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Yan R, Yang K, Zhang T, Sharif R, Yang S, Li S, Wang N, Liu J, Zhao S, Wang W, Zhang X, Dong Q, Luan H, Guo S, Wang Y, Qi G, Jia P. Comprehensive analysis of AHL genes in Malus domestica reveals the critical role of MdAHL6 in flowering induction. Int J Biol Macromol 2024:136387. [PMID: 39389506 DOI: 10.1016/j.ijbiomac.2024.136387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 10/04/2024] [Accepted: 10/05/2024] [Indexed: 10/12/2024]
Abstract
AT-hook motif nuclear localized (AHL) genes are crucial in various biological processes, yet the AHL gene family in apples has remained largely unexplored. In this study, we isolated 36 MdAHL genes from the apple genome and grouped them into two distinct clades. We characterized the gene structure, conserved motifs, protein biochemical properties, and promoter regions of the MdAHL genes. Transcriptional analysis revealed that MdAHL genes are preferentially and predominantly expressed in flowers and leaves. Notably, during the floral induction phase, the MdAHL6 gene exhibited remarkably high transcriptional activity. Overexpression of MdAHL6 resulted in shortened hypocotyls and delayed flowering by regulating hypocotyl- and floral-related genes. Y1H, EMSA, GUS activity, and molecular docking assays revealed that MdAHL6 directly binds to AT-rich regions, inhibiting the expression of FLOWERING LOCUS T (MdFT). Furthermore, Y2H, pull-down, and BiFC assays demonstrated a physical interaction between MdAHL6 and the class II knotted-like transcription factor MdKNOX19, which significantly enhances the inhibitory effect of MdAHL6 on MdFT expression. This comprehensive initial analysis unveils the critical role of the MdKNOX19-MdAHL6-MdFT module in flowering induction and lays a theoretical foundation for future functional exploration.
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Affiliation(s)
- Rui Yan
- Hebei Agricultural University, Baoding 071000, China
| | - Kaiyu Yang
- Hebei Agricultural University, Baoding 071000, China
| | - Tianle Zhang
- Hebei Agricultural University, Baoding 071000, China
| | - Rahat Sharif
- South China Agricultural University, Guangzhou 510642, China
| | - Siyu Yang
- Hebei Agricultural University, Baoding 071000, China
| | - Siyu Li
- Hebei Agricultural University, Baoding 071000, China
| | - Ning Wang
- Hebei Agricultural University, Baoding 071000, China
| | - Jiale Liu
- Hebei Agricultural University, Baoding 071000, China
| | - Shengnan Zhao
- Hebei Agricultural University, Baoding 071000, China
| | - Wenxiu Wang
- Hebei Agricultural University, Baoding 071000, China
| | - Xuemei Zhang
- Hebei Agricultural University, Baoding 071000, China
| | - Qinglong Dong
- Hebei Agricultural University, Baoding 071000, China
| | - Haoan Luan
- Hebei Agricultural University, Baoding 071000, China
| | - Suping Guo
- Hebei Agricultural University, Baoding 071000, China
| | - Yuan Wang
- Hebei Agricultural University, Baoding 071000, China.
| | - Guohui Qi
- Hebei Agricultural University, Baoding 071000, China.
| | - Peng Jia
- Hebei Agricultural University, Baoding 071000, China.
