution characteristics of both 5UIs and 3UIs and the distributions of cis-acting elements and transcription factor binding sites (TFBSs) in 5UIs were investigated. Moreover, PageMan enrichment analysis was applied to show the possible roles of transcripts containing UIs (UI-Ts). In total, 1077 5UIs and 866 3UIs were identified from 897 5UI-Ts and 670 3UI-Ts, respectively. Among them, 765 (85.28%) 5UI-Ts and 527 (78.66%) 3UI-Ts contained only one UI, and 94 (6.38%) UI-Ts contained both 5UI and 3UI. The UI density was lower than that of CDS introns, but their mean and median intron sizes were ~2 times those of the CDS introns. The A. buxifolia 5UIs were rich in gene-expression-enhancement-related elements and contained many TFBSs for BBR-BPC, MIKC_MADS, AP2 and Dof TFs, indicating that 5UIs play a role in regulating or enhancing the expression of downstream genes. Enrichment analysis revealed that UI-Ts involved in ‘not assigned’ and ‘RNA’ pathways were significantly enriched. Noteworthily, 119 (85.61%) of the 3UI-Ts were genes encoding pentatricopeptide (PPR) repeat-containing proteins. These results will be helpful for the future study of the regulatory roles of UIs in A. buxifolia.
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Diao P, Sun H, Bao Z, Li W, Niu N, Li W, Wuriyanghan H. Expression of an Antiviral Gene GmRUN1 from Soybean Is Regulated via Intron-Mediated Enhancement (IME). Viruses 2021; 13:2032. [PMID: 34696462 PMCID: PMC8539222 DOI: 10.3390/v13102032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/18/2022] Open
Abstract
Most of R (resistance) genes encode the protein containing NBS-LRR (nucleotide binding site and leucine-rich repeat) domains. Here, N. benthamiana plants were used for transient expression assays at 3-4 weeks of age. We identified a TNL (TIR-NBS-LRR) encoding gene GmRUN1 that was resistant to both soybean mosaic virus (SMV) and tobacco mosaic virus (TMV). Truncation analysis indicated the importance of all three canonical domains for GmRUN1-mediated antiviral activity. Promoter-GUS analysis showed that GmRUN1 expression is inducible by both salicylic acid (SA) and a transcription factor GmDREB3 via the cis-elements as-1 and ERE (ethylene response element), which are present in its promoter region. Interestingly, GmRUN1 gDNA (genomic DNA) shows higher viral resistance than its cDNA (complementary DNA), indicating the existence of intron-mediated enhancement (IME) for GmRUN1 regulation. We provided evidence that intron2 of GmRUN1 increased the mRNA level of native gene GmRUN1, a soybean antiviral gene SRC7 and also a reporter gene Luciferase, indicating the general transcriptional enhancement of intron2 in different genes. In summary, we identified an antiviral TNL type soybean gene GmRUN1, expression of which was regulated at different layers. The investigation of GmRUN1 gene regulatory network would help to explore the mechanism underlying soybean-SMV interactions.
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Affiliation(s)
- Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Hongyu Sun
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Zhuo Bao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Wenxia Li
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Niu Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
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16
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Ikeda C, Taku K, Miyazaki T, Shirai R, Nelson RS, Nyunoya H, Matsushita Y, Sasaki N. Cooperative roles of introns 1 and 2 of tobacco resistance gene N in enhanced N transcript expression and antiviral defense responses. Sci Rep 2021; 11:15424. [PMID: 34326371 PMCID: PMC8322402 DOI: 10.1038/s41598-021-94713-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/15/2021] [Indexed: 12/03/2022] Open
Abstract
The tobacco virus resistance gene N contains four introns. Transient expression of transcripts from an N transgene containing these introns and driven by the native promoter in the presence of the elicitor of tobacco mosaic virus resulted in its increased expression. The requirement of the native promoter, the elicitor, or the individual introns for enhanced expression of N has not been fully studied. Here, we determined that 35S promoter-driven N transcript expression could be enhanced in the presence of the four introns regardless of the co-expression of the virus elicitor in tobacco. Function analyses using a series of N transgenes with different combination of introns revealed that the presence of intron 1 more so than intron 2 allowed higher accumulation of premature and mature N transcripts; however, both introns were important for not only enhanced gene expression but also for induction of cell death in tobacco and induced local resistance to spread of virus in Nicotiana benthamiana. Our findings indicate that introns 1 and 2 cooperatively contribute to N expression and virus resistance.
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Affiliation(s)
- Chihiro Ikeda
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Kazuo Taku
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tsumugi Miyazaki
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Rikako Shirai
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Richard S Nelson
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Hiroshi Nyunoya
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
- Faculty of Science and Engineering, Waseda University, Okubo, Shinjuku, Tokyo, 169-8555, Japan
| | - Yasuhiko Matsushita
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Nobumitsu Sasaki
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
- Institute of Global Innovation Research (GIR), Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
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17
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Venisse JS, Õunapuu-Pikas E, Dupont M, Gousset-Dupont A, Saadaoui M, Faize M, Chen S, Chen S, Petel G, Fumanal B, Roeckel-Drevet P, Sellin A, Label P. Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. Int J Mol Sci 2021; 22:7269. [PMID: 34298887 PMCID: PMC8304918 DOI: 10.3390/ijms22147269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/12/2023] Open
Abstract
Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.
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Affiliation(s)
- Jean-Stéphane Venisse
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Eele Õunapuu-Pikas
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia; (E.Õ.-P.); (A.S.)
| | - Maxime Dupont
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Aurélie Gousset-Dupont
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Mouadh Saadaoui
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
- National Institute of Agronomy of Tunisia (INAT), Crop Improvement Laboratory, INRAT, Tunis CP 1004, Tunisia
| | - Mohamed Faize
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences, University Chouaib Doukkali, El Jadida 24000, Morocco;
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; (S.C.); (S.C.)
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; (S.C.); (S.C.)
| | - Gilles Petel
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Boris Fumanal
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Patricia Roeckel-Drevet
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Arne Sellin
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia; (E.Õ.-P.); (A.S.)
| | - Philippe Label
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
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18
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Kemppainen M, Chowdhury J, Lundberg-Felten J, Pardo A. Fluorescent protein expression in the ectomycorrhizal fungus Laccaria bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes. Curr Genet 2020; 66:791-811. [PMID: 32170354 DOI: 10.1007/s00294-020-01060-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 10/24/2022]
Abstract
For long time, studies on ectomycorrhiza (ECM) have been limited by inefficient expression of fluorescent proteins (FPs) in the fungal partner. To convert this situation, we have evaluated the basic requirements of FP expression in the model ECM homobasidiomycete Laccaria bicolor and established eGFP and mCherry as functional FP markers. Comparison of intron-containing and intronless FP-expression cassettes confirmed that intron-processing is indispensable for efficient FP expression in Laccaria. Nuclear FP localization was obtained via in-frame fusion of FPs between the intron-containing genomic gene sequences of Laccaria histone H2B, while cytosolic FP expression was produced by incorporating the intron-containing 5' fragment of the glyceraldehyde-3-phosphate dehydrogenase encoding gene. In addition, we have characterized the consensus Kozak sequence of strongly expressed genes in Laccaria and demonstrated its boosting effect on transgene mRNA accumulation. Based on these results, an Agrobacterium-mediated transformation compatible plasmid set was designed for easy use of FPs in Laccaria. The four cloning plasmids presented here allow fast and highly flexible construction of C-terminal in-frame fusions between the sequences of interest and the two FPs, expressed either from the endogenous gene promoter, allowing thus evaluation of the native regulation modes of the gene under study, or alternatively, from the constitutive Agaricus bisporus gpdII promoter for enhanced cellular protein localization assays. The molecular tools described here for cell-biological studies in Laccaria can also be exploited in studies of other biotrophic or saprotrophic basidiomycete species susceptible to genetic transformation.
