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Kattupalli D, Srinivasan A, Soniya EV. A Genome-Wide Analysis of Pathogenesis-Related Protein-1 ( PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection. Genes (Basel) 2021; 12:1007. [PMID: 34208836 PMCID: PMC8303604 DOI: 10.3390/genes12071007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 11/25/2022] Open
Abstract
Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.
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Affiliation(s)
| | | | - Eppurath Vasudevan Soniya
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India; (D.K.); (A.S.)
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Gomes Ferreira MD, Araújo Castro J, Santana Silva RJ, Micheli F. HVA22 from citrus: A small gene family whose some members are involved in plant response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:395-404. [PMID: 31408843 DOI: 10.1016/j.plaphy.2019.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 05/27/2023]
Abstract
The HVA22 gene has been isolated for the first time from the aleurone layer of barley (Hordeum vulgare). Here, we characterized the HVA22 family from citrus (C. clementina and C. sinensis). Twelve genes, 6 in each species, were identified as well as duplication events for some of them. The ORF size ranged from 235 to 804 bp and the protein molecular weight from 94 to 267 kDa. All the citrus HVA22 protein presented transmembrane location and conserved TB2/DP1/HVA22 region. Phylogenetic and gene expression analyses suggested that some citrus HVA22 play a role in flower and fruit development, and that gene expression may be regulated by hormone or environmental conditions. Other regulation levels were also predicted, such as alternative splicing and post-translational modifications. The overall data indicated that citrus HVA22 may be involved in vesicular traffic in stressed cells, and that CcHVA22d could be involved in dehydration tolerance.
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Affiliation(s)
| | - Jacqueline Araújo Castro
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil; Instituto Federal de Educação, Ciência e Tecnologia Baiano (IFBaiano), Governador Mangabeira, Bahia, Brazil
| | - Raner José Santana Silva
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil; CIRAD, UMR AGAP, F-34398, Montpellier, France.
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Watanabe KA, Homayouni A, Gu L, Huang KY, Ho THD, Shen QJ. Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element. PLANT, CELL & ENVIRONMENT 2017. [PMID: 28626890 DOI: 10.1111/pce.13006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA-induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements, and particle bombardment-mediated transient expression studies were performed to verify the function. Gene ontology analysis was performed to predict the roles of genes containing the novel ABREs. This study revealed 2443 ABA-inducible genes and a novel ABRE, designated as ABREN, which was experimentally verified to mediate ABA signalling in rice aleurone cells. Many of the ABREN-containing genes are predicted to be involved in stress responses and transcription. Analysis of other species suggests that the ABREN may be monocot specific. This study also revealed interesting expression patterns of genes involved in ABA metabolism and signalling. Collectively, this study advanced our understanding of diverse cis-regulatory sequences and the transcriptomes underlying ABA responses in rice aleurone cells.
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Affiliation(s)
- Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Arielle Homayouni
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Lingkun Gu
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Kuan-Ying Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV, 89154, USA
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Duraisamy GS, Mishra AK, Kocabek T, Matoušek J. Identification and characterization of promoters and cis-regulatory elements of genes involved in secondary metabolites production in hop (Humulus lupulus. L). Comput Biol Chem 2016; 64:346-352. [DOI: 10.1016/j.compbiolchem.2016.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/07/2016] [Accepted: 07/15/2016] [Indexed: 10/21/2022]
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Zhang L, Gu L, Ringler P, Smith S, Rushton PJ, Shen QJ. Three WRKY transcription factors additively repress abscisic acid and gibberellin signaling in aleurone cells. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:214-22. [PMID: 26025535 DOI: 10.1016/j.plantsci.2015.04.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 04/14/2015] [Accepted: 04/19/2015] [Indexed: 05/06/2023]
Abstract
Members of the WRKY transcription factor superfamily are essential for the regulation of many plant pathways. Functional redundancy due to duplications of WRKY transcription factors, however, complicates genetic analysis by allowing single-mutant plants to maintain wild-type phenotypes. Our analyses indicate that three group I WRKY genes, OsWRKY24, -53, and -70, act in a partially redundant manner. All three showed characteristics of typical WRKY transcription factors: each localized to nuclei and yeast one-hybrid assays indicated that they all bind to W-boxes, including those present in their own promoters. Quantitative real time-PCR (qRT-PCR) analyses indicated that the expression levels of the three WRKY genes varied in the different tissues tested. Particle bombardment-mediated transient expression analyses indicated that all three genes repress the GA and ABA signaling in a dosage-dependent manner. Combination of all three WRKY genes showed additive antagonism of ABA and GA signaling. These results suggest that these WRKY proteins function as negative transcriptional regulators of GA and ABA signaling. However, different combinations of these WRKY genes can lead to varied strengths in suppression of their targets.