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Shi X, Yang T, Ren M, Fu J, Bai J, Cui H. AT-hook motif nuclear localized transcription factors function redundantly in promoting root growth through modulation of redox homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:199-217. [PMID: 39136690 DOI: 10.1111/tpj.16981] [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: 09/06/2023] [Revised: 06/18/2024] [Accepted: 07/31/2024] [Indexed: 09/27/2024]
Abstract
Maintaining an optimal redox status is essential for plant growth and development, particularly when the plants are under stress. AT-hook motif nuclear localized (AHL) proteins are evolutionarily conserved transcription factors in plants. Much of our understanding about this gene family has been derived from studies on clade A members. To elucidate the functions of clade B genes, we first analyzed their spatial expression patterns using transgenic plants expressing a nuclear localized GFP under the control of their promoter sequences. AHL1, 2, 6, 7, and 10 were further functionally characterized owing to their high expression in the root apical meristem. Through mutant analyses and transgenic studies, we showed that these genes have the ability to promote root growth. Using yeast one-hybrid and dual luciferase assays, we demonstrated that AHL1, 2, 6, 7, and 10 are transcription regulators and this activity is required for their roles in root growth. Although mutants for these genes did not showed obvious defects in root growth, transgenic plants expressing their fusion proteins with the SRDX repressor motif exhibited a short-root phenotype. Through transcriptome analysis, histochemical staining and molecular genetics experiments, we found that AHL10 maintains redox homeostasis via direct regulation of glutathione transferase (GST) genes. When the transcript level of GSTF2, a top-ranked target of AHL10, was reduced by RNAi, the short-root phenotype in the AHL10-SRDX expressing plant was largely rescued. These results together suggest that AHL genes function redundantly in promoting root growth through direct regulation of redox homeostasis.
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Affiliation(s)
- Xiaowen Shi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ting Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mengfei Ren
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jing Fu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Juan Bai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hongchang Cui
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306, USA
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Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F. Plant-TFClass: a structural classification for plant transcription factors. TRENDS IN PLANT SCIENCE 2024; 29:40-51. [PMID: 37482504 DOI: 10.1016/j.tplants.2023.06.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.
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Affiliation(s)
- Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France.
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Yang Q, Li M, Hou Y, He H, Sun S. High-mobility group box 1 emerges as a therapeutic target for asthma. Immun Inflamm Dis 2023; 11:e1124. [PMID: 38156383 PMCID: PMC10739362 DOI: 10.1002/iid3.1124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023] Open
Abstract
High-mobility group box 1 (HMGB1) is a highly conserved nonhistone nuclear protein found in the calf thymus and participates in a variety of intracellular processes such as DNA transcription, replication and repair. In the cytoplasm, HMGB1 promotes mitochondrial autophagy and is involved in in cellular stress response. Once released into the extracellular, HMGB1 becomes an inflammatory factor that triggers inflammatory responses and a variety of immune responses. In addition, HMGB1 binding with the corresponding receptor can activate the downstream substrate to carry out several biological effects. Meanwhile, HMGB1 is involved in various signaling pathways, such as the HMGB1/RAGE pathway, HMGB1/NF-κB pathway, and HMGB1/JAK/STAT pathway, which ultimately promote inflammation. Moreover, HMGB1 may be involved in the pathogenesis of asthma by regulating downstream signaling pathways through corresponding receptors and mediates a number of signaling pathways in asthma, such as HMGB1/TLR4/NF-κB, HMGB1/RAGE, HMGB1/TGF-β, and so forth. Accordingly, HMGB1 emerges as a therapeutic target for asthma.
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Affiliation(s)
- Qianni Yang
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
- 2021 Class 2 of AnesthesiologyKunming Medical UniversityKunmingChina
| | - Min Li
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Yunjiao Hou
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Huilin He
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
| | - Shibo Sun
- Department of Pulmonary and Critical Care MedicineFirst Affiliated Hospital, Kunming Medical UniversityKunmingChina
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HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2021; 118:2021053118. [PMID: 33975946 PMCID: PMC8157925 DOI: 10.1073/pnas.2021053118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA-protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga Chlamydomonas reinhardtii identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the HBD1 gene by CRISPR-Cas9-mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast Δabf2 mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.