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Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina.
| | - Jamil Chowdhury
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Judith Lundberg-Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina
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19
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Jores T, Tonnies J, Dorrity MW, Cuperus JT, Fields S, Queitsch C. Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves. THE PLANT CELL 2020; 32:2120-2131. [PMID: 32409318 PMCID: PMC7346570 DOI: 10.1105/tpc.20.00155] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 05/04/2023]
Abstract
Genetic engineering of cis-regulatory elements in crop plants is a promising strategy to ensure food security. However, such engineering is currently hindered by our limited knowledge of plant cis-regulatory elements. Here, we adapted self-transcribing active regulatory region sequencing (STARR-seq)-a technology for the high-throughput identification of enhancers-for its use in transiently transformed tobacco (Nicotiana benthamiana) leaves. We demonstrate that the optimal placement in the reporter construct of enhancer sequences from a plant virus, pea (Pisum sativum) and wheat (Triticum aestivum), was just upstream of a minimal promoter and that none of these four known enhancers was active in the 3' untranslated region of the reporter gene. The optimized assay sensitively identified small DNA regions containing each of the four enhancers, including two whose activity was stimulated by light. Furthermore, we coupled the assay to saturation mutagenesis to pinpoint functional regions within an enhancer, which we recombined to create synthetic enhancers. Our results describe an approach to define enhancer properties that can be performed in potentially any plant species or tissue transformable by Agrobacterium and that can use regulatory DNA derived from any plant genome.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Graduate Program in Biology, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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20
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Faize M, Fumanal B, Luque F, Ramírez-Tejero JA, Zou Z, Qiao X, Faize L, Gousset-Dupont A, Roeckel-Drevet P, Label P, Venisse JS. Genome Wild Analysis and Molecular Understanding of the Aquaporin Diversity in Olive Trees ( Olea Europaea L.). Int J Mol Sci 2020; 21:E4183. [PMID: 32545387 PMCID: PMC7312470 DOI: 10.3390/ijms21114183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
Cellular aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life, playing important roles in the uptake of water and many solutes across the membranes. In olive trees, AQP diversity, protein features and their biological functions are still largely unknown. This study focuses on the structure and functional and evolution diversity of AQP subfamilies in two olive trees, the wild species Olea europaea var. sylvestris (OeuAQPs) and the domesticated species Olea europaea cv. Picual (OleurAQPs), and describes their involvement in different physiological processes of early plantlet development and in biotic and abiotic stress tolerance in the domesticated species. A scan of genomes from the wild and domesticated olive species revealed the presence of 52 and 79 genes encoding full-length AQP sequences, respectively. Cross-genera phylogenetic analysis with orthologous clustered OleaAQPs into five established subfamilies: PIP, TIP, NIP, SIP, and XIP. Subsequently, gene structures, protein motifs, substrate specificities and cellular localizations of the full length OleaAQPs were predicted. Functional prediction based on the NPA motif, ar/R selectivity filter, Froger's and specificity-determining positions suggested differences in substrate specificities of Olea AQPs. Expression analysis of the OleurAQP genes indicates that some genes are tissue-specific, whereas few others show differential expressions at different developmental stages and in response to various biotic and abiotic stresses. The current study presents the first detailed genome-wide analysis of the AQP gene family in olive trees and it provides valuable information for further functional analysis to infer the role of AQP in the adaptation of olive trees in diverse environmental conditions in order to help the genetic improvement of domesticated olive trees.
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Affiliation(s)
- Mohamed Faize
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences, University Chouaib Doukkali, El Jadida 24000, Morocco
| | - Boris Fumanal
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (B.F.); (A.G.-D.); (P.R.-D.); (P.L.)
| | - Francisco Luque
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of Jaén, 23071 Jaén, Spain; (F.L.); (J.A.R.-T.)
| | - Jorge A. Ramírez-Tejero
- Department of Experimental Biology, Center for Advanced Studies in Olive Grove and Olive Oils, University of Jaén, 23071 Jaén, Spain; (F.L.); (J.A.R.-T.)
| | - Zhi Zou
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China; (Z.Z.); (X.Q.)
| | - Xueying Qiao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China; (Z.Z.); (X.Q.)
| | - Lydia Faize
- Group of Fruit Tree Biotechnology, Department of Plant Breeding, Murcia University, CEBAS CSIC, 30100 Murcia, Spain;
| | - Aurélie Gousset-Dupont
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (B.F.); (A.G.-D.); (P.R.-D.); (P.L.)
| | - Patricia Roeckel-Drevet
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (B.F.); (A.G.-D.); (P.R.-D.); (P.L.)
| | - Philippe Label
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (B.F.); (A.G.-D.); (P.R.-D.); (P.L.)
| | - Jean-Stéphane Venisse
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (B.F.); (A.G.-D.); (P.R.-D.); (P.L.)
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21
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Shi X, Wu J, Mensah RA, Tian N, Liu J, Liu F, Chen J, Che J, Guo Y, Wu B, Zhong G, Cheng C. Genome-Wide Identification and Characterization of UTR-Introns of Citrus sinensis. Int J Mol Sci 2020; 21:E3088. [PMID: 32349372 PMCID: PMC7247714 DOI: 10.3390/ijms21093088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022] Open
Abstract
Introns exist not only in coding sequences (CDSs) but also in untranslated regions (UTRs) of a gene. Recent studies in animals and model plants such as Arabidopsis have revealed that the UTR-introns (UIs) are widely presented in most genomes and involved in regulation of gene expression or RNA stability. In the present study, we identified introns at both 5'UTRs (5UIs) and 3'UTRs (3UIs) of sweet orange genes, investigated their size and nucleotide distribution characteristics, and explored the distribution of cis-elements in the UI sequences. Functional category of genes with predicted UIs were further analyzed using GO, KEGG, and PageMan enrichment. In addition, the organ-dependent splicing and abundance of selected UI-containing genes in root, leaf, and stem were experimentally determined. Totally, we identified 825 UI- and 570 3UI-containing transcripts, corresponding to 617 and 469 genes, respectively. Among them, 74 genes contain both 5UI and 3UI. Nucleotide distribution analysis showed that 5UI distribution is biased at both ends of 5'UTR whiles 3UI distribution is biased close to the start site of 3'UTR. Cis- elements analysis revealed that 5UI and 3UI sequences were rich of promoter-enhancing related elements, indicating that they might function in regulating the expression through them. Function enrichment analysis revealed that genes containing 5UI are significantly enriched in the RNA transport pathway. While, genes containing 3UI are significantly enriched in splicesome. Notably, many pentatricopeptide repeat-containing protein genes and the disease resistance genes were identified to be 3UI-containing. RT-PCR result confirmed the existence of UIs in the eight selected gene transcripts whereas alternative splicing events were found in some of them. Meanwhile, qRT-PCR result showed that UIs were differentially expressed among organs, and significant correlation was found between some genes and their UIs, for example: The expression of VPS28 and its 3UI was significantly negative correlated. This is the first report about the UIs in sweet orange from genome-wide level, which could provide evidence for further understanding of the role of UIs in gene expression regulation.
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Affiliation(s)
- Xiaobao Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junwei Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Raphael Anue Mensah
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Na Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiapeng Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fan Liu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jialan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingru Che
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ye Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binghua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guangyan Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chunzhen Cheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Vemireddy LR, Kadambari G, Reddy GE, Kola VSR, Ramireddy E, Puram VRR, Badri J, Eslavath SN, Bollineni SN, Naik BJ, Chintala S, Pottepalem R, Akkareddy S, Nagireddy R, Reddy LVB, Bodanapu R, Lekkala SP, Chakravartty N, Siddiq EA. Uncovering of natural allelic variants of key yield contributing genes by targeted resequencing in rice (Oryza sativa L.). Sci Rep 2019; 9:8192. [PMID: 31160789 PMCID: PMC6547710 DOI: 10.1038/s41598-019-44708-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/13/2019] [Indexed: 11/09/2022] Open
Abstract
In rice (Oryza sativa L.), during the course of domestication, numerous beneficial alleles remain untapped in the progenitor wild species and landraces. This study aims at uncovering these promising alleles of six key genes influencing the yield, such as DEP1, Ghd7, Gn1a, GS3, qSW5 and sd1 by targeted resequencing of the 200 rice genotypes. In all, 543 nucleotide variations including single nucleotide polymorphisms and insertion and deletion polymorphisms were identified from the targeted genes. Of them, 225 were novel alleles, which identified in the present study only and 91 were beneficial alleles that showed significant association with the yield traits. Besides, we uncovered 128 population-specific alleles with indica being the highest of 79 alleles. The neutrality tests revealed that pleiotropic gene, Ghd7 and major grain size contributing gene, GS3 showed positive and balanced selection, respectively during the domestication. Further, the haplotype analysis revealed that some of the rice genotypes found to have rare haplotypes, especially the high yielding variety, BPT1768 has showed maximum of three genes such as Gn1a-8, qSW5-12 and GS3-29. The rice varieties with novel and beneficial alleles along with the rare haplotypes identified in the present study could be of immense value for yield improvement in the rice breeding programs.
