1
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Zerpa-Catanho D, Clough SJ, Ming R. Characterization and analysis of the promoter region of monodehydroascorbate reductase 4 (CpMDAR4) in papaya. PLANT REPRODUCTION 2022; 35:233-264. [PMID: 35920937 DOI: 10.1007/s00497-022-00447-2] [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: 01/07/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Differential spatial and temporal expression patterns due to regulatory cis-elements and two different isoforms are detected among CpMDAR4 alleles in papaya. The aim of this research was to study the effects of cis-element differences between the X, Y and Yh alleles on the expression of CpMDAR4, a potential candidate gene for sex differentiation in papaya, using a transcriptional reporter system in a model species Arabidopsis thaliana. Possible effects of a retrotransposon insertion in the Y and Yh alleles on the transcription and expression of CpMDAR4 alleles in papaya flowers were also examined. When comparing promoters and cis-regulatory elements among genes in the non-recombining region of the sex chromosomes, paired genes exhibited differences. Our results showed that differences in the promoter sequences of the CpMDAR4 alleles drove the expression of a reporter gene to different flower tissues in Arabidopsis. β-glucuronidase staining analysis of T2 and T3 lines for constructs containing 5' deletions of native Y and Yh allele promoters showed the loss of specific expression of the reporter gene in the anthers, confirming the existence and location of cis-regulatory element POLLEN1LELAT52. The expression analysis of CpMDAR4 alleles in papaya flowers also showed that all alleles are actively expressed in different flower tissues, with the existence of a shorter truncated isoform, with unknown function, for the Y and Yh alleles due to an LTR-RT insertion in the Y and Yh chromosomes. The observed expression patterns in Arabidopsis thaliana flowers and the expression patterns of CpMDAR4 alleles in papaya flowers suggest that MDAR4 might have a role on development of reproductive organs in papaya, and that it constitutes an important candidate for sex differentiation.
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Affiliation(s)
| | - Steven J Clough
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- United States Department of Agriculture, Agricultural Research Service, Urbana, IL, 61801, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA.
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2
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Yim WC, Swain ML, Ma D, An H, Bird KA, Curdie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, Cushman JC, Edger PP, Mason AS, Pires JC, Tang H, Zhang X. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. THE PLANT CELL 2022; 34:4143-4172. [PMID: 35961044 PMCID: PMC9614464 DOI: 10.1093/plcell/koac249] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/24/2022] [Indexed: 05/05/2023]
Abstract
Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.
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Affiliation(s)
| | | | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - David D Curdie
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel Wang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hyun Don Ham
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Juan K Q Solomon
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada, Reno, Nevada 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Annaliese S Mason
- Plant Breeding Department, INRES, The University of Bonn, Bonn 53115, Germany
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, , University of Missouri, Columbia, Missouri 65211, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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3
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Arce RC, Carrillo N, Pierella Karlusich JJ. The chloroplast redox-responsive transcriptome of solanaceous plants reveals significant nuclear gene regulatory motifs associated to stress acclimation. PLANT MOLECULAR BIOLOGY 2022; 108:513-530. [PMID: 35044587 DOI: 10.1007/s11103-022-01240-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Transcriptomes of solanaceous plants expressing a plastid-targeted antioxidant protein were analysed to identify chloroplast redox networks modulating the expression of nuclear genes associated with stress acclimation. Plastid functions depend on the coordinated expression of nuclear genes, many of them associated to developmental and stress response pathways. Plastid-generated signals mediate this coordination via retrograde signaling, which includes sensing of chloroplast redox state and levels of reactive oxygen species (ROS), although it remains a poorly understood process. Chloroplast redox poise and ROS build-up can be modified by recombinant expression of a plastid-targeted antioxidant protein, i.e., cyanobacterial flavodoxin, with the resulting plants displaying increased tolerance to multiple environmental challenges. Here we analysed the transcriptomes of these flavodoxin-expressing plants to study the coordinated transcriptional responses of the nucleus to the chloroplast redox status and ROS levels during normal growth and stress responses (drought or biotic stress) in tobacco and potato, members of the economically important Solanaceae family. We compared their transcriptomes against those from stressed and mutant plants accumulating ROS in different subcellular compartments and found distinct ROS-related imprints modulated by flavodoxin expression and/or stress. By introducing our datasets in a large-scale interaction network, we identified transcriptional factors related to ROS and stress responses potentially involved in flavodoxin-associated signaling. Finally, we discovered identical cis elements in the promoters of many genes that respond to flavodoxin in the same direction as in wild-type plants under stress, suggesting a priming effect of flavodoxin before stress manifestation. The results provide a genome-wide picture illustrating the relevance of chloroplast redox status on biotic and abiotic stress responses and suggest new cis and trans targets to generate stress-tolerant solanaceous crops.
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Affiliation(s)
- Rocío C Arce
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Juan J Pierella Karlusich
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, 75005, Paris, France.
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4
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Irigoyen S, Ramasamy M, Misra A, McKnight TD, Mandadi KK. A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers. PLANT PHYSIOLOGY 2022; 188:397-410. [PMID: 34597402 PMCID: PMC8774732 DOI: 10.1093/plphys/kiab450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) BTB-TAZ DOMAIN PROTEIN 2 (BT2) contains an N-terminal BTB domain, a central TAZ zinc-finger protein-protein interaction domain, and a C-terminal calmodulin-binding domain. We previously demonstrated that BT2 regulates telomerase activity and mediates multiple responses to nutrients, hormones, and abiotic stresses in Arabidopsis. Here, we describe the essential role of BT2 in activation of genes by multimerized Cauliflower mosaic virus 35S (35S) enhancers. Loss of BT2 function in several well-characterized 35S enhancer activation-tagged lines resulted in suppression of the activation phenotypes. Suppression of the phenotypes was associated with decreased transcript abundance of the tagged genes. Nuclear run-on assays, mRNA decay studies, and bisulfite sequencing revealed that BT2 is required to maintain the transcriptionally active state of the multimerized 35S enhancers, and lack of BT2 leads to hypermethylation of the 35S enhancers. The TAZ domain and the Ca++/calmodulin-binding domain of BT2 are critical for its function and 35S enhancer activity. We further demonstrate that BT2 requires CULLIN3 and two bromodomain-containing Global Transcription factor group E proteins (GTE9 and GTE11), to regulate 35S enhancer activity. We propose that the BT2-CULLIN3 ubiquitin ligase, through interactions with GTE9 and GTE11, regulates 35S enhancer activity in Arabidopsis.
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Affiliation(s)
- Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
| | | | - Anjali Misra
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Thomas D McKnight
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
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5
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Bai R, Luo Y, Wang L, Li J, Wu K, Zhao G, Duan D. A specific allele of MYB14 in grapevine correlates with high stilbene inducibility triggered by Al 3+ and UV-C radiation. PLANT CELL REPORTS 2019; 38:37-49. [PMID: 30302553 PMCID: PMC6320375 DOI: 10.1007/s00299-018-2347-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/01/2018] [Indexed: 05/13/2023]
Abstract
The structural differences of MYB14 promoter in two grapevine genotypes affect the expression of MYB14 and stilbene synthesis in response to Al3+ and UV-C radiation. Grapevines provide an important fruit crop worldwide, but production is often limited by pathogen infection. Stilbenes, a class of secondary metabolite, represent phytoalexins that contribute to defence against pathogens in many plants, including grapevine. It is known that the transcription factors MYB14 and MYB15 are required for the activation of the promoters of resveratrol synthase to regulate stilbene biosynthesis. In the current study, we observed that stilbene levels were more highly induced by Al3+ and UV-C radiation treatments in the cultivar Vitis labrusca 'Concord' than in the cultivar V. vinifera 'Cabernet Sauvignon'. We investigated whether genetic/structural variations in the MYB14 and MYB15 promoters between these two representative genotypes are responsible for the differences in stilbene accumulation. Significant differences in the structure and activity of the promoter of MYB14, but not MYB15 were identified between the two genotypes, following heterologous expression in Nicotiana benthamiana system and treatments with Al3+ and UV-C. Hydrogen peroxide (H2O2) was detected in Concord soon after the stress treatments, but after diphenyleneiodonium chloride pre-treatment, the expressing level of VlMYB14, the promoter activity of VlMYB14 and the accumulation of stilbenes was significantly reduced. A model is presented where the induction of MYB14 contributes to stilbene accumulation in Concord following Al3+ and UV-C treatments involving reactive oxygen species (ROS) production as an early signal.
