1
|
Liu X, Li S, Yang W, Mu B, Jiao Y, Zhou X, Zhang C, Fan Y, Chen R. Synthesis of Seed-Specific Bidirectional Promoters for Metabolic Engineering of Anthocyanin-Rich Maize. PLANT & CELL PHYSIOLOGY 2018; 59:1942-1955. [PMID: 29917151 DOI: 10.1093/pcp/pcy110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
Tissue-specific promoters play an important role in plant molecular farming. Here, we describe a strategy to modify the tissue specificity of a maize embryo-specific bidirectional promoter PZmBD1. Six types of cis-elements, i.e. RY repeats (R), GCN4 (G), the prolamin box (P), Skn-1 (S), and the ACGT and AACA (A) motifs, were collected and fused to PZmBD1 to generate eight chimeric putative bidirectional promoters. Qualitative and quantitative analysis of reporter genes driven by the promoters showed that two promoters exhibited high seed-specific bidirectional activity in maize transient and stable transformed systems. The stronger one was chosen and fused to the intergenic region of two gene clusters consisting of four anthocyanin biosynthesis-related genes (ZmBz1, ZmBz2, ZmC1 and ZmR2) and seven reporter genes, resulting in the first embryo and endosperm anthocyanin-rich purple maize. Anthocyanin analysis showed that the total anthocyanin content reaches 2,910 mg kg-1 DW in transgenic maize and cyanidin is the major anthocyanin in transgenic maize, as in natural varieties. The expression profile analysis of endogenous genes showed that the anthocyanin biosynthesis pathway was activated by two transgenic transcription factor genes ZmC1 and ZmR2. Our results indicate that both the modification strategy and these functionally characterized tissue-specific bidirectional promoters generated could be used for genetic research and development of plant biotechnology products. The anthocyanin-rich purple maize could provide economic natural colorants for the food and beverage industry, and valuable germplasm for developing anthocyanin-rich fresh corn.
Collapse
Affiliation(s)
- Xiaoqing Liu
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Suzhen Li
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Wenzhu Yang
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Bona Mu
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Yong Jiao
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaojin Zhou
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Chunyi Zhang
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Yunliu Fan
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| | - Rumei Chen
- Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, China
| |
Collapse
|
2
|
Stephenson SEM, Aumann TD, Taylor JM, Riseley JR, Li R, Mann JR, Tomas D, Lockhart PJ. Generation and characterisation of a parkin-Pacrg knockout mouse line and a Pacrg knockout mouse line. Sci Rep 2018; 8:7528. [PMID: 29760428 PMCID: PMC5951884 DOI: 10.1038/s41598-018-25766-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/25/2018] [Indexed: 11/24/2022] Open
Abstract
Mutations in PARK2 (parkin) can result in Parkinson's disease (PD). Parkin shares a bidirectional promoter with parkin coregulated gene (PACRG) and the transcriptional start sites are separated by only ~200 bp. Bidirectionally regulated genes have been shown to function in common biological pathways. Mice lacking parkin have largely failed to recapitulate the dopaminergic neuronal loss and movement impairments seen in individuals with parkin-mediated PD. We aimed to investigate the function of PACRG and test the hypothesis that parkin and PACRG function in a common pathway by generating and characterizing two novel knockout mouse lines harbouring loss of both parkin and Pacrg or Pacrg alone. Successful modification of the targeted allele was confirmed at the genomic, transcriptional and steady state protein levels for both genes. At 18-20 months of age, there were no significant differences in the behaviour of parental and mutant lines when assessed by openfield, rotarod and balance beam. Subsequent neuropathological examination suggested there was no gross abnormality of the dopaminergic system in the substantia nigra and no significant difference in the number of dopaminergic neurons in either knockout model compared to wildtype mice.
Collapse
Affiliation(s)
- Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Timothy D Aumann
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Juliet M Taylor
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jessica R Riseley
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia
| | - Ruili Li
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Surgical Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia
| | - Jeffrey R Mann
- Monash Genome Modification Platform, Monash University, Clayton, Victoria, Australia
| | - Doris Tomas
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria, Australia.