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Affiliation(s)
- Lakshminarayana R Vemireddy
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India. .,Regional Agricultural Research Station, ANGRAU, Tirupati, India.
| | - Gopalakrishnamurty Kadambari
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - G Eswar Reddy
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Vijaya Sudhakara Rao Kola
- Biology division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, India
| | - Eswarayya Ramireddy
- Biology division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, India
| | | | - Jyothi Badri
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Suresh N Eslavath
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Swarajyalakshmi N Bollineni
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Bukya J Naik
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | | | | | | | | | | | | | | | | | - E A Siddiq
- Institute of Biotechnology, PJTSAU, Hyderabad, India
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23
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Lu H, Cui X, Liu Z, Liu Y, Wang X, Zhou Z, Cai X, Zhang Z, Guo X, Hua J, Ma Z, Wang X, Zhang J, Zhang H, Liu F, Wang K. Discovery and annotation of a novel transposable element family in Gossypium. BMC PLANT BIOLOGY 2018; 18:307. [PMID: 30486783 PMCID: PMC6264596 DOI: 10.1186/s12870-018-1519-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 11/13/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Fluorescence in situ hybridization (FISH) is an efficient cytogenetic technology to study chromosome structure. Transposable element (TE) is an important component in eukaryotic genomes and can provide insights in the structure and evolution of eukaryotic genomes. RESULTS A FISH probe derived from bacterial artificial chromosome (BAC) clone 299N22 generated striking signals on all 26 chromosomes of the cotton diploid A genome (AA, 2x=26) but very few on the diploid D genome (DD, 2x=26). All 26 chromosomes of the A sub genome (At) of tetraploid cotton (AADD, 2n=4x=52) also gave positive signals with this FISH probe, whereas very few signals were observed on the D sub genome (Dt). Sequencing and annotation of BAC clone 299N22, revealed a novel Ty3/gypsy transposon family, which was named as 'CICR'. This family is a significant contributor to size expansion in the A (sub) genome but not in the D (sub) genome. Further FISH analysis with the LTR of CICR as a probe revealed that CICR is lineage-specific, since massive repeats were found in A and B genomic groups, but not in C-G genomic groups within the Gossypium genus. Molecular evolutionary analysis of CICR suggested that tetraploid cottons evolved after silence of the transposon family 1-1.5 million years ago (Mya). Furthermore, A genomes are more homologous with B genomes, and the C, E, F, and G genomes likely diverged from a common ancestor prior to 3.5-4 Mya, the time when CICR appeared. The genomic variation caused by the insertion of CICR in the A (sub) genome may have played an important role in the speciation of organisms with A genomes. CONCLUSIONS The CICR family is highly repetitive in A and B genomes of Gossypium, but not amplified in the C-G genomes. The differential amount of CICR family in At and Dt will aid in partitioning sub genome sequences for chromosome assemblies during tetraploid genome sequencing and will act as a method for assessing the accuracy of tetraploid genomes by looking at the proportion of CICR elements in resulting pseudochromosome sequences. The timeline of the expansion of CICR family provides a new reference for cotton evolutionary analysis, while the impact on gene function caused by the insertion of CICR elements will be a target for further analysis of investigating phenotypic differences between A genome and D genome species.
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Affiliation(s)
- Hejun Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
- Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Xinglei Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xinlei Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Jinping Hua
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhiying Ma
- Key Laboratory for Crop Germplasm Resources of Hebei province, Hebei Agricultural University, Baoding, 071000 Hebei China
| | - Xiyin Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000 Hebei China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 88003 USA
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, 79409 USA
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
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24
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Chang PK, Zhang Q, Scharfenstein L, Mack B, Yoshimi A, Miyazawa K, Abe K. Aspergillus flavus GPI-anchored protein-encoding ecm33 has a role in growth, development, aflatoxin biosynthesis, and maize infection. Appl Microbiol Biotechnol 2018; 102:5209-5220. [DOI: 10.1007/s00253-018-9012-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/21/2022]
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25
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Abstract
During differentiation of CD4+CD8+ double-positive (DP) thymocytes into the CD4-CD8+ single-positive (CD8SP) thymocytes committed to the cytotoxic T cell lineage, Cd8a transcription is temporally terminated after positive selection and is subsequently reinitiated, a process known as coreceptor reversal. Despite the identification of a transcriptional enhancer in the Cd8a gene that directs reporter transgene expression specifically in CD8SP thymocytes, the molecular mechanisms controlling reactivation of the Cd8a gene are not fully understood. Here, we show that, after positive selection, hCD2 reporter expression from the Cd8a locus, which was generated by insertion of hCD2 cDNA into the first exon of the Cd8a gene, requires the incorporation of intron sequences into the hCD2 transcript. The presence of polyadenylation signals after hCD2 cDNA inhibited hCD2 expression in mature CD8+ T cells, whereas hCD2 expression in DP thymocytes recapitulated the Cd8a expression. Incorporation of the endogenous short intron structure and heterologous intron structure of the Cd4 locus restored hCD2 expression in mature CD8+ T cells in a variegated manner. Interestingly, stage-specific DNA demethylation was impaired in Cd8a reporter alleles that failed to express hCD2 in CD8+ T cells, and intron sequences lacking RNA splicing signals still restored hCD2 expression. These observations indicate that "intron-mediated enhancement" is involved in a stage-specific reactivation of the Cd8a locus harboring hCD2 cDNA. However, the Cd8a gene was transcribed in mature CD8+ T cells, albeit at a lower level, from a mutant Cd8a locus lacking intron structures, suggesting that protein-coding sequences in transcripts affect sensitivity to intron-mediated enhancement.
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26
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Li H, Huang Y. Expression of brown-midrib in a spontaneous sorghum mutant is linked to a 5'-UTR deletion in lignin biosynthesis gene SbCAD2. Sci Rep 2017; 7:11664. [PMID: 28916814 PMCID: PMC5601950 DOI: 10.1038/s41598-017-10119-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022] Open
Abstract
Brown midrib (bmr) mutants in sorghum (Sorghum bicolor (L.) Moench) and several other C4 grasses are associated with reduced lignin concentration, altered lignin composition and improved cell wall digestibility, which are desirable properties in biomass development for the emerging lignocellulosic biofuel industry. Studying bmr mutants has considerably expanded our understanding of the molecular basis underlying lignin biosynthesis and perturbation in grasses. In this study, we performed quantitative trait locus (QTL) analysis, identified and cloned a novel cinnamyl alcohol dehydrogenase allele (SbCAD2) that has an 8-bp deletion in its 5'-untranslated region (UTR), conferring the spontaneous brown midrib trait and lignin reduction in the sorghum germplasm line PI 595743. Complementation test and gene expression analysis revealed that this non-coding region alteration is associated with the significantly reduced expression of the SbCAD2 in PI 595743 throughout its growth stages. Moreover, a promoter-GUS fusion study with transgenic Arabidopsis thaliana plants found that SbCAD2 promoter is functionally conserved, driving a specific expression pattern in lignifying vascular tissues. Taken together, our results revealed the genetic basis of bmr occurrence in this spontaneous sorghum mutant and suggested the regulatory region of the SbCAD2 can be a target site for optimizing lignin modification in sorghum and other bioenergy crops.