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Aguilar M, Prieto P. Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:672489. [PMID: 34149773 PMCID: PMC8212018 DOI: 10.3389/fpls.2021.672489] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/06/2021] [Indexed: 05/08/2023]
Abstract
Genomic architecture facilitates chromosome recognition, pairing, and recombination. Telomeres and subtelomeres play an important role at the beginning of meiosis in specific chromosome recognition and pairing, which are critical processes that allow chromosome recombination between homologs (equivalent chromosomes in the same genome) in later stages. In plant polyploids, these terminal regions are even more important in terms of homologous chromosome recognition, due to the presence of homoeologs (equivalent chromosomes from related genomes). Although telomeres interaction seems to assist homologous pairing and consequently, the progression of meiosis, other chromosome regions, such as subtelomeres, need to be considered, because the DNA sequence of telomeres is not chromosome-specific. In addition, recombination operates at subtelomeres and, as it happens in rye and wheat, homologous recognition and pairing is more often correlated with recombining regions than with crossover-poor regions. In a plant breeding context, the knowledge of how homologous chromosomes initiate pairing at the beginning of meiosis can contribute to chromosome manipulation in hybrids or interspecific genetic crosses. Thus, recombination in interspecific chromosome associations could be promoted with the aim of transferring desirable agronomic traits from related genetic donor species into crops. In this review, we summarize the importance of telomeres and subtelomeres on chromatin dynamics during early meiosis stages and their implications in recombination in a plant breeding framework.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
- *Correspondence: Pilar Prieto, ; orcid.org/0000-0002-8160-808X
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Pal Negi A, Singh R, Sharma A, Negi VS. Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs. Comput Biol Chem 2020; 87:107306. [PMID: 32559639 DOI: 10.1016/j.compbiolchem.2020.107306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022]
Abstract
High mobility group (HMG) proteins are the major architectural proteins. Among HMG proteins, High Mobility Group A (HMGA) is characterized by AT-hook (ATH) motifs, which have an affinity for AT-rich DNA. In this study, we characterized the plant HMGAs from the Poaceae family using in silico methods. The protein sequences for rice HMGAs were retrieved and the corresponding orthologs from grasses were extracted. The phylogenetic analysis identified three major evolutionary clades of grass HMGAs and their ATH motif analysis revealed that HMGAs from clade 1 and 2, except for clade 2 HMGAs, are devoid of high-affinity DNA-binding domain. The clade 2 HMGAs also displayed a highly conserved length of all the spacers and the length of the C-terminal tail following the last ATH. Moreover, the C-terminal tail in clade 2 HMGAs is smaller than HMGAs from any other clade. Unlike clade 2, other clades of Poaceae HMGAs displayed high variability in the length of spacers. Despite several differences among HMGAs of different clades in Poaceae, the H1/H5 domain was found to be highly conserved. This study has revealed the detailed analyses of Poaceae HMGAs and it will be useful for further investigation aiming at the determination of precise biological functions and molecular mechanisms of grass HMGAs.
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Affiliation(s)
- Archana Pal Negi
- School of Sciences, PP Savani University, Surat, Gujarat, 394125, India
| | | | | | - Vishal Singh Negi
- School of Sciences, PP Savani University, Surat, Gujarat, 394125, India.
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Zhu Y, Luo X, Liu X, Wu W, Cui X, He Y, Huang J. Arabidopsis PEAPODs function with LIKE HETEROCHROMATIN PROTEIN1 to regulate lateral organ growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:812-831. [PMID: 31099089 DOI: 10.1111/jipb.12841] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
In higher plants, lateral organs are usually of determinate growth. It remains largely elusive how the determinate growth is achieved and maintained. Previous reports have shown that Arabidopsis PEAPOD (PPD) proteins suppress proliferation of dispersed meristematic cells partly through a TOPLESS corepressor complex. Here, we identified a new PPD-interacting partner, LIKE HETEROCHROMATIN PROTEIN1 (LHP1), using the yeast two-hybrid system, and their interaction is mediated by the chromo shadow domain and the Jas domain in LHP1 and PPD2, respectively. Our genetic data demonstrate that the phenotype of ppd2 lhp1 is more similar to lhp1 than to ppd2, indicating epistasis of lhp1 to ppd2. Microarray analysis reveals that PPD2 and LHP1 can regulate expression of a common set of genes directly or indirectly. Consistently, chromatin immunoprecipitation results confirm that PPD2 and LHP1 are coenriched at the promoter region of their targets such as D3-TYPE CYCLINS and HIGH MOBILITY GROUP A, which are upregulated in ppd2, lhp1 and ppd2 lhp1 mutants, and that PPDs mediate repressive histone 3 lysine-27 trimethylation at these loci. Taken together, our data provide evidence that PPD and LHP1 form a corepressor complex that regulates lateral organ growth.