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
3
|
Meersseman C, Letaief R, Léjard V, Rebours E, Guillocheau G, Esquerré D, Djari A, Chamberlain A, Vander Jagt C, Klopp C, Boussaha M, Renand G, Maftah A, Petit D, Rocha D. Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. DNA Res 2017; 24:221-233. [PMID: 28338730 PMCID: PMC5499805 DOI: 10.1093/dnares/dsx004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
Collapse
Affiliation(s)
- Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Léjard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gabriel Guillocheau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Anis Djari
- SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France
| | - Amanda Chamberlain
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | - Christy Vander Jagt
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | | | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Daniel Petit
- GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| |
Collapse
|
4
|
Wang R, Yan Y, Zhu M, Yang M, Zhou F, Chen H, Lin Y. Isolation and Functional Characterization of Bidirectional Promoters in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:766. [PMID: 27303432 PMCID: PMC4885881 DOI: 10.3389/fpls.2016.00766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/17/2016] [Indexed: 05/19/2023]
Abstract
Bidirectional promoters, which show great application potential in genetic improvement of plants, have aroused great research interest recently. However, most bidirectional promoters were cloned individually in the studies of single genes. Here, we initiatively combined RNA-seq data and cDNA microarray data to discover the potential bidirectional promoters in rice genome. Based on the expression level and correlation of each adjacent and oppositely transcribed gene pair, we selected four candidate gene pairs. Then, the intergenic region between each pair was isolated and cloned into a dual reporter vector pDX2181 for functional identification. GUS and GFP assays of the transgenic plants indicated that all the intergenic regions showed bidirectional expression activity in various tissues. Through 5' and 3' deletion analysis on one of the above bidirectional promoters, we identified the enhancing region which sharply increased its bidirectional expression efficiency and the essential regions respectively responsible for its 5' and 3' basic expression activity. The bidirectional arrangement of the four gene pairs in six gramineous plants was also analyzed, showing the conserved characteristics of the four bidirectional promoters identified in our study. In addition, two novel cis-sequences conserved in the four bidirectional promoters were discovered by bioinformatic identification. Our study proposes a feasible method for selecting, cloning, and functionally identifying bidirectional promoters as well as for discovering their bidirectional regulatory regions and conserved sequences in rice.
Collapse
Affiliation(s)
- Rui Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Yan Yan
- Chinese Academy of Tropical Agricultural SciencesHainan, China
| | - Menglin Zhu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Mei Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Yongjun Lin
| |
Collapse
|
5
|
Liu X, Zhou X, Li Y, Tian J, Zhang Q, Li S, Wang L, Zhao J, Chen R, Fan Y. Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize. BMC Genomics 2014; 15:338. [PMID: 24886269 PMCID: PMC4035068 DOI: 10.1186/1471-2164-15-338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/25/2014] [Indexed: 11/21/2022] Open
Abstract
Background Bidirectional gene pairs exist as a specific form of gene organization in microorganisms and mammals as well as in model plant species, such as Arabidopsis and rice. Little is known about bidirectional gene pairs in maize, which has a large genome and is one of the most important grain crops. Results We conducted a genome-wide search in maize using genome sequencing results from the inbred line B73. In total, 1696 bidirectional transcript pairs were identified using a modified search model. We functionally characterized the promoter activity of the intergenic regions of most of the bidirectional transcript pairs that were expressed in embryos using a maize embryo transient expression system. A comparative study of bidirectional gene pairs performed for three monocot (Zea mays, Sorghum bicolor and Oryza sativa) and two dicot (Arabidopsis thaliana and Glycine max) plant genomes showed that bidirectional gene pairs were abundant in the five plant species. Orthologous bidirectional gene pairs were clearly distinguishable between the monocot and dicot species although the total numbers of orthologous bidirectional genes were similar. Analysis of the gene pairs using the Blast2GO software suite showed that the molecular functions (MF), cellular components (CC), and biological processes (BP) associated with the bidirectional transcripts were similar among the five plant species. Conclusions The evolutionary analysis of the function and structure of orthologous bidirectional gene pairs in various plant species revealed a potential pathway of their origin, which may be required for the evolution of a new species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-338) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Rumei Chen