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Affiliation(s)
- Huang Li
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yinghua Huang
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA.
- United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Science Research Laboratory, Stillwater, OK, 74075, USA.
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27
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Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol 2017; 91:145-155. [PMID: 28673892 DOI: 10.1016/j.biocel.2017.06.016] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 01/18/2023]
Abstract
In many eukaryotes, including mammals, plants, yeast, and insects, introns can increase gene expression without functioning as a binding site for transcription factors. This phenomenon was termed 'intron-mediated enhancement'. Introns can increase transcript levels by affecting the rate of transcription, nuclear export, and transcript stability. Moreover, introns can also increase the efficiency of mRNA translation. This review discusses the current knowledge about these processes. The role of splicing in IME and the significance of intron position relative to the sites of transcription and translation initiation are elaborated. Particular emphasis is placed on the question why different introns, present at the same location of the same genes and spliced at a similar high efficiency, can have very different impacts on expression - from almost no effect to considerable stimulation. This situation can be at least partly accounted for by the identification of splicing-unrelated intronic elements with a special ability to enhance mRNA accumulation or translational efficiency. The many factors that could lead to the large variation observed between the impact of introns in different genes and experimental systems are highlighted. It is suggested that there is no sole, definite answer to the question "how do introns enhance gene expression". Rather, each intron-gene combination might undergo its own unique mixture of processes that lead to the perceptible outcome.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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28
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Grant TNL, De La Torre CM, Zhang N, Finer JJ. Synthetic introns help identify sequences in the 5' UTR intron of the Glycine max polyubiquitin (Gmubi) promoter that give increased promoter activity. PLANTA 2017; 245:849-860. [PMID: 28070655 DOI: 10.1007/s00425-016-2646-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/26/2016] [Indexed: 05/03/2023]
Abstract
MAIN CONCLUSION Specific sequences within the leader intron of a soybean polyubiquitin gene stimulated gene expression when placed either within a synthetic intron or upstream of a core promoter. The intron in the 5' untranslated region of the soybean polyubiquitin promoter, Gmubi, seems to contribute to the high activity of this promoter. To identify the stimulatory sequences within the intron, ten different sequential intronic sequences of 40 nt were isolated, cloned as tetrameric repeats and placed upstream of a minimal cauliflower mosaic virus 35S (35S) core promoter, which was used to control expression of the green fluorescent protein. Intron fragment tetramers were also cloned within a modified, native intron, creating a Synthetic INtron Cassette (SINC), which was then placed downstream of Gmubi and 35S core promoters. Intron fragment tetramers and SINC constructs were evaluated using transient expression in lima bean cotyledons and stable expression in soybean hairy roots. Intron fragments, used as tetramers upstream of the 35S core promoter, yielded up to 80 times higher expression than the core promoter in transient expression analyses and ten times higher expression in stably transformed hairy roots. Tetrameric intronic fragments, cloned downstream of the Gmubi and 35S core promoters and within the synthetic intron, also yielded increased transient and stable GFP expression that was up to 4 times higher than Gmubi alone and up to 40 times higher than the 35S core promoter alone. These intron fragments contain sequences that seem to act as promoter regulatory elements and may contribute to the increased expression observed with this native strong promoter. Intron regulatory elements and synthetic introns may provide additional tools for increasing transgene expression in plants.
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Affiliation(s)
- Trudi N L Grant
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA
- Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 2725 Binion Road, Apopka, FL, 32703-8504, USA
| | - Carola M De La Torre
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA
- Division of Plant Sciences, 315 Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Ning Zhang
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Rd, Ithaca, NY, 14853, USA
| | - John J Finer
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA.
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29
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Laxa M. Intron-Mediated Enhancement: A Tool for Heterologous Gene Expression in Plants? FRONTIERS IN PLANT SCIENCE 2017; 7:1977. [PMID: 28111580 PMCID: PMC5216049 DOI: 10.3389/fpls.2016.01977] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/13/2016] [Indexed: 05/03/2023]
Abstract
Many plant promoters were characterized and used for transgene expression in plants. Even though these promoters drive high levels of transgene expression in plants, the expression patterns are rarely constitutive but restricted to some tissues and developmental stages. In terms of crop improvement not only the enhancement of expression per se but, in particular, tissue-specific and spatial expression of genes plays an important role. Introns were used to boost expression in transgenic plants in the field of crop improvement for a long time. However, the mechanism behind this so called intron-mediated enhancement (IME) is still largely unknown. This review highlights the complexity of IME on the levels of its regulation and modes of action and gives an overview on IME methodology, examples in fundamental research and models of proposed mechanisms. In addition, the application of IME in heterologous gene expression is discussed.
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Affiliation(s)
- Miriam Laxa
- Institute of Botany, Leibniz University HannoverHannover, Germany
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30
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Mathai J, Mittal SPK, Alam A, Ranade P, Mogare D, Patel S, Saxena S, Ghorai S, Kulkarni AP, Chattopadhyay S. SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster. Sci Rep 2016; 6:33779. [PMID: 27671416 PMCID: PMC5037395 DOI: 10.1038/srep33779] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 08/18/2016] [Indexed: 12/19/2022] Open
Abstract
Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-373.
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Affiliation(s)
- Jinumary Mathai
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Smriti P K Mittal
- Department of Zoology, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Aftab Alam
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Payal Ranade
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Devraj Mogare
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Sonal Patel
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Smita Saxena
- Bioinformatics Centre, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Suvankar Ghorai
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
| | - Abhijeet P Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University Campus, Pune 411007, India
| | - Samit Chattopadhyay
- Chromatin and Disease Biology Lab, National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune-411007, India
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31
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Laxa M, Müller K, Lange N, Doering L, Pruscha JT, Peterhänsel C. The 5'UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II. PLANT PHYSIOLOGY 2016; 172:313-27. [PMID: 27418588 PMCID: PMC5074633 DOI: 10.1104/pp.16.00881] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/07/2016] [Indexed: 05/19/2023]
Abstract
Photorespiration is essential for the detoxification of glycolate and recycling of carbon to the Calvin Benson Bassham cycle. Enzymes participating in the pathway have been identified, and investigations now focus on the regulation of photorespiration by transporters and metabolites. However, regulation of photorespiration on the gene level has not been intensively studied. Here, we show that maximum transcript abundance of Glu:glyoxylate aminotransferase 1 (GGT1) is regulated by intron-mediated enhancement (IME) of the 5' leader intron rather than by regulatory elements in the 5' upstream region. The intron is rich in CT-stretches and contains the motif TGTGATTTG that is highly similar to the IME-related motif TTNGATYTG. The GGT1 intron also confers leaf-specific expression of foreign promoters. Quantitative PCR analysis and GUS activity measurements revealed that IME of the GGT1 5'UTR intron is controlled on the transcriptional level. IME by the GGT1 5'UTR intron was at least 2-fold. Chromatin immunoprecipitation experiments showed that the abundance of RNA polymerase II binding to the intron-less construct is reduced.