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Affiliation(s)
- Liyuan Zhang
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Lingkun Gu
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Patricia Ringler
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Stanley Smith
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, TX 75252, USA
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA.
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Sohrabi M, Zebarjadi A, Najaphy A, Kahrizi D. Isolation and sequence analysis of napin seed specific promoter from Iranian Rapeseed (Brassica napus L.). Gene 2015; 563:160-4. [PMID: 25797503 DOI: 10.1016/j.gene.2015.03.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/06/2015] [Accepted: 03/13/2015] [Indexed: 10/23/2022]
Abstract
Rapeseed (Brassica napus L.) has become an important crop during the last 30years. In addition to a high lipid level, the seeds also have a significant protein content, which constitutes 20-25% of the dry seed weight. The synthesis of storage proteins is primarily controlled at transcriptional level and seed-specific expression has been shown to be conferred upon the promoter regions of many storage protein genes. Napin is one of the main storage proteins in rapeseed(')s embryo that is produced in seed developing stage. Its promoter region located at 5' upstream of the napin gene has already been isolated (GenBank number, EU416279.1). In current research, seed-specific promoter (napin) of Iranian B. napus L. was isolated from the genomic DNA and cloned into pBI121 plant binary vector to use in future researches. For this purpose, the napin promoter was amplified by PCR method using specific primers, cloned in pSK(+) vector and sequenced. Sequencing analysis showed that the cloned promoter contained all of conserved motifs such as TATA box (TATAAA), RY repeats (CATGCA), dist-B (TCAAACACC) and prox-B elements (GCCACTTGTC), G-box (CACGTG) and CAAT Motifs, which constituted the seed-specific promoter activity and according to this analysis, the seed-specific promoter activity of cloned sequence was predicted. Based on sequence distances of nucleotide sequences, our sequence had the highest similarity (99.8%) whit B. napus sequence (with EU416279.1 accession number). Finally the promoter obtained might be interesting not only as a useful tool for biotechnological application but also for fundamental research.
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Affiliation(s)
- Maryam Sohrabi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Razi University, Kermanshah, Iran
| | - Alireza Zebarjadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Razi University, Kermanshah, Iran; Department of Biotechnology for Drought Resistance, Razi University, Kermanshah, Iran.
| | - Abdollah Najaphy
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Razi University, Kermanshah, Iran; Department of Biotechnology for Drought Resistance, Razi University, Kermanshah, Iran
| | - Danial Kahrizi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Razi University, Kermanshah, Iran; Department of Biotechnology for Drought Resistance, Razi University, Kermanshah, Iran
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RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds. Genomics 2013; 103:122-34. [PMID: 24200500 DOI: 10.1016/j.ygeno.2013.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/03/2013] [Accepted: 10/25/2013] [Indexed: 01/14/2023]
Abstract
The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germination growth. Herein, we report transcriptomes of aleurone cells treated with the hormones abscisic acid, gibberellic acid, or both. Using a comprehensive approach, we identified hundreds of novel genes. To minimize the number of false positives, only transcripts that did not overlap with existing annotations, had a high level of expression, and showed a high level of uniqueness within the rice genome were considered to be novel genes. This approach led to the identification of 553 novel genes that encode proteins and/or microRNAs. The transcriptome data reported here will help to further improve the annotation of the rice genome.
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Li Q, Liu J, Tan D, Allan AC, Jiang Y, Xu X, Han Z, Kong J. A genome-wide expression profile of salt-responsive genes in the apple rootstock Malus zumi. Int J Mol Sci 2013; 14:21053-70. [PMID: 24145753 PMCID: PMC3821658 DOI: 10.3390/ijms141021053] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/09/2013] [Accepted: 09/23/2013] [Indexed: 02/07/2023] Open
Abstract
In some areas of cultivation, a lack of salt tolerance severely affects plant productivity. Apple, Malus x domestica Borkh., is sensitive to salt, and, as a perennial woody plant the mechanism of salt stress adaption will be different from that of annual herbal model plants, such as Arabidopsis. Malus zumi is a salt tolerant apple rootstock, which survives high salinity (up to 0.6% NaCl). To examine the mechanism underlying this tolerance, a genome-wide expression analysis was performed, using a cDNA library constructed from salt-treated seedlings of Malus zumi. A total of 15,000 cDNA clones were selected for microarray analysis. In total a group of 576 cDNAs, of which expression changed more than four-fold, were sequenced and 18 genes were selected to verify their expression pattern under salt stress by semi-quantitative RT-PCR. Our genome-wide expression analysis resulted in the isolation of 50 novel Malus genes and the elucidation of a new apple-specific mechanism of salt tolerance, including the stabilization of photosynthesis under stress, involvement of phenolic compounds, and sorbitol in ROS scavenging and osmoprotection. The promoter regions of 111 genes were analyzed by PlantCARE, suggesting an intensive cross-talking of abiotic stress in Malus zumi. An interaction network of salt responsive genes was constructed and molecular regulatory pathways of apple were deduced. Our research will contribute to gene function analysis and further the understanding of salt-tolerance mechanisms in fruit trees.