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Affiliation(s)
- Ying Zhu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiao Luo
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xuxin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenjuan Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences,, Shanghai Normal University,, Shanghai, 200234, China
| | - Xiaofeng Cui
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuehui He
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences,, Shanghai Normal University,, Shanghai, 200234, China
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HMGA Genes and Proteins in Development and Evolution. Int J Mol Sci 2020; 21:ijms21020654. [PMID: 31963852 PMCID: PMC7013770 DOI: 10.3390/ijms21020654] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
HMGA (high mobility group A) (HMGA1 and HMGA2) are small non-histone proteins that can bind DNA and modify chromatin state, thus modulating the accessibility of regulatory factors to the DNA and contributing to the overall panorama of gene expression tuning. In general, they are abundantly expressed during embryogenesis, but are downregulated in the adult differentiated tissues. In the present review, we summarize some aspects of their role during development, also dealing with relevant studies that have shed light on their functioning in cell biology and with emerging possible involvement of HMGA1 and HMGA2 in evolutionary biology.
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Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize. Genomics 2019; 112:1233-1244. [PMID: 31323298 DOI: 10.1016/j.ygeno.2019.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/26/2019] [Accepted: 07/15/2019] [Indexed: 11/23/2022]
Abstract
AT-hook motif nuclear localized (AHL) genes have diverse but poorly understood biological functions. We identified and analyzed 37 AHL genes in maize. We also discovered four and one additional AHLs in rice and sorghum, respectively, besides those reported earlier. The maize AHLs were classified into two clades (A and B) and three distinct types (I, II, and III) as also reported in Arabidopsis. Phylogenetic and ortholog analyses showed that, while the evolutionary classification was conserved in plants, expansion of the AHL gene family in maize was accompanied with new biological functions. Gene structure analysis showed that, while all but one Type-I AHLs lacked an intron, origin of Type-II and Type-III AHLs was associated with the gain of introns suggesting evolutionarily distinct temporal and spatial expression patterns and, likely, neofunctionalization. Gene duplication analysis revealed that AHLs in maize expanded via dispersive duplication further supporting their functional diversity. To discern these functions, we analyzed 71 transcriptomes from diverse tissues and developmental stages of maize and classified AHLs into eight groups with distinct temporal/spatial expression profiles. Coexpression analysis implicated 5 AHLs and 33 novel genes in networks specific to endosperm, seed, root, leaf, and reproductive tissues indicating their role in the development of these organs. Major processes coregulated by AHLs include pollen development, drought response, senescence, and wound response. We also identified interactions of AHL proteins in coregulating important processes including stress response. These novel insights into the role of AHLs in plant development provide a platform for functional analyses in maize and related grasses.