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Affiliation(s)
- Miriam Laxa
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Kristin Müller
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Natalie Lange
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Lennart Doering
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Jan Thomas Pruscha
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
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32
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Chakravarthi M, Syamaladevi DP, Harunipriya P, Augustine SM, Subramonian N. A novel PR10 promoter from Erianthus arundinaceus directs high constitutive transgene expression and is enhanced upon wounding in heterologous plant systems. Mol Biol Rep 2016; 43:17-30. [PMID: 26671655 DOI: 10.1007/s11033-015-3934-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
In genetic engineering, inducible promoters play an important role as the expression of genes driven by them can be turned on or off under situations like biotic or abiotic factors. There are few reports on inducible promoters that can be employed in the development of transgenic plants, particularly in sugarcane. In the present study, four wound inducible genes (Chitinase, PR1A, PR10 and HRGP) were selected and were amplified from Erianthus arundinaceus, a distant relative of sugarcane. In order to determine the gene that is highly induced upon wounding, RT-qPCR was performed, which showed that PR10 gene expression was instantaneous and higher upon wounding when compared to the other three genes. Using the random amplification of genomic ends technique, a 592 bp promoter sequence was obtained and in silico analysis of the upstream regulatory region revealed a 469 bp promoter and 123 bp of 5' untranslated region (UTR). Functional analyses of the promoter sequence (with and without 5' UTR) in tobacco, rice and sugarcane using β-glucuronidase (GUS) as the reporter gene revealed the constitutive and inducible nature of the PR10 promoter. Our studies have demonstrated that the PR10 promoter, though highly constitutive, was quickly induced upon wounding as well as on treatment with abscisic acid and methyl jasmonate hormones. This is the first report on the isolation and characterization of a PR10 promoter from a wild grass and is expected to have application for development of transgenic plants.
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Affiliation(s)
- M Chakravarthi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India
| | - Divya P Syamaladevi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India
- Directorate of Rice Research (ICAR), Rajendranagar, Hyderabad, 500 030, India
| | - P Harunipriya
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India
| | | | - N Subramonian
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India.
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33
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Kage U, Kumar A, Dhokane D, Karre S, Kushalappa AC. Functional molecular markers for crop improvement. Crit Rev Biotechnol 2015; 36:917-30. [DOI: 10.3109/07388551.2015.1062743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Udaykumar Kage
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Arun Kumar
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Dhananjay Dhokane
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Shailesh Karre
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
| | - Ajjamada C. Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada, H9X3V9
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De La Torre CM, Finer JJ. The intron and 5' distal region of the soybean Gmubi promoter contribute to very high levels of gene expression in transiently and stably transformed tissues. PLANT CELL REPORTS 2015; 34:111-20. [PMID: 25292438 DOI: 10.1007/s00299-014-1691-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 06/03/2023]
Abstract
KEY MESSAGE An extended version of an intron-containing soybean polyubiquitin promoter gave very high levels of gene expression using three different validation tools. The intron-containing Glycine max polyubiquitin promoter (Gmubi) is able to regulate expression levels five times higher than the widely used CaMV35S promoter. In this study, eleven Gmubi derivatives were designed and evaluated to determine which regions contributed to the high levels of gene expression, observed with this promoter. Derivative constructs regulating GFP were evaluated using transient expression in lima bean cotyledons and stable expression in soybean hairy roots. With both expression systems, removal of the intron in the 5'UTR led to reduced levels of gene expression suggesting a role of the intron in promoter activity. Promoter constructs containing an internal intron duplication and upstream translocations of the intron resulted in higher and similar expression levels to Gmubi, respectively, indicating the presence of enhancers within the intron. Evaluation of 5' distal extensions of the Gmubi promoter resulted in significantly higher levels of GFP expression, suggesting the presence of upstream regulatory elements. A twofold increase in promoter strength was obtained when Gmubi was extended 1.5 kb upstream to generate GmubiXL (2.4 kb total length). In stably transformed soybean plants containing GFP regulated by CaMV35S, Gmubi and GmubiXL, the GmubiXL promoter clearly produced the highest levels of gene expression, with especially high GFP fluorescence in the vascular tissue and root tips. Use of GmubiXL leads to very high levels of gene expression in soybean and represents a native soybean promoter, which may be useful for regulating transgene expression for both basic and applied research.
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Affiliation(s)
- Carola M De La Torre
- Department of Horticulture and Crop Science, OARDC/The Ohio State University, 1680 Madison Ave, Wooster, OH, 44691, USA,
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Akua T, Shaul O. The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5' UTR intron. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4255-70. [PMID: 24006416 PMCID: PMC3808313 DOI: 10.1093/jxb/ert235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The mechanisms that underlie the ability of some introns to increase gene expression, a phenomenon called intron-mediated enhancement (IME), are not fully understood. It is also not known why introns localized in the 5'-untranslated region (5' UTR) are considerably longer than downstream eukaryotic introns. It was hypothesized that this extra length results from the presence of some functional intronic elements. However, deletion analyses studies carried out thus far were unable to identify specific intronic regions necessary for IME. Using deletion analysis and a gain-of-function approach, an internal element that considerably increases translational efficiency, without affecting splicing, was identified in the 5' UTR intron of the Arabidopsis thaliana MHX gene. Moreover, the ability of this element to enhance translation was diminished by a minor downstream shift in the position of introns containing it from the 5' UTR into the coding sequence. These data suggest that some of the extra length of 5' UTR introns results from the presence of elements that enhance translation, and, moreover, from the ability of 5' UTR introns to provide preferable platforms for such elements over downstream introns. The impact of the identified intronic element on translational efficiency was augmented upon removal of neighbouring intronic elements. Interference between different intronic elements had not been reported thus far. This interference may support the bioinformatics-based idea that some of the extra sequence of 5' UTR introns is also necessary for separating different functional intronic elements.
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Affiliation(s)
- Tsofit Akua
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA. Association of loblolly pine xylem development gene expression with single-nucleotide polymorphisms. TREE PHYSIOLOGY 2013; 33:763-74. [PMID: 23933831 DOI: 10.1093/treephys/tpt054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Variation in the expression of genes with putative roles in wood development was associated with single-nucleotide polymorphisms (SNPs) using a population of loblolly pine (Pinus taeda L.) that included individuals from much of the native range. Association studies were performed using 3938 SNPs and expression data obtained using quantitative real-time polymerase chain reaction (PCR) (qRT-PCR) for 106 xylem development genes in 400 clonally replicated loblolly pine individuals. A general linear model (GLM) approach, which takes the underlying population structure into consideration, was used to discover significant associations. After adjustment for multiple testing using a false discovery rate correction, 88 statistically significant associations (Q<0.05) were observed for 80 SNPs with the expression data of 33 xylem development genes. Thirty SNPs caused nonsynonymous mutations, 18 resulted in synonymous mutations, 11 were in 3' untranslated regions (UTRs), 1 was in a 5' UTR and 20 were in introns. Using AraNet, we found that Arabidopsis genes with high similarity to the loblolly pine genes involved in 21 of the 88 statistically significant associations are connected in functional gene networks. Comparisons of gene expression values revealed that in most cases the average expression in plants homozygous for the rare SNP allele was lower than that of plants that were heterozygous or homozygous for the abundant allele. Although there are association studies of SNPs and expression profiles for humans, Arabidopsis and white spruce, to the best of our knowledge, this is the first example of such an association genetic study in pines. Functional validation of these associations will lead to a deeper understanding of the molecular basis of phenotypic differences in wood development among individuals in conifer populations.
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Affiliation(s)
- Sreenath R Palle
- Department of Ecosystem Science and Management, Molecular and Environmental Plant Sciences, Texas A&M University, TAMU 2138, College Station, TX 77843, USA
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Bianchi M, Crinelli R, Giacomini E, Carloni E, Radici L, Magnani M. Yin Yang 1 intronic binding sequences and splicing elicit intron-mediated enhancement of ubiquitin C gene expression. PLoS One 2013; 8:e65932. [PMID: 23776572 PMCID: PMC3680475 DOI: 10.1371/journal.pone.0065932] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 05/02/2013] [Indexed: 12/28/2022] Open
Abstract
In a number of organisms, introns affect expression of the gene in which they are contained. Our previous studies revealed that the 5′-UTR intron of human ubiquitin C (UbC) gene is responsible for the boost of reporter gene expression and is able to bind, in vitro, Yin Yang 1 (YY1) trans-acting factor. In this work, we demonstrate that intact YY1 binding sequences are required for maximal promoter activity and YY1 silencing causes downregulation of luciferase mRNA levels. However, YY1 motifs fail to enhance gene expression when the intron is moved upstream of the proximal promoter, excluding the typical enhancer hypothesis and supporting a context-dependent action, like intron-mediated enhancement (IME). Yet, almost no expression is seen in the construct containing an unspliceable version of UbC intron, indicating that splicing is essential for promoter activity. Moreover, mutagenesis of YY1 binding sites and YY1 knockdown negatively affect UbC intron removal from both endogenous and reporter transcripts. Modulation of splicing efficiency by YY1 cis-elements and protein factor may thus be part of the mechanism(s) by which YY1 controls UbC promoter activity. Our data highlight the first evidence of the involvement of a sequence-specific DNA binding factor in IME.