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Affiliation(s)
- Ru Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yangyang Luo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Lixin Wang
- Research Center of Chinese Jujube, Agricultural University of Hebei, Baoding, 071001, Hebei, China
| | - Jing Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Kerun Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Dong Duan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China.
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6
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Trapero‐Mozos A, Morris WL, Ducreux LJM, McLean K, Stephens J, Torrance L, Bryan GJ, Hancock RD, Taylor MA. Engineering heat tolerance in potato by temperature-dependent expression of a specific allele of HEAT-SHOCK COGNATE 70. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:197-207. [PMID: 28509353 PMCID: PMC5785350 DOI: 10.1111/pbi.12760] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/03/2017] [Accepted: 05/11/2017] [Indexed: 05/23/2023]
Abstract
For many commercial potato cultivars, tuber yield is optimal at average daytime temperatures in the range of 14-22 °C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. The aim of this study was to use a genetic screen based on a model tuberization assay to identify quantitative trait loci (QTL) associated with enhanced tuber yield. A candidate gene encoding HSc70 was identified within one of the three QTL intervals associated with elevated yield in a Phureja-Tuberosum hybrid diploid potato population (06H1). A particular HSc70 allelic variant was linked to elevated yield in the 06H1 progeny. Expression of this allelic variant was much higher than other alleles, particularly on exposure to moderately elevated temperature. Transient expression of this allele in Nicotiana benthamiana resulted in significantly enhanced tolerance to elevated temperature. An TA repeat element was present in the promoter of this allele, but not in other HSc70 alleles identified in the population. Expression of the HSc70 allelic variant under its native promoter in the potato cultivar Desiree resulted in enhanced HSc70 expression at elevated temperature. This was reflected in greater tolerance to heat stress as determined by improved yield under moderately elevated temperature in a model nodal cutting tuberization system and in plants grown from stem cuttings. Our results identify HSc70 expression level as a significant factor influencing yield stability under moderately elevated temperature and identify specific allelic variants of HSc70 for the induction of thermotolerance via conventional introgression or molecular breeding approaches.
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Affiliation(s)
| | - Wayne L. Morris
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | | | - Karen McLean
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | | | - Lesley Torrance
- School of BiologyUniversity of St AndrewsSt AndrewsFifeUK
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | - Glenn J. Bryan
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | | | - Mark A. Taylor
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
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7
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Li D, Lei Z, Xue J, Zhou G, Hang Y, Sun X. Regulation of FATTY ACID ELONGATION1 expression and production in Brassica oleracea and Capsella rubella. PLANTA 2017; 246:763-778. [PMID: 28674753 DOI: 10.1007/s00425-017-2731-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The contribution of variations in coding regions or promoters to the changes in FAE1 expression levels have be quantified and compared in parallel by specifically designed swapping constructs. FATTY ACID ELONGATION1 (FAE1) is a key gene in control of erucic acid synthesis in plant seeds. The expression of FAE1 genes in Brassica oleracea and Capsella rubella, representatives of high and low erucic acid species, respectively, was characterized to provide insight into the regulation of very long-chain fatty-acid biosynthesis in seeds. Virtually, no methylation was detected either in B. oleracea or in C. rubella, suggesting that modification of promoter methylation might not be a predominant mechanism. Swapping constructs were specifically designed to quantify and compare the contribution of variations in coding regions or promoters to the changes in FAE1 expression levels in parallel. A significantly higher fold change in erucic acid content was observed when swapping coding regions rather than when swapping promoters, indicating that the coding region is a major determinant of the catalytic power of β-ketoacyl-CoA synthase proteins. Common motifs have been proposed as essential for the preservation of basic gene expression patterns, such as seed-specific expression. However, the occurrence of variation in common cis-elements or the presence of species-specific cis-elements might be plausible mechanisms for changes in the expression levels in different organisms. In addition, conflicting observations in previous reports associated with FAE1 expression are discussed, and we suggest that caution should be taken when selecting a plant transformation vector and in interpreting the results obtained from vectors carrying the CaMV 35S promoter.
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Affiliation(s)
- Dinghong Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Zhao Lei
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Jiayu Xue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Guangcan Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Yueyu Hang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Xiaoqin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China.
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8
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Hwang SG, Kim DS, Kim JB, Hwang JE, Park HM, Kim JH, Jang CS. Transcriptome analysis of reproductive-stage Arabidopsis plants exposed gamma-ray irradiation at various doses. Int J Radiat Biol 2016; 92:451-65. [PMID: 27151538 DOI: 10.1080/09553002.2016.1178865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sun-Goo Hwang
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Korea
| | - Dong Sub Kim
- NJ Solar Plant Group, NJ Biopia Co., Gwangju, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, South Korea
| | - Jung Eun Hwang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, South Korea
| | - Hyun Mi Park
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Korea
| | - Jin Hyuk Kim
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Korea
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9
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Duan D, Fischer S, Merz P, Bogs J, Riemann M, Nick P. An ancestral allele of grapevine transcription factor MYB14 promotes plant defence. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1795-804. [PMID: 26842984 PMCID: PMC4783363 DOI: 10.1093/jxb/erv569] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Stilbene synthase is a key enzyme for the production of the phytoalexin resveratrol. Some clones of Vitis sylvestris, a wild European grapevine species which is almost extinct, have been shown to accumulate more resveratrol in response to different forms of stress. In the current study, we asked whether the induction of stilbene synthase transcripts in Hoe29, one of the V. sylvestris clones with elevated stilbene inducibility, might result from the elevated induction of the transcription factor MYB14. The MYB14 promoter of Hoe29 and of Ke83 (a second stilbene-inducible genotype) harboured distinct regions and were applied to a promoter-reporter system. We show that stilbene synthase inducibility correlates with differences in the induction of MYB14 transcripts for these two genotypes. Both alleles were induced by UV in a promoter-reporter assay, but only the MYB14 promoter from Hoe29 was induced by flg22, consistent with the stilbene synthase expression of the donor genotypes, where both respond to UV but only Hoe29 is responsive to Plasmopara viticola during defence. We mapped upstream signals and found that a RboH-dependent oxidative burst, calcium influx, a MAPK cascade, and jasmonate activated the MYB14 promoter, whereas salicylic acid was ineffective. Our data suggest that the Hoe29 allele of the MYB14 promoter has potential as a candidate target for resistance breeding.