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Affiliation(s)
- Qingtian Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; E-Mails: (Q.L.); (Y.J.); (X.X.); (Z.H.)
| | - Jia Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; E-Mails: (Q.L.); (Y.J.); (X.X.); (Z.H.)
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China; E-Mail:
| | - Dunxian Tan
- Department of Cellular & Structural Biology, the UT Health Science Center, San Antonio, TX 78229-3900, USA; E-Mail:
| | - Andrew C. Allan
- Plant & Food Research, Private Bag 92169, Auckland, New Zealand; E-Mail:
| | - Yuzhuang Jiang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; E-Mails: (Q.L.); (Y.J.); (X.X.); (Z.H.)
| | - Xuefeng Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; E-Mails: (Q.L.); (Y.J.); (X.X.); (Z.H.)
| | - Zhenhai Han
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; E-Mails: (Q.L.); (Y.J.); (X.X.); (Z.H.)
| | - Jin Kong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; E-Mails: (Q.L.); (Y.J.); (X.X.); (Z.H.)
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9
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Miller-Coleman RL, Dodsworth JA, Ross CA, Shock EL, Williams AJ, Hartnett HE, McDonald AI, Havig JR, Hedlund BP. Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning. PLoS One 2012; 7:e35964. [PMID: 22574130 PMCID: PMC3344838 DOI: 10.1371/journal.pone.0035964] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/28/2012] [Indexed: 11/18/2022] Open
Abstract
Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7–8.5 at concentrations up to 6.6×106 16S rRNA gene copies g−1 wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.
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Affiliation(s)
| | - Jeremy A. Dodsworth
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America
| | - Christian A. Ross
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America
| | - Everett L. Shock
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, United States of America
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America
| | - Amanda J. Williams
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America
| | - Hilairy E. Hartnett
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, United States of America
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America
| | - Austin I. McDonald
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America
| | - Jeff R. Havig
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, United States of America
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America
- * E-mail:
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Woodrow P, Pontecorvo G, Ciarmiello LF, Fuggi A, Carillo P. Ttd1a promoter is involved in DNA–protein binding by salt and light stresses. Mol Biol Rep 2010; 38:3787-94. [PMID: 21104438 DOI: 10.1007/s11033-010-0494-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
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LIU YX, HAN YP, CHANG W, ZOU Q, GUO MZ, LI WB. Genomic Analysis of MicroRNA Promoters and Their Cis-Acting Elements in Soybean. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1671-2927(09)60252-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Woodrow P, Pontecorvo G, Fantaccione S, Fuggi A, Kafantaris I, Parisi D, Carillo P. Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:311-22. [PMID: 20237753 DOI: 10.1007/s00122-010-1311-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 02/22/2010] [Indexed: 05/18/2023]
Abstract
Long terminal repeat retrotransposons are the most abundant mobile elements in the plant genome and play an important role in the genome reorganization induced by environmental challenges. Their success depends on the ability of their promoters to respond to different signaling pathways that regulate plant adaptation to biotic and abiotic stresses. We have isolated a new Ty1-copia-like retrotransposon, named Ttd1a from the Triticum durum L. genome. To get insight into stress activation pathways in Ttd1a, we investigated the effect of salt and light stresses by RT-PCR and S-SAP profiling. We screened for Ttd1a insertion polymorphisms in plants grown to stress and showed that one new insertion was located near the resistance gene. Our analysis showed that the activation and mobilization of Ttd1a was controlled by salt and light stresses, which strengthened the hypothesis that stress mobilization of this element might play a role in the defense response to environmental stresses.