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Affiliation(s)
- Marzia Bianchi
- Department of Biomolecular Sciences, Biochemistry and Molecular Biology Section, University of Urbino Carlo Bo, Urbino, Italy.
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Koo JC. Isolation of an actin promoter for strong expression of transgenes in the orchid genus Dendrobium. ACTA ACUST UNITED AC 2013. [DOI: 10.5010/jpb.2013.40.1.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Azad MAK, Morita K, Ohnishi JI, Kore-eda S. Isolation and characterization of a polyubiquitin gene and its promoter region from Mesembryanthemum crystallinum. Biosci Biotechnol Biochem 2013; 77:551-9. [PMID: 23470760 DOI: 10.1271/bbb.120807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transcript levels of the polyubiquitin gene McUBI1 had been reported to be constant during Crassulacean acid metabolism (CAM) induction in the facultative CAM plant, Mesembryanthemum crystallinum. Here, we report the sequences of the full-length cDNA of McUBI1 and its promoter, and validation of the McUBI1 promoter as an internal control driving constitutive expression in transient assays using the dual-luciferase system to investigate the regulation of CAM-related gene expression. The McUBI1 promoter drove strong, constitutive expression during CAM induction. We compared the activities of this promoter with those of the cauliflower mosaic virus (CaMV) 35S promoter in detached C3- and CAM-performing M. crystallinum and tobacco leaves. We confirmed stable expression of the genes controlled by the McUBI1 promoter with far less variability than under the CaMV 35S promoter in M. crystallinum, whereas both promoters worked well in tobacco. We found the McUBI1 promoter more suitable than the CaMV 35S promoter as an internal control for transient expression assays in M. crystallinum.
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Affiliation(s)
- Muhammad Abul Kalam Azad
- Division of Life Sciences, Graduate School of Science and Engineering, Saitama University, Japan
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Almeida T, Menéndez E, Capote T, Ribeiro T, Santos C, Gonçalves S. Molecular characterization of Quercus suber MYB1, a transcription factor up-regulated in cork tissues. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:172-8. [PMID: 23218545 DOI: 10.1016/j.jplph.2012.08.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 08/13/2012] [Accepted: 08/13/2012] [Indexed: 05/20/2023]
Abstract
The molecular processes associated with cork development in Quercus suber L. are poorly understood. A previous molecular approach identified a list of genes potentially important for cork formation and differentiation, providing a new basis for further molecular studies. This report is the first molecular characterization of one of these candidate genes, QsMYB1, coding for an R2R3-MYB transcription factor. The R2R3-MYB gene sub-family has been described as being involved in the phenylpropanoid and lignin pathways, both involved in cork biosynthesis. The results showed that the expression of QsMYB1 is putatively mediated by an alternative splicing (AS) mechanism that originates two different transcripts (QsMYB1.1 and QsMYB1.2), differing only in the 5'-untranslated region, due to retention of the first intron in one of the variants. Moreover, within the retained intron, a simple sequence repeat (SSR) was identified. The upstream regulatory region of QsMYB1 was extended by a genome walking approach, which allowed the identification of the putative gene promoter region. The relative expression pattern of QsMYB1 transcripts determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR) revealed that both transcripts were up-regulated in cork tissues; the detected expression was several times higher in newly formed cork harvested from trees producing virgin, second or reproduction cork when compared with wood. Moreover, the expression analysis of QsMYB1 in several Q. suber organs showed very low expression in young branches and roots, whereas in leaves, immature acorns or male flowers, no expression was detected. These preliminary results suggest that QsMYB1 may be related to secondary growth and, in particular, with the cork biosynthesis process with a possible alternative splicing mechanism associated with its regulatory function.
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Affiliation(s)
- Tânia Almeida
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Baixo Alentejo e Litoral (CEBAL)/Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal
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Greenham T, Altosaar I. Molecular strategies to engineer transgenic rice seed compartments for large-scale production of plant-made pharmaceuticals. Methods Mol Biol 2013; 956:311-26. [PMID: 23135861 DOI: 10.1007/978-1-62703-194-3_22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of plants as bioreactors for the large-scale production of recombinant proteins has emerged as an exciting area of research. The current shortages in protein therapeutics due to the capacity and economic bottlenecks faced with modern protein production platforms (microbial, yeast, mammalian) has driven considerable attention towards molecular pharming. Utilizing plants for the large-scale production of recombinant proteins is estimated to be 2-10% the cost of microbial platforms, and up to 1,000-fold more cost effective than mammalian platforms (Twyman et al. Trends Biotechnol 21:570-578, 2003; Sharma and Sharma, Biotechnol Adv 27:811-832, 2009). In order to achieve an economically feasible plant production host, protein expression and accumulation must be optimized. The seed, and more specifically the rice seed has emerged as an ideal candidate in molecular pharming due to its low protease activity, low water content, stable protein storage environment, relatively high biomass, and the molecular tools available for manipulation (Lau and Sun, Biotechnol Adv 27:1015-1022, 2009).
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Affiliation(s)
- Trevor Greenham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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Ye R, Zhou F, Lin Y. Two novel positive cis-regulatory elements involved in green tissue-specific promoter activity in rice (Oryza sativa L ssp.). PLANT CELL REPORTS 2012; 31:1159-72. [PMID: 22388917 DOI: 10.1007/s00299-012-1238-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/05/2012] [Accepted: 02/06/2012] [Indexed: 05/23/2023]
Abstract
UNLABELLED In plant genetic engineering, using tissue-specific promoters to control the expression of target gene is an effective way to avoid potential negative effects of using constitutive promoter, such as metabolic burden and so on. However, until now, there are few tissue-specific promoters with strong and reliable expression that could be used in crop biotechnology application. In this study, based on microarray and RT-PCR data, we identified a rice green tissue-specific expression gene DX1 (LOC_Os12g33120). The expression pattern of DX1 gene promoter was examined by using the β-glucuronidase (GUS) reporter gene and analyzed in transgenic rice plants in different tissues. Histochemical assays and quantitative analyses of GUS activity confirmed that P (DX1):GUS was highly expressed in green tissues. To identify the regulatory elements controlling the expression of the DX1 gene, a series of 5' and 3' deletions of DX1 promoter were fused to GUS gene and stably introduced into rice plants. In addition, gel mobility shift assays and site-directed mutagenesis studies were used, allowing for the identification of two novel tissue-specific cis-acting elements (GSE1 and GSE2) within P(DX1). GSE1 acted as a positive regulator in all green tissues (leaf, sheath, stem and panicle). Compared with GSE1, GSE2 acted as a positive regulator only in sheath and stem tissue, and had a weaker effect on gene expression. In addition, P(DX1):GUS was not expressed in anther and seed, this characteristic reduced the potential ecological risk and potential food safety issues. Taken together, our results strongly suggest that the identified promoter, P(DX1), and its cis regulatory elements, GSE1 and GSE2, are potentially useful in the field of rice transgenic breeding. KEY MESSAGE We have isolated and characterized the rice green tissue-specific promoter P(DX1), and identified two novel positive cis-acting elements in P(DX1).