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Affiliation(s)
- Dong Duan
- Molecular Cell Biology, Botanical Institute 1, Karlsruhe Institute of Technology, Kaiserstr. 2, D-76131 Karlsruhe, Germany College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Sabine Fischer
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, J.-J.-Becherweg 32, D-55128 Mainz, Germany
| | - Patrick Merz
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Breitenweg 71, Viticulture and Enology Group, D-67435 Neustadt, Germany
| | - Jochen Bogs
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Breitenweg 71, Viticulture and Enology Group, D-67435 Neustadt, Germany Fachhochschule Bingen, D-55411 Bingen am Rhein, Germany
| | - Michael Riemann
- Molecular Cell Biology, Botanical Institute 1, Karlsruhe Institute of Technology, Kaiserstr. 2, D-76131 Karlsruhe, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute 1, Karlsruhe Institute of Technology, Kaiserstr. 2, D-76131 Karlsruhe, Germany
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10
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Yan G, Li D, Cai M, Gao G, Chen B, Xu K, Li J, Li F, Wang N, Qiao J, Li H, Zhang T, Wu X. Characterization of FAE1 in the zero erucic acid germplasm of Brassica rapa L. BREEDING SCIENCE 2015; 65:257-64. [PMID: 26175623 PMCID: PMC4482176 DOI: 10.1270/jsbbs.65.257] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/01/2015] [Indexed: 05/07/2023]
Abstract
The modification of erucic acid content in seeds is one of the major goals for quality breeding in oil-yielding Brassica species. However, few low erucic acid (LEA) resources are available, and novel LEA genetic resources are being sought. Fatty acid elongase 1 (FAE1) is the key gene that controls erucic acid synthesis. However, the mechanism for erucic acid synthesis in B. rapa lacks systematic study. Here, we isolated zero erucic acid lines from 1981 Chinese landraces of B. rapa and found that the formation of LEA is not attributable to variations in FAE1 coding sequences, as reported for B. napus, but may be attributable to the decrease in FAE1 expression. Moreover, the FAE1 promoter sequences of LEA and high erucic acid materials shared 95% similarity. Twenty-eight bases deletions (containing a 24-base AT-rich region) were identified approximately 1300 bp upstream from the FAE1 start codon in the LEA accessions. The genotype with the deletions co-segregated with the LEA trait in the segregating population. This study isolated an LEA B. rapa resource that can be exploited in Brassica cultivation. The promoter variations might modify the expression level of FAE1, and the results shed light on novel regulation mechanisms for erucic acid synthesis.
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11
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Chiron H, Wilmer J, Lucas MO, Nesi N, Delseny M, Devic M, Roscoe TJ. Regulation of FATTY ACID ELONGATION1 expression in embryonic and vascular tissues of Brassica napus. PLANT MOLECULAR BIOLOGY 2015; 88:65-83. [PMID: 25795129 PMCID: PMC4408364 DOI: 10.1007/s11103-015-0309-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/13/2015] [Indexed: 05/09/2023]
Abstract
The expression of the FATTY ACID ELONGATION1 genes was characterised to provide insight into the regulation of very long chain fatty acid (VLCFA) biosynthesis in Brassica napus embryos. Each of the two rapeseed homoeologous genes (Bn-FAE1.1 and Bn-FAE1.2) encoding isozymes of 3-keto-acylCoA synthase, a subunit of the cytoplasmic acyl-CoA elongase complex that controls the production of elongated fatty acids, are expressed predominantly in developing seeds. The proximal regions of the Bn-FAE1.1 and Bn-FAE1.2 promoters possess strong sequence identity suggesting that transcriptional control of expression is mediated by this region which contains putative cis-elements characteristic of those found in the promoters of genes expressed in embryo and endosperm. Histochemical staining of rapeseed lines expressing Bn-FAE1.1 promoter:reporter gene fusions revealed a strong expression in the embryo cotyledon and axis throughout the maturation phase. Quantitative analyses revealed the region, -331 to -149, exerts a major control on cotyledon specific expression and the level of expression. A second region, -640 to -475, acts positively to enhance expression levels and extends expression of Bn-FAE1.1 into the axis and hypocotyl but also acts negatively to repress expression in the root meristem. The expression of the Bn-FAE1.1 gene was not restricted to the seed but was also detected in the vascular tissues of germinating seedlings and mature plants in the fascicular cambium tissue present in roots, stem and leaf petiole. We propose that Bn-FAE1.1 expression in vascular tissue may contribute VLCFA for barrier lipid synthesis and reflects the ancestral function of FAE1 encoded 3-keto-acylCoA synthase.
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Affiliation(s)
- Hélène Chiron
- Laboratoire Genome et Developpement des Plantes, CNRS-UP UMR5096, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France
| | - Jeroen Wilmer
- BIOGEMMA, Chappes Research Centre, Route d’Ennezat, 63720 Chappes, France
| | - Marie-Odile Lucas
- UMR1349 INRA-Agrocampus Ouest-Université de Rennes, Institut de Génétique, Environnement et Protection des Plantes, BP 35327, 35653 Le Rheu Cedex, France
| | - Nathalie Nesi
- UMR1349 INRA-Agrocampus Ouest-Université de Rennes, Institut de Génétique, Environnement et Protection des Plantes, BP 35327, 35653 Le Rheu Cedex, France
| | - Michel Delseny
- Laboratoire Genome et Developpement des Plantes, CNRS-UP UMR5096, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France
| | - Martine Devic
- Laboratoire Genome et Developpement des Plantes, CNRS-UP UMR5096, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France
- Present Address: CNRS ERL5300 Epigenetic Regulation and Seed Development Group, IRD UMR232 DIADE, Institute de Recherche pour le Développment, 911 Avenue Agropolis, 34032 Montpellier Cedex 1, France
| | - Thomas J. Roscoe
- Laboratoire Genome et Developpement des Plantes, CNRS-UP UMR5096, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France
- Present Address: CNRS ERL5300 Epigenetic Regulation and Seed Development Group, IRD UMR232 DIADE, Institute de Recherche pour le Développment, 911 Avenue Agropolis, 34032 Montpellier Cedex 1, France
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12
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Li X, Sui X, Zhao W, Huang H, Chen Y, Zhang Z. Characterization of cucumber violaxanthin de-epoxidase gene promoter in Arabidopsis. J Biosci Bioeng 2015; 119:470-7. [DOI: 10.1016/j.jbiosc.2014.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 11/26/2022]
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13
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Cserhati M. Motif content comparison between monocot and dicot species. GENOMICS DATA 2015; 3:128-36. [PMID: 26484161 PMCID: PMC4535654 DOI: 10.1016/j.gdata.2014.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 01/04/2023]
Abstract
While a number of DNA sequence motifs have been functionally characterized, the full repertoire of motifs in an organism (the motifome) is yet to be characterized. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include both rice species, Brachypodium, corn, wheat as monocots and Arabidopsis, Lotus japonica, Medicago truncatula, and Populus tremula as dicots. All possible existing motifs were analyzed in different regions of genomes such as were found in different sets of sequences in these species: the whole genome, core proximal and distal promoters, 5′ and 3′ UTRs, and the 1st introns. Due to the increased number of species involved in this study compared to previous works, species relationships were analyzed based on the similarity of common motif content. Certain secondary structure elements were inferred in the genomes of these species as well as new unknown motifs. The distribution of 20 motifs common to the studied species were found to have a significantly larger occurrence within the promoters and 3′ UTRs of genes, both being regulatory regions. Motifs common to the promoter regions of japonica rice, Brachypodium, and corn were also found in a number of orthologous and paralogous genes. Some of our motifs were found to be complementary to miRNA elements in Brachypodium distachyon and japonica rice.
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Affiliation(s)
- Matyas Cserhati
- Department of Genetics, Cell Biology, and Anatomy, 985805 Nebraska Medical Center, Omaha, NE, 68198-5805, United States
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14
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Davies JP, Reddy V, Liu XL, Reddy AS, Ainley WM, Thompson M, Sastry-Dent L, Cao Z, Connell J, Gonzalez DO, Wagner DR. Identification and use of the sugarcane bacilliform virus enhancer in transgenic maize. BMC PLANT BIOLOGY 2014; 14:359. [PMID: 25526789 PMCID: PMC4302606 DOI: 10.1186/s12870-014-0359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Transcriptional enhancers are able to increase transcription from heterologous promoters when placed upstream, downstream and in either orientation, relative to the promoter. Transcriptional enhancers have been used to enhance expression of specific promoters in transgenic plants and in activation tagging studies to help elucidate gene function. RESULTS A transcriptional enhancer from the Sugarcane Bacilliform Virus - Ireng Maleng isolate (SCBV-IM) that can cause increased transcription when integrated into the the genome near maize genes has been identified. In transgenic maize, the SCBV-IM promoter was shown to be comparable in strength to the maize ubiquitin 1 promoter in young leaf and root tissues. The promoter was dissected to identify sequences that confer high activity in transient assays. Enhancer sequences were identified and shown to increase the activity of a heterologous truncated promoter. These enhancer sequences were shown to be more active when arrayed in 4 copy arrays than in 1 or 2 copy arrays. When the enhancer array was transformed into maize plants it caused an increase in accumulation of transcripts of genes near the site of integration in the genome. CONCLUSIONS The SCBV-IM enhancer can activate transcription upstream or downstream of genes and in either orientation. It may be a useful tool to activate enhance from specific promoters or in activation tagging.