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Affiliation(s)
- Pasqualina Woodrow
- Department of Life Science, II University of Naples, via Vivaldi 43, Caserta, Italy
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Analysis of the Wsi18, a stress-inducible promoter that is active in the whole grain of transgenic rice. Transgenic Res 2010; 20:153-63. [DOI: 10.1007/s11248-010-9400-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022]
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14
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Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci U S A 2010; 107:5792-7. [PMID: 20220098 DOI: 10.1073/pnas.0911965107] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Seed dormancy provides a strategy for flowering plants to survive adverse natural conditions. It is also an important agronomic trait affecting grain yield, quality, and processing performance. We cloned a rice quantitative trait locus, Sdr4, which contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. These results are discussed with respect to possible selection of the allele during the domestication process.
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Lenka SK, Lohia B, Kumar A, Chinnusamy V, Bansal KC. Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes. PLANT MOLECULAR BIOLOGY 2009; 69:261-271. [PMID: 18998058 DOI: 10.1007/s11103-008-9423-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 10/16/2008] [Indexed: 05/27/2023]
Abstract
Abscisic acid (ABA), the popular plant stress hormone, plays a key role in regulation of sub-set of stress responsive genes. These genes respond to ABA through specific transcription factors which bind to cis-regulatory elements present in their promoters. We discovered the ABA Responsive Element (ABRE) core (ACGT) containing CGMCACGTGB motif as over-represented motif among the promoters of ABA responsive co-expressed genes in rice. Targeted gene prediction strategy using this motif led to the identification of 402 protein coding genes potentially regulated by ABA-dependent molecular genetic network. RT-PCR analysis of arbitrarily chosen 45 genes from the predicted 402 genes confirmed 80% accuracy of our prediction. Plant Gene Ontology (GO) analysis of ABA responsive genes showed enrichment of signal transduction and stress related genes among diverse functional categories.
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Affiliation(s)
- Sangram K Lenka
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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16
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Roychoudhury A, Gupta B, Sengupta DN. Trans-acting factor designated OSBZ8 interacts with both typical abscisic acid responsive elements as well as abscisic acid responsive element-like sequences in the vegetative tissues of indica rice cultivars. PLANT CELL REPORTS 2008; 27:779-94. [PMID: 18183401 DOI: 10.1007/s00299-007-0498-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/22/2007] [Accepted: 12/15/2007] [Indexed: 05/21/2023]
Abstract
Specific cis-acting elements, identified in the stress-regulated promoters, can respond to the changes in the levels of abscisic acid. Most of our previous works were done with ACGT-containing typical abscisic acid responsive elements (ABREs) but not with non-ACGT, GC-rich sequences also present in such promoters. The current communication shows a comparative analysis performed on the binding of rice nuclear proteins, together with the purified transcription factor OSBZ8, to the cis-elements in the promoters of Rab16A (Motif I/Motif II), Osem (Motif A-1/Motif B) and Em (4X ABRE/2X ABRC). Our data show that the extent of binding of nuclear protein from salt-tolerant rice to both typical ABREs and non-ACGT, ABRE-like sequences such as Motif IIa, is much higher than that from salt-sensitive rice and occurs constitutively, i.e., even with the protein from unstressed plants. The complex formation is low and inducible only by salt in the salt-sensitive variety. While Motif I bind to a single 38 kDa protein, Motif IIa bind to two polypeptides of 38 and 29 kDa. We also show here that the activation and binding of OSBZ8 to the upstream regions of salt-inducible genes depends on its phosphorylated state. The novelty of our work is that it shows rice OSBZ8 as the prime factor interacting with both typical ABRE(s) and ABRE-like sequences. To our knowledge, this is also the first report for the detection and identification of Motif IIa (non-ACGT, coupling element-like)-binding factor(s) from rice and their expression pattern in different rice cultivars.
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Gómez-Porras JL, Riaño-Pachón DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 2007; 8:260. [PMID: 17672917 PMCID: PMC2000901 DOI: 10.1186/1471-2164-8-260] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 08/01/2007] [Indexed: 11/16/2022] Open
Abstract
Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.
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Affiliation(s)
- Judith L Gómez-Porras
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- University of Bielefeld, Institute of Molecular Cell Physiology, Department of Biology, Universitätsstr. 25, D-33501 Germany
| | - Diego Mauricio Riaño-Pachón
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ingo Dreyer
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Jorge E Mayer
- Center for Applied Biosciences, University of Freiburg, Stefan-Meier-Str. 8, D-79104 Freiburg, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Haus 20, D-14476 Potsdam-Golm, Germany
- Cooperative Research Group of the Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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