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Affiliation(s)
- Rongjian Ye
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Kamo K, Kim AY, Park SH, Joung YH. The 5'UTR-intron of the Gladiolus polyubiquitin promoter GUBQ1 enhances translation efficiency in Gladiolus and Arabidopsis. BMC PLANT BIOLOGY 2012; 12:79. [PMID: 22672685 PMCID: PMC3406973 DOI: 10.1186/1471-2229-12-79] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/06/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND There are many non-cereal monocots of agronomic, horticultural, and biofuel importance. Successful transformation of these species requires an understanding of factors controlling expression of their genes. Introns have been known to affect both the level and tissue-specific expression of genes in dicots and cereal monocots, but there have been no studies on an intron isolated from a non-cereal monocot. This study characterizes the levels of GUS expression and levels of uidA mRNA that code for β-glucuronidase (GUS) expression in leaves of Gladiolus and Arabidopsis using GUBQ1, a polyubiquitin promoter with a 1.234 kb intron, isolated from the non-cereal monocot Gladiolus, and an intronless version of this promoter. RESULTS Gladiolus and Arabidopsis were verified by Southern hybridization to be transformed with the uidA gene that was under control of either the GUBQ1 promoter (1.9 kb), a 5' GUBQ1 promoter missing its 1.234 kb intron (0.68 kb), or the CaMV 35 S promoter. Histochemical staining showed that GUS was expressed throughout leaves and roots of Gladiolus and Arabidopsis with the 1.9 kb GUBQ1 promoter. GUS expression was significantly decreased in Gladiolus and abolished in Arabidopsis when the 5'UTR-intron was absent. In Arabidopsis and Gladiolus, the presence of uidA mRNA was independent of the presence of the 5'UTR-intron. The 5'-UTR intron enhanced translation efficiency for both Gladiolus and Arabidopsis. CONCLUSIONS The GUBQ1 promoter directs high levels of GUS expression in young leaves of both Gladiolus and Arabidopsis. The 5'UTR-intron from GUBQ1 resulted in a similar pattern of β-glucuronidase translation efficiency for both species even though the intron resulted in different patterns of uidA mRNA accumulation for each species.
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Affiliation(s)
- Kathryn Kamo
- U.S. Department of Agriculture, Floral and Nursery Plants Research Unit, Beltsville, MD, 20705-2350, USA
| | - Ah-Young Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Se Hee Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Young Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 500-757, South Korea
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Hara T, Iwata H, Okuno K, Matsui K, Ohsawa R. QTL analysis of photoperiod sensitivity in common buckwheat by using markers for expressed sequence tags and photoperiod-sensitivity candidate genes. BREEDING SCIENCE 2011; 61:394-404. [PMID: 23136477 PMCID: PMC3406765 DOI: 10.1270/jsbbs.61.394] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 09/16/2011] [Indexed: 05/08/2023]
Abstract
Photoperiod sensitivity is an important trait related to crop adaptation and ecological breeding in common buckwheat (Fagopyrum esculentum Moench). Although photoperiod sensitivity in this species is thought to be controlled by quantitative trait loci (QTLs), no genes or regions related to photoperiod sensitivity had been identified until now. Here, we identified QTLs controlling photoperiod sensitivity by QTL analysis in a segregating F(4) population (n = 100) derived from a cross of two autogamous lines, 02AL113(Kyukei SC2)LH.self and C0408-0 RP. The F(4) progenies were genotyped with three markers for photoperiod-sensitivity candidate genes, which were identified based on homology to photoperiod-sensitivity genes in Arabidopsis and 76 expressed sequence tag markers. Among the three photoperiod-sensitivity candidate genes (FeCCA1, FeELF3 and FeCOL3) identified in common buckwheat, FeELF3 was associated with photoperiod sensitivity. Two EST regions, Fest_L0606_4 and Fest_L0337_6, were associated with photoperiod sensitivity and explained 20.0% and 14.2% of the phenotypic variation, respectively. For both EST regions, the allele from 02AL113(Kyukei SC2)LH.self led to early flowering. An epistatic interaction was also confirmed between Fest_L0606_4 and Fest_L0337_6. These results demonstrate that photoperiod sensitivity in common buckwheat is controlled by a pathway consisting of photoperiod-sensitivity candidate genes as well as multiple gene action.
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Affiliation(s)
- Takashi Hara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennondai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agriculture and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Kazutoshi Okuno
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennondai, Tsukuba, Ibaraki 305-8572, Japan
| | - Katsuhiro Matsui
- National Agricultural and Food Research Organization, National Agricultural Research Center for Kyushu Okinawa Region, 2421 Suya, Koushi, Kumamoto 861-1192, Japan
| | - Ryo Ohsawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennondai, Tsukuba, Ibaraki 305-8572, Japan
- Corresponding author (e-mail: )
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Viana AAB, Fragoso RR, Guimarães LM, Pontes N, Oliveira-Neto OB, Artico S, Nardeli SM, Alves-Ferreira M, Batista JAN, Silva MCM, Grossi-de-Sa MF. Isolation and functional characterization of a cotton ubiquitination-related promoter and 5'UTR that drives high levels of expression in root and flower tissues. BMC Biotechnol 2011; 11:115. [PMID: 22115195 PMCID: PMC3239415 DOI: 10.1186/1472-6750-11-115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 11/24/2011] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) is an important crop worldwide that provides raw material to 40% of the textile fiber industry. Important traits have been studied aiming the development of genetically modified crops including resistance to insect and diseases, and tolerance to drought, cold and herbicide. Therefore, the characterization of promoters and regulatory regions is also important to achieve high gene expression and/or a specific expression pattern. Commonly, genes involved in ubiquitination pathways are highly and differentially expressed. In this study, we analyzed the expression of a cotton ubiquitin-conjugating enzyme (E2) family member with no previous characterization. RESULTS Nucleotide analysis revealed high identity with cotton E2 homologues. Multiple alignment showed a premature stop codon, which prevents the encoding of the conserved cysteine residue at the E2 active site, and an intron that is spliced in E2 homologues, but not in GhGDRP85. The GhGDRP85 gene is highly expressed in different organs of cotton plants, and has high transcript levels in roots. Its promoter (uceApro2) and the 5'UTR compose a regulatory region named uceA1.7, and were isolated from cotton and studied in Arabidopsis thaliana. uceA1.7 shows strong expression levels, equaling or surpassing the expression levels of CaMV35S. The uceA1.7 regulatory sequence drives GUS expression 7-fold higher in flowers, 2-fold in roots and at similar levels in leaves and stems. GUS expression levels are decreased 7- to 15-fold when its 5'UTR is absent in uceApro2. CONCLUSIONS uceA1.7 is a strong constitutive regulatory sequence composed of a promoter (uceApro2) and its 5'UTR that will be useful in genetic transformation of dicots, having high potential to drive high levels of transgene expression in crops, particularly for traits desirable in flower and root tissues.