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The HMGA gene family in chordates: evolutionary perspectives from amphioxus. Dev Genes Evol 2017; 227:201-211. [DOI: 10.1007/s00427-017-0581-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 04/24/2017] [Indexed: 02/07/2023]
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12
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Hao X, Yang Y, Yue C, Wang L, Horvath DP, Wang X. Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages. FRONTIERS IN PLANT SCIENCE 2017; 8:553. [PMID: 28458678 PMCID: PMC5394108 DOI: 10.3389/fpls.2017.00553] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of tea plant, one of the few woody plants in the world whose leaves are harvested and one of the few non-conifer evergreen species with characterized dormancies. To discover the bud dormancy regulation mechanism of tea plant in winter, we analyzed the global gene expression profiles of axillary buds at the paradormancy, endodormancy, ecodormancy, and bud flush stages by RNA-Seq analysis. In total, 16,125 differentially expressed genes (DEGs) were identified among the different measured conditions. Gene set enrichment analysis was performed on the DEGs identified from each dormancy transition. Enriched gene ontology terms, gene sets and transcription factors were mainly associated with epigenetic mechanisms, phytohormone signaling pathways, and callose-related cellular communication regulation. Furthermore, differentially expressed transcription factors as well as chromatin- and phytohormone-associated genes were identified. GI-, CAL-, SVP-, PHYB-, SFR6-, LHY-, ZTL-, PIF4/6-, ABI4-, EIN3-, ETR1-, CCA1-, PIN3-, CDK-, and CO-related gene sets were enriched. Based on sequence homology analysis, we summarized the key genes with significant expression differences in poplar and tea plant. The major molecular pathways involved in tea plant dormancy regulation are consistent with those of poplar to a certain extent; however, the gene expression patterns varied. This study provides the global transcriptome profiles of overwintering buds at different dormancy stages and is meaningful for improving the understanding of bud dormancy in tea plant.
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Affiliation(s)
- Xinyuan Hao
- Tea Research Institute, Chinese Academy of Agricultural SciencesHangzhou, China
- National Center for Tea Improvement, Key Laboratory of Tea Biology and Resources Utilization, Ministry of AgricultureHangzhou, China
| | - Yajun Yang
- Tea Research Institute, Chinese Academy of Agricultural SciencesHangzhou, China
- National Center for Tea Improvement, Key Laboratory of Tea Biology and Resources Utilization, Ministry of AgricultureHangzhou, China
| | - Chuan Yue
- Tea Research Institute, Chinese Academy of Agricultural SciencesHangzhou, China
- National Center for Tea Improvement, Key Laboratory of Tea Biology and Resources Utilization, Ministry of AgricultureHangzhou, China
| | - Lu Wang
- Tea Research Institute, Chinese Academy of Agricultural SciencesHangzhou, China
- National Center for Tea Improvement, Key Laboratory of Tea Biology and Resources Utilization, Ministry of AgricultureHangzhou, China
| | - David P. Horvath
- Biosciences Research Laboratory, Sunflower and Plant Biology Research Unit, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
- *Correspondence: David P. Horvath, Xinchao Wang,
| | - Xinchao Wang
- Tea Research Institute, Chinese Academy of Agricultural SciencesHangzhou, China
- National Center for Tea Improvement, Key Laboratory of Tea Biology and Resources Utilization, Ministry of AgricultureHangzhou, China
- *Correspondence: David P. Horvath, Xinchao Wang,
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Kasahara K, Higashino A, Unzai S, Yoshikawa H, Kokubo T. Oligomerization of Hmo1 mediated by box A is essential for DNA binding in vitro and in vivo. Genes Cells 2016; 21:1333-1352. [PMID: 27860073 DOI: 10.1111/gtc.12449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/05/2016] [Indexed: 11/30/2022]
Abstract
Hmo1, a member of HMGB family proteins in Saccharomyces cerevisiae, binds to and regulates the transcription of genes encoding ribosomal RNA and ribosomal proteins. The functional motifs of Hmo1 include two HMG-like motifs, box A and box B, and a C-terminal tail. To elucidate the molecular roles of the HMG-like boxes in DNA binding in vivo, we analyzed the DNA-binding activity of various Hmo1 mutants using ChIP or reporter assays that enabled us to conveniently detect Hmo1 binding to the promoter of RPS5, a major target gene of Hmo1. Our mutational analyses showed that box B is a bona fide DNA-binding motif and that it also plays other important roles in cell growth. However, box A, especially its first α-helix, contributes to DNA binding of Hmo1 by inducing self-assembly of Hmo1. Intriguingly, box A mediated formation of oligomers of more than two proteins on DNA in vivo. Furthermore, duplication of the box B partially alleviates the requirement for box A. These findings suggest that the principal role of box A is to assemble multiple box B in the appropriate orientation, thereby stabilizing the binding of Hmo1 to DNA and nucleating specific chromosomal architecture on its target genes.