- Department of crop genomics and genetic improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | | |
Collapse
|
6
|
Petridis M, Chatzidimitriou D. Characterization of an intergenic polymorphic site (pp-hC1A_5) in Wolbachia pipientis (wPip). Mol Ecol Resour 2011; 11:753-6. [PMID: 21676204 DOI: 10.1111/j.1755-0998.2011.02991.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Wolbachia pipientis (wPip) is an intracellular bacterium causing cytoplasmic incompatibility in arthropods, including mosquitoes of the Culex pipiens complex. Here, we present a method useful for genotyping within the wPip group. Primers were designed using a Tandem Repeat Finder program to amplify an intergenic, polymorphic site (pp-hC1A_5) of wPip. The polymorphic site is located between genes that code for polynucleotide phosphorylase and a hypothetical protein (C1A_5). Comparison of these wPip genomic regions from C. pipiens mosquitoes sampled in different geographic regions revealed deletions of fragments that proved useful in phylogenetic analysis.
Collapse
Affiliation(s)
- Michael Petridis
- Department of Parasitology and Infectious Diseases, Veterinary School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | | |
Collapse
|
7
|
Oh-Hashi K, Koga H, Ikeda S, Shimada K, Hirata Y, Kiuchi K. Role of an ER stress response element in regulating the bidirectional promoter of the mouse CRELD2 - ALG12 gene pair. BMC Genomics 2010; 11:664. [PMID: 21106106 PMCID: PMC3091781 DOI: 10.1186/1471-2164-11-664] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/25/2010] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Recently, we identified cysteine-rich with EGF-like domains 2 (CRELD2) as a novel endoplasmic reticulum (ER) stress-inducible gene and characterized its transcriptional regulation by ATF6 under ER stress conditions. Interestingly, the CRELD2 and asparagine-linked glycosylation 12 homolog (ALG12) genes are arranged as a bidirectional (head-to-head) gene pair and are separated by less than 400 bp. In this study, we characterized the transcriptional regulation of the mouse CRELD2 and ALG12 genes that is mediated by a common bidirectional promoter. RESULTS This short intergenic region contains an ER stress response element (ERSE) sequence and is well conserved among the human, rat and mouse genomes. Microarray analysis revealed that CRELD2 and ALG12 mRNAs were induced in Neuro2a cells by treatment with thapsigargin (Tg), an ER stress inducer, in a time-dependent manner. Other ER stress inducers, tunicamycin and brefeldin A, also increased the expression of these two mRNAs in Neuro2a cells. We then tested for the possible involvement of the ERSE motif and other regulatory sites of the intergenic region in the transcriptional regulation of the mouse CRELD2 and ALG12 genes by using variants of the bidirectional reporter construct. With regards to the promoter activities of the CRELD2-ALG12 gene pair, the entire intergenic region hardly responded to Tg, whereas the CRELD2 promoter constructs of the proximal region containing the ERSE motif showed a marked responsiveness to Tg. The same ERSE motif of ALG12 gene in the opposite direction was less responsive to Tg. The direction and the distance of this motif from each transcriptional start site, however, has no impact on the responsiveness of either gene to Tg treatment. Additionally, we found three putative sequences in the intergenic region that antagonize the ERSE-mediated transcriptional activation. CONCLUSIONS These results show that the mouse CRELD2 and ALG12 genes are arranged as a unique bidirectional gene pair and that they may be regulated by the combined interactions between ATF6 and multiple other transcriptional factors. Our studies provide new insights into the complex transcriptional regulation of bidirectional gene pairs under pathophysiological conditions.
Collapse
Affiliation(s)
- Kentaro Oh-Hashi
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | | | | | | | | | | |
Collapse
|