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Affiliation(s)
- Antonio AB Viana
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB final W5 Norte, Brasília/DF, 70770-900, Brasil
- Universidade Católica de Brasília, QS 07 Lote 01 EPCT, Taguatinga/DF, 71966-700, Brasil
| | - Rodrigo R Fragoso
- Embrapa Cerrados, Rodovia Brasília/Fortaleza BR 020, Km18, Planaltina/DF, 73310-970, Brasil
- Depto. Biologia Celular, Universidade de Brasília, IB, Campus Universitário Darcy Ribeiro, Brasília/DF, 70910-900, Brasil
| | - Luciane M Guimarães
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB final W5 Norte, Brasília/DF, 70770-900, Brasil
| | - Naiara Pontes
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB final W5 Norte, Brasília/DF, 70770-900, Brasil
| | - Osmundo B Oliveira-Neto
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB final W5 Norte, Brasília/DF, 70770-900, Brasil
| | - Sinara Artico
- Depto. Genética, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde (CCS), Bloco A, 2° andar, Sala 85, Ilha do Fundão, Rio de Janeiro/RJ, 21941-570, Brasil
| | - Sarah M Nardeli
- Depto. Genética, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde (CCS), Bloco A, 2° andar, Sala 85, Ilha do Fundão, Rio de Janeiro/RJ, 21941-570, Brasil
| | - Marcio Alves-Ferreira
- Depto. Genética, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde (CCS), Bloco A, 2° andar, Sala 85, Ilha do Fundão, Rio de Janeiro/RJ, 21941-570, Brasil
| | - João AN Batista
- Depto. Botânica, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte/MG, 31270-901, Brasil
| | - Maria CM Silva
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB final W5 Norte, Brasília/DF, 70770-900, Brasil
| | - Maria F Grossi-de-Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB final W5 Norte, Brasília/DF, 70770-900, Brasil
- Universidade Católica de Brasília, QS 07 Lote 01 EPCT, Taguatinga/DF, 71966-700, Brasil
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Morello L, Gianì S, Troina F, Breviario D. Testing the IMEter on rice introns and other aspects of intron-mediated enhancement of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:533-44. [PMID: 20855457 PMCID: PMC3003800 DOI: 10.1093/jxb/erq273] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 08/12/2010] [Accepted: 08/12/2010] [Indexed: 05/19/2023]
Abstract
In many eukaryotes, spliceosomal introns are able to influence the level and site of gene expression. The mechanism of this Intron Mediated Enhancement (IME) has not yet been elucidated, but regulation of gene expression is likely to occur at several steps during and after transcription. Different introns have different intrinsic enhancing properties, but the determinants of these differences remain unknown. Recently, an algorithm called IMEter, which is able to predict the IME potential of introns without direct testing, has been proposed. A computer program was developed for Arabidopsis thaliana and rice (Oryza sativa L.), but was only tested experimentally in Arabidopsis by measuring the enhancement effect on GUS expression of different introns inserted within otherwise identical plasmids. To test the IMEter potential in rice, a vector bearing the upstream regulatory sequence of a rice β-tubulin gene (OsTub6) fused to the GUS reporter gene was used. The enhancing intron interrupting the OsTub6 5'-UTR was precisely replaced by seven other introns carrying different features. GUS expression level in transiently transformed rice calli does not significantly correlate with the calculated IMEter score. It was also found that enhanced GUS expression was mainly due to a strong increase in the mRNA steady-state level and that mutations at the splice recognition sites almost completely abolished the enhancing effect. Splicing also appeared to be required for IME in Arabidopsis cell cultures, where failure of the OsTub6 5' region to drive high level gene expression could be rescued by replacing the poorly spliced rice intron with one from Arabidopsis.
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Affiliation(s)
- Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, I-20133 Milano, Italy.
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Seabra AR, Vieira CP, Cullimore JV, Carvalho HG. Medicago truncatula contains a second gene encoding a plastid located glutamine synthetase exclusively expressed in developing seeds. BMC PLANT BIOLOGY 2010; 10:183. [PMID: 20723225 PMCID: PMC3095313 DOI: 10.1186/1471-2229-10-183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 08/19/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Nitrogen is a crucial nutrient that is both essential and rate limiting for plant growth and seed production. Glutamine synthetase (GS), occupies a central position in nitrogen assimilation and recycling, justifying the extensive number of studies that have been dedicated to this enzyme from several plant sources. All plants species studied to date have been reported as containing a single, nuclear gene encoding a plastid located GS isoenzyme per haploid genome. This study reports the existence of a second nuclear gene encoding a plastid located GS in Medicago truncatula. RESULTS This study characterizes a new, second gene encoding a plastid located glutamine synthetase (GS2) in M. truncatula. The gene encodes a functional GS isoenzyme with unique kinetic properties, which is exclusively expressed in developing seeds. Based on molecular data and the assumption of a molecular clock, it is estimated that the gene arose from a duplication event that occurred about 10 My ago, after legume speciation and that duplicated sequences are also present in closely related species of the Vicioide subclade. Expression analysis by RT-PCR and western blot indicate that the gene is exclusively expressed in developing seeds and its expression is related to seed filling, suggesting a specific function of the enzyme associated to legume seed metabolism. Interestingly, the gene was found to be subjected to alternative splicing over the first intron, leading to the formation of two transcripts with similar open reading frames but varying 5' UTR lengths, due to retention of the first intron. To our knowledge, this is the first report of alternative splicing on a plant GS gene. CONCLUSIONS This study shows that Medicago truncatula contains an additional GS gene encoding a plastid located isoenzyme, which is functional and exclusively expressed during seed development. Legumes produce protein-rich seeds requiring high amounts of nitrogen, we postulate that this gene duplication represents a functional innovation of plastid located GS related to storage protein accumulation exclusive to legume seed metabolism.
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Affiliation(s)
- Ana R Seabra
- Instituto de Biologia Molecular e Celular da Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular da Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Julie V Cullimore
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique - Centre National de la Recherche Scientifique, Boite Postale 52627, 31326 Castanet-Tolosan Cedex, France
| | - Helena G Carvalho
- Instituto de Biologia Molecular e Celular da Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
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Kumar GR, Sakthivel K, Sundaram R, Neeraja C, Balachandran S, Rani NS, Viraktamath B, Madhav M. Allele mining in crops: Prospects and potentials. Biotechnol Adv 2010; 28:451-61. [DOI: 10.1016/j.biotechadv.2010.02.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 09/21/2009] [Accepted: 09/25/2009] [Indexed: 12/26/2022]
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Guo L, Yu Y, Xia X, Yin W. Identification and functional characterisation of the promoter of the calcium sensor gene CBL1 from the xerophyte Ammopiptanthus mongolicus. BMC PLANT BIOLOGY 2010; 10:18. [PMID: 20113489 PMCID: PMC2844064 DOI: 10.1186/1471-2229-10-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 01/29/2010] [Indexed: 05/06/2023]
Abstract
BACKGROUND CBL1 is a calcium sensor that regulates drought, cold and salt signals in Arabidopsis. Overexpression of CBL1 gene in Arabidopsis and in Ammopiptanthus mongolicus showed different tolerant activities. We are interested in understanding the molecular mechanism of the upstream region of the CBL1 gene of A. mongolicus (AmCBL1). We investigated and characterized the promoter of the AmCBL1 gene, for promoters play a very important role in regulating gene expression in eukaryotes. RESULTS A 1683-bp 5' flanking region was isolated from A. mongolicus. The sequence was identified as AmCBL1 promoter. Analysis of the promoter sequence indicated a 690-bp intron and some basic cis-acting elements were related to various environmental stresses and plant hormones. To identify the functional region of the AmCBL1 promoter, five plant expression vectors fused with the GUS (beta-glucuronidase) gene, driven by series deleted fragments of AmCBL1 promoter at different lengths from -1659, -1414, -1048, -296 to -167 bp relative to the transcriptional start site were constructed and transformed into Nicotiana tabacum L. cv. 89. Functional properties of each promoter segment were examined by GUS staining and fluorescence quantitative analyses using at least three single-copy PCR-positive plants of transgenic tobacco, treated with various environmental stresses and plant hormones for different times. We demonstrated that the AmCBL1 promoter was a vascular-specific and multiple-stress-inducible promoter. Our results further imply that the promoter fragment B1S3 possessed sufficient essential cis-acting elements, accounting for vascular-specific and stress-induced expression patterns. It may also indicate that for response to some stresses certain cis-elements are required in tissues outside the region of the B1S3 construct. CONCLUSIONS To help resolve uncertainties about the upstream regulatory mechanism of the CBL1 gene in desert plants, we suggest that the function of the AmCBL1 promoter, particularly under conditions of abiotic stress, to be examined for possible usefulness in molecular breeding. Regardless of the outcome, the allocation and relative quantification of the GUS-fusion AmCBL1 promoter segments at transcriptional levels in different tissues under various stresses across separate promoter segments suggests that the AmCBL1 promoter is a phloem-specific and multiple-stress-inducible promoter. These data coupled with the ongoing AmCBL1 5' UTR intron analyses provide a solid foundation for their future use in molecular breeding as new promoters of stress-resistance genes from desert plants.
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Affiliation(s)
- Lili Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, PR China
| | - Yanhua Yu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, PR China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, PR China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, PR China
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A potent enhancer element in the 5′-UTR intron is crucial for transcriptional regulation of the human ubiquitin C gene. Gene 2009; 448:88-101. [DOI: 10.1016/j.gene.2009.08.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 08/26/2009] [Accepted: 08/28/2009] [Indexed: 02/01/2023]
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