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Affiliation(s)
- Koji Kasahara
- Isotope Center, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Ayako Higashino
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | | | - Tetsuro Kokubo
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
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14
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Chinpongpanich A, Phean-O-Pas S, Thongchuang M, Qu LJ, Buaboocha T. C-terminal extension of calmodulin-like 3 protein from Oryza sativa L.: interaction with a high mobility group target protein. Acta Biochim Biophys Sin (Shanghai) 2015; 47:880-9. [PMID: 26423116 DOI: 10.1093/abbs/gmv097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/28/2015] [Indexed: 11/14/2022] Open
Abstract
A large number of calmodulin-like (CML) proteins are present in plants, but there is little detailed information on the functions of these proteins in rice (Oryza sativa L.). Here, the CML3 protein from rice (OsCML3) and its truncated form lacking the C-terminal extension (OsCML3m) were found to exhibit a Ca2+-binding property and subsequent conformational change, but the ability to bind the CaM kinase II peptide was only observed for OsCML3m. Changes in their secondary structure upon Ca2+-binding measured by circular dichroism revealed that OsCML3m had a higher helical content than OsCML3. Moreover, OsCML3 was mainly localized in the plasma membrane, whereas OsCML3m was found in the nucleus. The rice high mobility group B1 (OsHMGB1) protein was identified as one of the putative OsCML3 target proteins. Bimolecular fluorescence complementation analysis revealed that OsHMGB1 bound OsCML3, OsCML3m or OsCML3s (cysteine to serine mutation at the prenylation site) in the nucleus presumably through the methionine and phenylalanine-rich hydrophobic patches, confirming that OsHMGB1 is a target protein in planta. The effect of OsCML3 or OsCML3m on the DNA-binding ability of OsHMGB1 was measured using an electrophoretic mobility shift assay. OsCML3m decreased the level of OsHMGB1 binding to pUC19 double-stranded DNA whereas OsCML3 did not. Taken together, OsCML3 probably provides a mechanism for manipulating the DNA-binding ability of OsHMGB1 in the nucleus and its C-terminal extension provides an intracellular Ca2+ regulatory switch.
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Affiliation(s)
- Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Srivilai Phean-O-Pas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mayura Thongchuang
- Division of Food Safety Management and Technology, Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Krungthep, Bangkok 10120, Thailand
| | - Li-Jia Qu
- National Laboratory for Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Teerapong Buaboocha
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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15
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Liu B, Pang B, Liu H, Arakawa Y, Zhang R, Feng B, Zhong P, Murata D, Fan H, Xin T, Zhao G, Liu W, Guo H, Luan L, Xu S, Miyamoto S, Pang Q. High mobility group A1 expression shows negative correlation with recurrence time in patients with glioblastoma multiforme. Pathol Res Pract 2015; 211:596-600. [PMID: 26092597 DOI: 10.1016/j.prp.2015.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/22/2015] [Accepted: 05/13/2015] [Indexed: 01/24/2023]
Abstract
The aim of this study was to explore the difference in high mobility group A1 (HMGA1) expression and isocitrate dehydrogenase (IDH) 1 R132H point mutation in initial and recurrent glioblastoma multiforme (GBM), and to further identify whether the expression of HMGA1 has a role in the malignant progression of GBM. Paired initial and recurrent GBM specimens from the same patient were evaluated using immunohistochemical analysis. The association between HMGA1 expression and progression-free survival time (PFST) was analyzed. Three patients were confirmed with IDH-1 R132H mutations in both initial and recurrent groups (3/25, 12%). There was a significant difference in HMGA1 expression between initial and recurrent GBM (P=0.002), and patients with tumors expressing HMGA1 at higher level had a significantly shorter PFST (7.3 months versus 11.1months; P=0.044). Our study indicates that recurrent GBM express HMGA1 at a higher level and that HMGA1 overexpressoin is associated with shorter PFST in patients with GBM. These findings suggest that HMGA1 potentially plays an important role in the treatment of GBM.