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Affiliation(s)
- John P Davies
- />Dow AgroSciences, 16160 SW Upper Boones Ferry Rd, Portland, OR 97224 USA
| | - Vaka Reddy
- />Dow AgroSciences, 16160 SW Upper Boones Ferry Rd, Portland, OR 97224 USA
- />Current address: GEVO, Inc., 345 Inverness Dr S C-310, Englewood, CO 80112 USA
| | - Xing L Liu
- />Dow AgroSciences, 16160 SW Upper Boones Ferry Rd, Portland, OR 97224 USA
| | - Avutu S Reddy
- />Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | | | - Mark Thompson
- />Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | | | - Zehui Cao
- />Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - James Connell
- />Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | | | - Douglas Ry Wagner
- />Dow AgroSciences, 16160 SW Upper Boones Ferry Rd, Portland, OR 97224 USA
- />Dow AgroSciences, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
- />Current address: Agrinos, Inc, 279 Cousteau Place, Davis, CA 95618 USA
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15
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Cserháti M, Turóczy Z, Dudits D, Györgyey J. The rice word landscape: a detailed catalogue of the rice motif content in the non-coding regions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:334-42. [PMID: 22702246 DOI: 10.1089/omi.2011.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Among the different areas of molecular biology concerning the detailed study of different parts of the cell, such as genomics, proteomics, and metabolomics, different new areas of study are emerging which entail the analysis of different parts of the genome, such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study was to construct and analyze a catalogue of all statistically relevant putative functional octamer words or motifs (which we have termed the "motifome" of a given organism) found within first introns, promoters, the 5' and 3' untranslated regions (UTRs), and the entire genome of japonica rice, and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of non-coding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. While common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.
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Affiliation(s)
- Mátyás Cserháti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary.
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16
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Cserháti M, Turóczy Z, Dudits D, Györgyey J. The rice word landscape--a detailed catalog of the rice motif content in the noncoding regions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 15:819-28. [PMID: 22122670 DOI: 10.1089/omi.2011.0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Among the different areas of molecular biology concerning the detailed study of different parts of the cell such as genomics, proteomics, or metabolomics, different new areas of study are emerging that entail the analysis of different parts of the genome such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study is to draw up and analyze a catalog of all statistically relevant putative functional octamer words or motifs found within first introns, promoters, the 5' and 3' UTRs, and the entire genome of japonica rice and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of noncoding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. Although common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.
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Affiliation(s)
- Mátyás Cserháti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary.
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17
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Vézina LP, Faye L, Lerouge P, D'Aoust MA, Marquet-Blouin E, Burel C, Lavoie PO, Bardor M, Gomord V. Transient co-expression for fast and high-yield production of antibodies with human-like N-glycans in plants. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:442-55. [PMID: 19422604 DOI: 10.1111/j.1467-7652.2009.00414.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant-based transient expression is potentially the most rapid and cost-efficient system for the production of recombinant pharmaceutical proteins, but safety concerns associated with plant-specific N-glycosylation have hampered its adoption as a commercial production system. In this article, we describe an approach based on the simultaneous transient co-expression of an antibody, a suppressor of silencing and a chimaeric human beta1,4-galactosyltransferase targeted for optimal activity to the early secretory pathway in agroinfiltrated Nicotiana benthamiana leaves. This strategy allows fast and high-yield production of antibodies with human-like N-glycans and, more generally, provides solutions to many critical problems posed by the large-scale production of therapeutic and vaccinal proteins, specifically yield, volume and quality.
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18
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Lai C, Xiong J, Li X, Qin X. A 43-bp A/T-rich element upstream of the kinesin gene AtKP1 promoter functions as a silencer in Arabidopsis. PLANT CELL REPORTS 2009; 28:851-860. [PMID: 19306002 DOI: 10.1007/s00299-009-0689-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 01/23/2009] [Accepted: 02/19/2009] [Indexed: 05/27/2023]
Abstract
The expression of the Arabidopsis thaliana kinesin-like protein 1 (AtKP1) gene is restricted to tender tissues. We used a 5'-deletion assay to identify and characterize the regulatory regions controlling tissue-specific AtKP1 expression. Multiple enhancer regions, located 470- and 2,808-bp upstream of the translational start codon, were critical for activation, while a silencer region located at -2,987 to -2,808 (A + T = 71%) was required for repression. Within this 180-bp fragment, a 43-bp element (termed KPRE, A + T = 58%) mediated repression of the CaMV35S promoter by using a gain-of-function approach that was orientation-dependent in leaves and orientation-independent in roots. Electrophoretic mobility shift assay (EMSA) showed that the GAGAAATT octamer (corresponding to neucleotides -2,908 - -2,900) in KPRE was the core negative regulatory motif for interacting with DNA-binding proteins in leaves and roots. However, using a second gain-of-function experiment with KPRE fused to CaMV35S, we found that the mutant negatively affected transcription in transgenic leaves and positively affected transcription in transgenic roots. This indicated that these two modes mediate repressive regulation in leaves and roots, respectively. The EMSA experiment using different mutant KPRE as probes confirmed that two distinct sets of proteins bound to KPRE at an overlapping site AGAAAT in the leaf. Taken together, these data suggest that two different modes control the negatively transcriptional regulation of KPRE in leaves and roots, and provide new insight into the mechanism of transcriptional repression of A/T-rich sequences in higher plants.
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Affiliation(s)
- Chengxia Lai
- College of Biological Sciences, China Agricultural University, Beijing, China.
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19
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Abstract
Regions of DNA that bind to the nuclear matrix, or nucleoskeleton, are known as Matrix Attachment Regions (MARs). MARs are thought to play an important role in higher-order structure and chromatin organization within the nucleus. MARs are also thought to act as boundaries of chromosomal domains that act to separate regions of gene-rich, decondensed euchromatin from highly repetitive, condensed heterochromatin. Herein I will present evidence that MARs do indeed act as domain boundaries and can prevent the spread of silencing into active genes. Many fundamental questions remain unanswered about how MARs function in the nucleus. New findings in epigenetics indicate that MARs may also play an important role in the organization of genes and the eventual transport of their mRNAs through the nuclear pore.
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20
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Luo K, Deng W, Xu S, Pei Y. Functional analysis of the Arabidopsis thaliana poly(A) binding protein PAB5 gene promoter in Nicotiana tabacum. PLANT CELL REPORTS 2008; 27:1811-9. [PMID: 18779966 DOI: 10.1007/s00299-008-0597-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2008] [Revised: 06/09/2008] [Accepted: 08/05/2008] [Indexed: 05/26/2023]
Abstract
Poly(A) binding (PAB) proteins play an important role in posttranscriptional regulation by stabilizing mRNA and initiating translation in eukaryotes. Previous studies have shown that the expression of PAB5 gene encoding one of the poly(A) binding proteins (PABPs) in Arabidopsis thaliana is restricted to pollen, ovule and early embryogenesis. To investigate the tissue-specific expression of the PAB5 promoter, a series of promoter deletions (from -1,804, -1,653, -1,334, -1,014, -715, -424 and -175 to +185) were fused to the uidA reporter gene (GUS) and transformed into tobacco plants (Nicotiana tabacum L.). The results showed that GUS expression driven by the full-length PAB5 promoter was detected in floral organs (pollen, ovule, anther, stigma) and immature seeds, but not in vegetative tissues (root, stem, leaf) and mature seeds. Deletion analysis of the PAB5 promoter region revealed that promoters longer than -1,334 had the similar GUS expression level in pollen, ovule and immature seeds, whereas further 5' deletions resulted in a considerable reduction in GUS activity. These results indicated that the region between -1,653 and -1,014 was necessary to direct the tissue-specific expression of PAB5 promoter during development.