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Affiliation(s)
- Bin Liu
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China; Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto 606-8527, Japan
| | - Bo Pang
- Department of Neurosurgery, Shandong University Graduate School of Medicine, Jinan 250012, PR China
| | - Huajie Liu
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Yoshiki Arakawa
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto 606-8527, Japan
| | - Rui Zhang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Bin Feng
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Peng Zhong
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Daiki Murata
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto 606-8527, Japan
| | - Haitao Fan
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Tao Xin
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Guangyu Zhao
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Wei Liu
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Hua Guo
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China.
| | - Liming Luan
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Shangchen Xu
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Susumu Miyamoto
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto 606-8527, Japan
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China.
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16
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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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17
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Vriet C, Hennig L, Laloi C. Stress-induced chromatin changes in plants: of memories, metabolites and crop improvement. Cell Mol Life Sci 2015; 72:1261-73. [PMID: 25578097 PMCID: PMC11113909 DOI: 10.1007/s00018-014-1792-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 01/18/2023]
Abstract
Exposure of plants to adverse environmental conditions leads to extensive transcriptional changes. Genome-wide approaches and gene function studies have revealed the importance of chromatin-level control in the regulation of stress-responsive gene expression. Advances in understanding chromatin modifications implicated in plant stress response and identifying proteins involved in chromatin-mediated transcriptional responses to stress are briefly presented in this review. We then highlight how chromatin-mediated gene expression changes can be coupled to the metabolic status of the cell, since many of the chromatin-modifying proteins involved in transcriptional regulation depend on cofactors and metabolites that are shared with enzymes in basic metabolism. Lastly, we discuss the stability and heritability of stress-induced chromatin changes and the potential of chromatin-based strategies for increasing stress tolerance of crops.
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Affiliation(s)
- Cécile Vriet
- BVME UMR 7265, Lab Genet Biophys Plantes, Aix Marseille Université, Marseille, 13284, France,
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18
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Higashino A, Shiwa Y, Yoshikawa H, Kokubo T, Kasahara K. Both HMG boxes in Hmo1 are essential for DNA binding in vitro and in vivo. Biosci Biotechnol Biochem 2014; 79:384-93. [PMID: 25410521 DOI: 10.1080/09168451.2014.978258] [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] [Indexed: 10/24/2022]
Abstract
Hmo1, a member of the high mobility group B family proteins in Saccharomyces cerevisiae, associates with the promoters of ribosomal protein genes (RPGs) to direct accurate transcriptional initiation. Here, to identify factors involved in the binding of Hmo1 to its targets and the mechanism of Hmo1-dependent transcriptional initiation, we developed a novel reporter system using the promoter of the RPG RPS5. A genetic screen did not identify any factors that influence Hmo1 binding, but did identify a number of mutations in Hmo1 that impair its DNA binding activity in vivo and in vitro. These results suggest that Hmo1 binds to its target promoters autonomously without any aid of additional factors. Furthermore, characterization of Hmo1 mutants showed that the box A domain plays a pivotal role in DNA binding and may be required for the recognition of structural properties of target promoters that occur in native chromatin.