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Affiliation(s)
- Keming Luo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, 400715 Chongqing, China
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21
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Pimentel C, Van Der Straeten D, Pires E, Faro C, Rodrigues-Pousada C. Characterization and expression analysis of the aspartic protease gene family of Cynara cardunculus L. FEBS J 2007; 274:2523-39. [PMID: 17433048 DOI: 10.1111/j.1742-4658.2007.05787.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cardosin A and cardosin B are two aspartic proteases mainly found in the pistils of cardoon Cynara cardunculus L., whose flowers are traditionally used in several Mediterranean countries in the manufacture of ewe's cheese. We have been characterizing cardosins at the biochemical, structural and molecular levels. In this study, we show that the cardoon aspartic proteases are encoded by a multigene family. The genes for cardosin A and cardosin B, as well as those for two new cardoon aspartic proteases, designated cardosin C and cardosin D, were characterized, and their expression in C. cardunculus L. was analyzed by RT-PCR. Together with cardosins, a partial clone of the cyprosin B gene was isolated, revealing that cardosin and cyprosin genes coexist in the genome of the same plant. As a first approach to understanding what dictates the flower-specific pattern of cardosin genes, the respective gene 5' regulatory sequences were fused with the reporter beta-glucuronidase and introduced into Arabidopsis thaliana. A subsequent deletion analysis of the promoter region of the cardosin A gene allowed the identification of a region of approximately 500 bp essential for gene expression in transgenic flowers. Additionally, the relevance of the leader intron of the cardosin A and B genes for gene expression was evaluated. Our data showed that the leader intron is essential for cardosin B gene expression in A. thaliana. In silico analysis revealed the presence of potential regulatory motifs that lay within the aforementioned regions and therefore might be important in the regulation of cardosin expression.
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Affiliation(s)
- Catarina Pimentel
- Departamento de Biologia Molecular e Biotecnologia do Centro de Neurociências de Coimbra, Universidade de Coimbra, Coimbra, Portugal
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22
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Komarnytsky S, Borisjuk N. Functional analysis of promoter elements in plants. GENETIC ENGINEERING 2004; 25:113-41. [PMID: 15260236 DOI: 10.1007/978-1-4615-0073-5_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Affiliation(s)
- Slavko Komarnytsky
- Biotech Center, Cook College, Rutgers University, 59 Dudley Rd., New Brunswick, NJ 08901-8520, USA
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23
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Hemleben V, Volkov RA, Zentgraf U, Medina FJ. Molecular Cell Biology: Organization and Molecular Evolution of rDNA, Nucleolar Dominance, and Nucleolus Structure. PROGRESS IN BOTANY 2004. [DOI: 10.1007/978-3-642-18819-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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24
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Chua YL, Watson LA, Gray JC. The transcriptional enhancer of the pea plastocyanin gene associates with the nuclear matrix and regulates gene expression through histone acetylation. THE PLANT CELL 2003; 15:1468-79. [PMID: 12782737 PMCID: PMC156380 DOI: 10.1105/tpc.011825] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2003] [Accepted: 04/11/2003] [Indexed: 05/17/2023]
Abstract
The influence of the transcriptional enhancer of the pea plastocyanin gene (PetE) on the acetylation of histones was examined with chromatin immunoprecipitation (ChIP) experiments using antibodies that recognize acetylated or nonacetylated histones H3 and H4. In transgenic tobacco plants containing the pea PetE promoter fused to uidA, both acetylated and nonacetylated histones H3 and H4 were present on the integrated transgene. Linking the PetE enhancer to the transgene resulted in increased beta-glucuronidase activity and increased amounts of acetylated histones H3 and H4 present on the promoter, suggesting that the enhancer may increase transcription by mediating the acetylation of histones. Trichostatin A and sodium butyrate, which are potent inhibitors of histone deacetylases (HDAs), activated expression from the PetE promoter by fourfold, with a concomitant increase in the acetylation states of histones H3 and H4, as determined by ChIP, indicating that the acetylation of histones has a direct positive effect on transcription. The HDA inhibitors did not increase expression from the PetE promoter when it was linked to the enhancer, consistent with preexisting hyperacetylated histones on the transgene. Mapping of histone acetylation states along the reporter gene indicated that the histones H3 and H4 associated with the promoter and the 5' region of uidA were hyperacetylated in the presence of the PetE enhancer. The PetE enhancer bound to isolated tobacco nuclear matrices in vitro and was associated with the nuclear matrix in nuclei isolated from transgenic tobacco plants. These results suggest that the pea PetE enhancer activates transcription by associating with the nuclear matrix, mediating the acetylation of histones on the promoter and the nearby coding region and resulting in an altered chromatin structure.
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Affiliation(s)
- Yii Leng Chua
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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25
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Mathieu M, Neutelings G, Hawkins S, Grenier E, David H. Cloning of a pine germin-like protein (GLP) gene promoter and analysis of its activity in transgenic tobacco Bright Yellow 2 cells. PHYSIOLOGIA PLANTARUM 2003; 117:425-434. [PMID: 12654044 DOI: 10.1034/j.1399-3054.2003.00050.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Germins and germin-like proteins (GLPs) constitute a large and highly diverse family of ubiquitous plant cell wall proteins. These proteins seem to be involved in many developmental stages and stress-related processes, but their exact participation in these processes generally remains obscure. In Pinus caribaea Morelet, the PcGER1 gene is expressed uniquely in embryo tissues, and encodes a GLP ionically bound to the walls of pine embryo cells maintained in 2,4-D-containing medium. We have cloned a genomic fragment including the 1520 bp 5'-upstream promoter region of PcGER1. This sequence contains, in its 1200 bp distal part, several cis elements (e.g. SEF4, 60 kDa protein, ABA RE and Dof recognition sites) present in genes responding to hormones and/or expressed in embryo or seed tissues, or during germination. The PcGER1 promoter sequence was cloned upstream of the GUS (beta-glucuronidase) reporter gene and transferred to tobacco Bright Yellow 2 (BY-2) cells via Agrobacterium tumefaciens-mediated transformation. Promoter activity and growth performances of transgenic asynchronous cell suspensions were analysed in the presence or absence of 2,4-D and/or BA. Optimal growth, maximum cell-wall yield and PcGER1 promoter activity were observed in the presence of 2,4-D and BA at day 4, the end of the exponential growth phase where 70-75% cells have a 2C DNA content. Analysis of promoter activity during the cell cycle in an aphidicoline-synchronized culture suggested that the expression is maximum in G1 cells. We also showed that under optimal growth conditions, 5' promoter deletions decreased the activity of the reporter gene. We discuss the function of this gene with regards to cell growth. Accession number: The PcGER1 promoter sequence was submitted to the genbank database under the accession number AY077704.
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Affiliation(s)
- Mélanie Mathieu
- Laboratoire de Physiologie des Parois Végétales UPRES EA-USC INRA, Université des Sciences et Technologies de Lille, Bât SN2, 59655 Villeneuve d'Ascq cedex, France Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA-1207, Antenne Scientifique Universitaire de Chartres, 21, rue de Loigny la Bataille, 28000 Chartres, France Cellule Statistique et Traitement Informatique des Données, Institut Supérieur Agricole de Beauvais, rue Pierre Waguet, 60026 Beauvais cedex, France
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Uthman A, Rezaie S, Dockal M, Ban J, Söltz-Szöts J, Tschachler E. Fluconazole downregulates metallothionein expression and increases copper cytotoxicity in Microsporum canis. Biochem Biophys Res Commun 2002; 299:688-92. [PMID: 12470632 DOI: 10.1016/s0006-291x(02)02724-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Azole antifungals are widely used to treat infections with dermatophyte fungi. Whereas it is well established that this class of drugs interferes with fungal ergosterol synthesis, little is known about its potential other biological effects. Here we report the isolation and structural organization of Microsporum canis metallothionein gene and demonstrate that fluconazole is able to downregulate the baseline as well as copper-induced expression of this gene. Since this effect occurred within 30 min after exposure of the fungus to fluconazole, it is unlikely that it is due to impaired ergosterol synthesis. Our additional demonstration that fluconazole enhances copper toxicity for M. canis suggests that inhibition of metallothionein expression by fluconazole is biologically relevant and may represent an important additional mode of the antifungal action of this drug. Therefore our data indicate that antifungal effects of azole derivatives might not only be due to interference with cell wall synthesis but may also affect other biological circuits within the fungal cells.
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Affiliation(s)
- Aumaid Uthman
- Ludwig Boltzmann Institute for venero-dermatological infection, University of Vienna Medical School, Währinger Gürtel 18-20, A-1090, Vienna, Austria
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27
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Reisdorf-Cren M, Carrayol E, Tercé-Laforgue T, Hirel B. A novel HMG A-like protein binds differentially to the AT-rich regions located in the far distal and proximal parts of a soybean glutamine synthetase gene (GS15) promoter. PLANT & CELL PHYSIOLOGY 2002; 43:1006-16. [PMID: 12354918 DOI: 10.1093/pcp/pcf123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In soybean (Glycine max L.) ammonium provided externally or as the result of symbiotic nitrogen fixation stimulates the transcription of GS15, a gene encoding cytosolic glutamine synthetase. Strong constitutive positive expression (SCPE), silencer-like and organ-specific elements, located respectively in the distal, the central and the proximal region of the promoter are required to control the ammonium responsiveness of the gene expression [Tercé-Laforgue et al. (1999) Plant Mol. Biol. 39: 551]. It was hypothesized that the correct spatial conformation of the promoter permitted the cooperative action of these three cis-acting elements. Further investigations were therefore required to ascertain this hypothesis. A nodule nuclear protein, binding to a 66 bp AT-rich DNA fragment containing a 13 bp AT-rich repeated sequence (AT-1) and located just downstream of the SCPE element, was identified using a gel retardation assay. A cDNA clone likely to code for this protein was isolated using the yeast one-hybrid system. It encodes a novel DNA binding protein (AT-1SNBP) similar to HMG A proteins but exhibiting a higher molecular weight. AT-1SNBP appears to be encoded by a single gene that is expressed in roots, root nodules and leaves of soybean. Since two other 13 bp AT-rich repeated sequences (AT-2 and AT-3) were localized in the organ-specific element, we have quantified the binding affinity of AT-1SNBP to these sequences. We demonstrate that AT-1SNBP binds differentially to DNA fragments containing AT-1, AT-2 and AT-3 and that its binding affinity depends on the presence of adjacent sequences. This result suggests that AT-1SNBP may be an architectural protein involved in maintaining the spatial conformation of the GS15 promoter, thus facilitating the interaction between the distal and proximal regulatory elements.
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MESH Headings
- AT Rich Sequence/genetics
- AT-Hook Motifs/genetics
- Amino Acid Sequence
- Base Sequence
- Bradyrhizobium/growth & development
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cytosol/enzymology
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Regulation, Enzymologic/drug effects
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant/genetics
- Glutamate-Ammonia Ligase/genetics
- Glutamate-Ammonia Ligase/metabolism
- HMGA Proteins/genetics
- HMGA Proteins/metabolism
- Lotus/enzymology
- Lotus/genetics
- Lotus/microbiology
- Molecular Sequence Data
- Plants, Genetically Modified
- Promoter Regions, Genetic
- Quaternary Ammonium Compounds/pharmacology
- Rhizobium/growth & development
- Sequence Analysis, DNA
- Sequence Deletion
- Soybean Proteins/genetics
- Soybean Proteins/metabolism
- Glycine max/enzymology
- Glycine max/genetics
- Glycine max/microbiology
- Transcription Factors/genetics
- Two-Hybrid System Techniques
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Affiliation(s)
- Michèle Reisdorf-Cren
- Laboratoire de la Nutrition Azotée des Plantes, INRA, centre de Versailles, Route de Saint Cyr, F-78026 Versailles Cedex, France.
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28
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Schroda M, Beck CF, Vallon O. Sequence elements within an HSP70 promoter counteract transcriptional transgene silencing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 31:445-55. [PMID: 12182703 DOI: 10.1046/j.1365-313x.2002.01371.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have shown previously that the HSP70A (A) promoter, when fused upstream of other promoters, significantly improves their performance in driving transgene expression in Chlamydomonas. Here, we employed the bacterial resistance gene ble, driven by the RBCS2 (R) promoter or an AR promoter fusion, to determine, by which mechanism(s) the A promoter may exert its enhancing effect. We observed that transformation rates of AR-ble constructs were significantly higher than those of R-ble constructs. However, ble mRNA levels in pools of transformants generated with either construct type were the same. Co-transformation experiments revealed that the R-ble transgene was silenced in 80% of the transformants, whereas this fraction was reduced to 36% in transformants harbouring the AR-ble transgene. We conclude that the A promoter acts by decreasing the probability that a transgene becomes transcriptionally silenced. We mapped two elements within the A promoter that are responsible for this effect. The core of the first element appears to be located between nucleotides - 7 and + 67 relative to the HSP70A transcriptional start site. Its activity is strongly dependent on its spatial setting with respect to the R promoter and is increased by upstream sequences (- 196 to - 8). The second element is independent of the first and is located to the region from - 754 to - 197. Its activity is spacing-independent and additive to the first element.
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Affiliation(s)
- Michael Schroda
- Institut de Biologie Physico-Chimique UPR 1261, 13, rue Pierre et Marie Curie, 75005 Paris, France.
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29
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Nagano Y, Furuhashi H, Inaba T, Sasaki Y. A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. Nucleic Acids Res 2001; 29:4097-105. [PMID: 11600698 PMCID: PMC60209 DOI: 10.1093/nar/29.20.4097] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2001] [Revised: 08/21/2001] [Accepted: 08/21/2001] [Indexed: 11/13/2022] Open
Abstract
Complementary DNA encoding a DNA-binding protein, designated PLATZ1 (plant AT-rich sequence- and zinc-binding protein 1), was isolated from peas. The amino acid sequence of the protein is similar to those of other uncharacterized proteins predicted from the genome sequences of higher plants. However, no paralogous sequences have been found outside the plant kingdom. Multiple alignments among these paralogous proteins show that several cysteine and histidine residues are invariant, suggesting that these proteins are a novel class of zinc-dependent DNA-binding proteins with two distantly located regions, C-x(2)-H-x(11)-C-x(2)-C-x((4-5))-C-x(2)-C-x((3-7))-H-x(2)-H and C-x(2)-C-x((10-11))-C-x(3)-C. In an electrophoretic mobility shift assay, the zinc chelator 1,10-o-phenanthroline inhibited DNA binding, and two distant zinc-binding regions were required for DNA binding. A protein blot with (65)ZnCl(2) showed that both regions are required for zinc-binding activity. The PLATZ1 protein non-specifically binds to A/T-rich sequences, including the upstream region of the pea GTPase pra2 and plastocyanin petE genes. Expression of the PLATZ1 repressed those of the reporter constructs containing the coding sequence of luciferase gene driven by the cauliflower mosaic virus (CaMV) 35S90 promoter fused to the tandem repeat of the A/T-rich sequences. These results indicate that PLATZ1 is a novel class of plant-specific zinc-dependent DNA-binding protein responsible for A/T-rich sequence-mediated transcriptional repression.
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Affiliation(s)
- Y Nagano
- Graduate School of Agricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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30
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Webster CI, Packman LC, Gray JC. HMG-1 enhances HMG-I/Y binding to an A/T-rich enhancer element from the pea plastocyanin gene. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:3154-62. [PMID: 11389716 DOI: 10.1046/j.1432-1327.2001.02191.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
High-mobility-group proteins HMG-1 and HMG-I/Y bind at overlapping sites within the A/T-rich enhancer element of the pea plastocyanin gene. Competition binding experiments revealed that HMG-1 enhanced the binding of HMG-I/Y to a 31-bp region (P31) of the enhancer. Circularization assays showed that HMG-1, but not HMG-I/Y, was able to bend a linear 100-bp DNA containing P31 so that the ends could be ligated. HMG-1, but not HMG-I/Y, showed preferential binding to the circular 100-bp DNA compared with the equivalent linear DNA, indicating that alteration of the conformation of the DNA by HMG-1 was not responsible for enhanced binding of HMG-I/Y. Direct interaction of HMG-I/Y and HMG-1 in the absence of DNA was demonstrated by binding of 35S-labeled proteins to immobilized histidine-tagged proteins, and this was due to an interaction of the N-terminal HMG-box-containing region of HMG-1 and the C-terminal AT-hook region of HMG-I/Y. Kinetic analysis using the IAsys biosensor revealed that HMG-1 had an affinity for immobilized HMG-I/Y (Kd = 28 nM) similar to that for immobilized P31 DNA. HMG-1-enhanced binding of HMG-I/Y to the enhancer element appears to be mediated by the formation of an HMG-1-HMG-I/Y complex, which binds to DNA with the rapid loss of HMG-1.
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Affiliation(s)
- C I Webster
- Cambridge Centre for Molecular Recognition and Department of Plant Sciences, University of Cambridge, UK
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31
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Han J, Lühs W, Sonntag K, Zähringer U, Borchardt DS, Wolter FP, Heinz E, Frentzen M. Functional characterization of beta-ketoacyl-CoA synthase genes from Brassica napus L. PLANT MOLECULAR BIOLOGY 2001; 46:229-39. [PMID: 11442062 DOI: 10.1023/a:1010665121980] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seed-specifically expressed beta-ketoacyl-CoA synthase genes of Brassica napus (Bn-FAE1.1 genes) were cloned from two cultivars, namely Askari, a high-erucic-acid type, and Drakkar, a low-erucic-acid type. The genes from the two cultivars were found to be nearly identical. They encode proteins of 507 amino acids, the sequences of which differ only at position 282. The Bn-FAE1.1 gene of Askari, unlike that of Drakkar, was functionally expressed in yeast cells suggesting that the single amino acid exchange effects the low erucic acid phenotype at the E1 gene locus. In yeast cells the beta-ketoacyl-CoA synthase of Askari elongated not only oleoyl but also palmitoleoyl groups as well as saturated acyl groups in such a way that monounsaturated acyl groups of 22 carbons and saturated ones of 26 carbons were formed as main products. A reporter gene fused to the promoter region of the Bn-FAE1.1 gene from Askari showed seed-specific expression in transgenic rapeseed plants. Over-expression of the coding region of the Askari gene in developing seeds of transgenic Drakkar plants resulted in a significant increase in the levels of eicosenoic acid and erucic acid esterified in the seed oil. On the other hand, in transgenic high-erucic-acid rapeseed plants the increase in erucic acid level was at most 60% although the chimeric Bn-FAE1.1 gene was co-expressed with an erucoyl-CoA-specific lysophosphatidate acyltransferase gene enabling trierucoyl glycerol to accumulate in the seed oil.
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Affiliation(s)
- J Han
- Universität Hamburg, Institut für Allgemeine Botanik, Germany
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32
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Chua YL, Pwee KH, Kini RM. DNA binding mediated by the wheat HMGa protein: a novel instance of selectivity against alternating GC sequence. PLANT MOLECULAR BIOLOGY 2001; 46:193-204. [PMID: 11442059 DOI: 10.1023/a:1010696604330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The high-mobility-group (HMG) chromosomal protein wheat HMGa was purified to homogeneity and tested for its binding characteristics to double-stranded DNA. Wheat HMGa was able to bind to P268, an A/T-rich fragment derived from the pea plastocyanin gene promoter, producing a small mobility shift in gel retardation assays where the bound complex was sensitive to addition of proteinase K but resistant to heat treatment of the protein, consistent with the identity of wheat HMGa as a putative HMG-I/Y protein. Gel retardation assays and southwestern hybridization analysis revealed that wheat HMGa could selectively interact with the DNA polynucleotides poly(dA).poly(dT), poly(dAdT).poly(dAdT), and poly(dG).poly(dC), but not with poly(dGdC).poly(dGdC). Surface plasmon resonance analysis determined the kinetic and affinity constants of sensor chip-immobilized wheat HMGa for double-stranded DNA 10-mers, revealing a good affinity of the protein for various dinucleotide combinations, except that of alternating GC sequence. Thus contrary to prior reports of a selectivity of wheat HMGa for A/T-rich DNA, the protein appears to be able to interact with sequences containing guanine and cytosine residues as well, except where G/C residues alternate directly in the primary sequence.
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Affiliation(s)
- Y L Chua
- Plant Molecular Biology Laboratory, National University of Singapore, Republic of Singapore
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33
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Chua YL, Brown AP, Gray JC. Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene. THE PLANT CELL 2001; 13:599-612. [PMID: 11251099 PMCID: PMC135505 DOI: 10.1105/tpc.13.3.599] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2000] [Accepted: 01/09/2001] [Indexed: 05/17/2023]
Abstract
The chromatin structure of the pea plastocyanin gene (PetE) was examined at three different transcriptional states by investigating the acetylation states of histones H3 and H4 and the nuclease accessibility of the gene in pea roots, etiolated shoots, and green shoots. The acetylation states of histones associated with different regions of PetE were analyzed by chromatin immunoprecipitation with antibodies specific for acetylated or nonacetylated histone H3 or H4 tails, followed by polymerase chain reaction quantification. Comparison of pea tissues indicated that histone hyperacetylation was associated with increased PetE transcription in green shoots. Moreover, hyperacetylation of both histones H3 and H4 was targeted to the enhancer/promoter region in green shoots, suggesting that only specific nucleosomes along the gene were modified. Time-course digestions of nuclei with micrococcal nuclease and DNaseI indicated that the enhancer/promoter region was more resistant to digestion in the inactive gene in pea roots than was the same region in the active gene in shoots, whereas the transcribed region of PetE was digested similarly among the tissues. This finding indicates that transcription is accompanied by changes in the nuclease accessibility of the enhancer/promoter region only. Moreover, these results indicate that the changes in nuclease accessibility are organ specific, whereas histone hyperacetylation is light dependent, and they suggest that changes in nuclease accessibility precede histone hyperacetylation during PetE activation.
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Affiliation(s)
- Y L Chua
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
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34
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Chua YL, Brown AP, Gray JC. Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene. THE PLANT CELL 2001; 13:599-612. [PMID: 11251099 DOI: 10.2307/3871409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The chromatin structure of the pea plastocyanin gene (PetE) was examined at three different transcriptional states by investigating the acetylation states of histones H3 and H4 and the nuclease accessibility of the gene in pea roots, etiolated shoots, and green shoots. The acetylation states of histones associated with different regions of PetE were analyzed by chromatin immunoprecipitation with antibodies specific for acetylated or nonacetylated histone H3 or H4 tails, followed by polymerase chain reaction quantification. Comparison of pea tissues indicated that histone hyperacetylation was associated with increased PetE transcription in green shoots. Moreover, hyperacetylation of both histones H3 and H4 was targeted to the enhancer/promoter region in green shoots, suggesting that only specific nucleosomes along the gene were modified. Time-course digestions of nuclei with micrococcal nuclease and DNaseI indicated that the enhancer/promoter region was more resistant to digestion in the inactive gene in pea roots than was the same region in the active gene in shoots, whereas the transcribed region of PetE was digested similarly among the tissues. This finding indicates that transcription is accompanied by changes in the nuclease accessibility of the enhancer/promoter region only. Moreover, these results indicate that the changes in nuclease accessibility are organ specific, whereas histone hyperacetylation is light dependent, and they suggest that changes in nuclease accessibility precede histone hyperacetylation during PetE activation.
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Affiliation(s)
- Y L Chua
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
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35
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Choi KR, Roh K, Kim J, Sim W. Genomic cloning and characterization of mitochondrial elongation factor Tu (EF-Tu) gene (tufM) from maize (Zea mays L.). Gene 2000; 257:233-42. [PMID: 11080589 DOI: 10.1016/s0378-1119(00)00404-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have cloned and characterized a mitochondrial elongation factor Tu (EF-Tu) gene (tufM) in maize (Zea mays L.). This maize tufM gene encoded a polypeptide of 452 amino acid residues, consisting of a putative transit peptide of 55 residues and a mature EF-Tu of 397 residues. The coding region was composed of 12 exons and 11 introns that ranged from 76 to 1673bp in length. The deduced amino acid sequence showed 85.9% and 61.2% identity with Arabidopsis mitochondrial EF-Tu and Arabidopsis chloroplast EF-Tu sequence respectively. The transcription initiation site was determined to be 165bp upstream of the AUG initiation codon by primer extension analysis. Southern blot analysis revealed that the cloned EF-Tu gene was encoded by the members of small gene family in maize. Although this gene does not resemble the Arabidopsis nuclear tufA gene, which encodes the plastid EF-Tu, and does not contain sequence elements found in all cyanobacterial and plastid tufA genes, the predicted amino acid sequence includes an N-terminal extension that resembles a mitochondrial targeting sequence, and shares three unique sequence elements with mitochondrial EF-Tu's from Arabidopsis thaliana, Saccharomyces cerevisiae, and Homo sapiens. Therefore, we concluded that this gene encodes the maize mitochondrial EF-Tu.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Southern
- Cloning, Molecular
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Genes, Plant/genetics
- Mitochondria/chemistry
- Molecular Sequence Data
- Peptide Elongation Factor Tu/genetics
- Phylogeny
- Promoter Regions, Genetic
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transcription, Genetic
- Zea mays/genetics
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Affiliation(s)
- K R Choi
- Department of Biology, Korea University, 136-701, Seoul, South Korea
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36
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Webster CI, Cooper MA, Packman LC, Williams DH, Gray JC. Kinetic analysis of high-mobility-group proteins HMG-1 and HMG-I/Y binding to cholesterol-tagged DNA on a supported lipid monolayer. Nucleic Acids Res 2000; 28:1618-24. [PMID: 10710428 PMCID: PMC102798 DOI: 10.1093/nar/28.7.1618] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/1999] [Revised: 02/16/2000] [Accepted: 02/16/2000] [Indexed: 01/18/2023] Open
Abstract
High-mobility-group proteins HMG-1 and HMG-I/Y bind to multiple sites within a 268 bp A/T-rich enhancer element of the pea plastocyanin gene ( PetE ). Within a 31 bp region of the enhancer, the binding site for HMG-1 overlaps with the binding site for HMG-I/Y. The kinetics of binding and the affinities of HMG-1 and HMG-I/Y for the 31 bp DNA were determined using surface plasmon resonance. Due to very high non-specific interactions of the HMG proteins with a carboxymethyl-dextran matrix, a novel method using a cholesterol tag to anchor the DNA in a supported lipid monolayer on a thin gold film was devised. The phosphatidylcholine monolayer produced a surface that reduced background interactions to a minimum and permitted the measurement of highly reproducible protein-DNA interactions. The association rate constant ( k (a)) of HMG-I/Y with the 31 bp DNA was approximately 5-fold higher than the rate constant for HMG-1, whereas the dissociation constant ( K (D)) for HMG-I/Y (3.1 nM) was approximately 7-fold lower than that for HMG-1 (20.1 nM). This suggests that HMG-I/Y should bind preferentially at the overlapping binding site within this region of the PetE enhancer.
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Affiliation(s)
- C I Webster
- Cambridge Centre for Molecular Recognition, University of Cambridge, UK
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37
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Strömvik MV, Sundararaman VP, Vodkin LO. A novel promoter from soybean that is active in a complex developmental pattern with and without its proximal 650 base pairs. PLANT MOLECULAR BIOLOGY 1999; 41:217-31. [PMID: 10579489 DOI: 10.1023/a:1006312228617] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report the isolation of a novel soybean gene, Msg, which is highly expressed in developing soybean pods. The gene shows significant homology to a family of fruit- and flower-specific genes, designated the major latex protein (MLP) homologues, so far reported in only a few species and whose functions are unknown. The MLPs are more distantly related to a group of pathogenesis-related proteins (IPR or PR-10) whose functions are likewise unknown. This is the first report of a MLP homologue in a plant for which there is already an IPR-protein reported. We performed an analysis of the Msg promoter with 14 different promoter fragments ranging from 0.65 kb to 2.26 kb, fused to the uidA (GUS) gene. High transient expression was obtained with all the constructs upon particle bombardment in soybean and green bean pods. Stable Arabidopsis transformants were obtained with the Agrobacterium vacuum infiltration method. The promoter is fully active in Arabidopsis only in plants transformed with the 2.26 kb fragment promoter, expressing GUS in nectaries, nodes, short style and in guard cells of the silique, pedicel and stem but not in mature leaves. Surprisingly, the proximal 650 bp TATA-containing region cannot function on its own in Arabidopsis and can be deleted without a change in expression pattern in both Arabidopsis and soybean. Thus, tissue-specific regions of the complex Msg promoter reside in the distal 5' regions upstream of a dispensable TATA box in contrast to many examples of tissue-specific elements that reside much closer to the TATA box.
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Affiliation(s)
- M V Strömvik
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana 61801, USA
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38
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Krech AB, Wurz A, Stemmer C, Feix G, Grasser KD. Structure of genes encoding chromosomal HMG1 proteins from maize. Gene 1999; 234:45-50. [PMID: 10393237 DOI: 10.1016/s0378-1119(99)00187-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The high mobility group (HMG) proteins of the HMG1 family are architectural proteins in chromatin that are considered to facilitate the formation of complex nucleoprotein structures in various biological processes such as transcription and recombination. Plants express a variety of these non-sequence-specific DNA-bending proteins. The sequences encoding the maize HMGa and HMGc1 proteins were isolated from a genomic DNA library. Determination of the nucleotide sequences of these genes revealed that the coding region of both genes has a similar genomic structure, comprising seven exons and six introns. The positioning of the introns is conserved between the two genes, whereas the number of introns and their positions are entirely different in the related animal genes. In the 5' flanking region of the hmgc1 gene, a copia-like retrotransposon was identified. In addition to the genes encoding HMGa and HMGc1, several genomic fragments (retropseudo gene, fragments of the genes) were isolated and characterised.
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Affiliation(s)
- A B Krech
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
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