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Affiliation(s)
- Ayako Higashino
- a Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
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19
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Kim HB, Oh CJ, Park YC, Lee Y, Choe S, An CS, Choi SB. Comprehensive analysis of AHL homologous genes encoding AT-hook motif nuclear localized protein in rice. BMB Rep 2012; 44:680-5. [PMID: 22027003 DOI: 10.5483/bmbrep.2011.44.10.680] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The AT-hook motif is a small DNA-binding protein motif that has been found in the high mobility group of non-histone chromosomal proteins. The Arabidopsis genome contains 29 genes encoding the AT-hook motif DNA-binding protein (AHL). Recent studies of Arabidopsis genes (AtAHLs) have revealed that they might play diverse functional roles during plant growth and development. In this report, we mined 20 AHL genes (OsAHLs) from the rice genome database using AtAHL genes as queries and characterized their molecular features. A phylogenetic tree revealed that OsAHL proteins can be classified into 2 evolutionary clades. Tissue expression pattern analysis revealed that all of the OsAHL genes might be functionally expressed genes with 3 distinct expression patterns. Nuclear localization analysis using transgenic Arabidopsis showed that several OsAHL proteins are exclusively localized in the nucleus, indicating that they may act as architectural transcription factors to regulate expression of their target genes during plant growth and development.
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Affiliation(s)
- Ho Bang Kim
- The Natural Science Research Institute, Myongji University, Yongin, Korea.
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20
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Lee S, Song H, Kim HA, Oh B, Lee DY, Lee M. The box a domain of high mobility group box-1 protein as an efficient siRNA carrier with anti-inflammatory effects. J Cell Biochem 2011; 113:122-31. [DOI: 10.1002/jcb.23334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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HMGA1 expression in human gliomas and its correlation with tumor proliferation, invasion and angiogenesis. J Neurooncol 2011; 106:543-9. [PMID: 21984063 DOI: 10.1007/s11060-011-0710-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 09/12/2011] [Indexed: 12/21/2022]
Abstract
High-mobility group A1 (HMGA1) protein is an architectural transcription factor widely expressed during embryonic development and tumor progression. The purpose of this research was to investigate the expression of HMGA1 in malignant gliomas with different WHO classification and to study the correlation of HMGA1 expression with tumor proliferation, invasion, and angiogenesis. Expression of HMGA1, Ki-67, MMP-9, VEGF-A, and MVD in malignant gliomas and their correlation were studied in 60 samples of different WHO classification by use of immunohistochemistry, and in 27 randomly selected samples by use of real-time quantitative PCR. Immunohistochemistry results showed that nuclear immunostaining of HMGA1 protein was not observed in normal brain tissues but was observed in 96.7% (58 of 60) of malignant gliomas including high (+++) in 15 (25.0%), moderate (++) in 28 (46.7%), and negligible to low (0-+) in 17 (28.3%) samples. Expression of HMGA1 protein was significantly higher in glioblastoma multiforme than in WHO grade II (P = 0.002) and WHO grade III gliomas (P = 0.024). HMGA1 protein expression correlated significantly with expression of Ki-67 (r = 0.530, P = 0.000), MMP-9 (r = 0.508, P = 0.000), VEGF-A (r = 0.316, P = 0.014), and MVD (r = 0.321, P = 0.012), but not with sex (r = 0.087, P = 0.510) and age (r = -0.121, P = 0.358). Real-time quantitative PCR results, also, were indicative of HMGA1 overexpression in glioblastoma multiforme compared with WHO grade II (P = 0.043) and WHO grade III (P = 0.031) gliomas. HMGA1 gene expression correlated significantly with gene expression of Ki-67 (r = 0.429, P = 0.025), MMP-9 (r = 0.443, P = 0.024), and VEGF-A (r = 0.409, P = 0.034). These results indicated that expression of HMGA1 correlates significantly with malignancy, proliferation, invasion, and angiogenesis of gliomas. We conclude that HMGA1 may be a potential biomarker and rational therapeutic target for human tumors.
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22
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Finnie C, Sultan A, Grasser KD. From protein catalogues towards targeted proteomics approaches in cereal grains. PHYTOCHEMISTRY 2011; 72:1145-1153. [PMID: 21134685 DOI: 10.1016/j.phytochem.2010.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 05/27/2023]
Abstract
Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain proteomes, mostly derived using 2D-gel based technologies, have been described and hundreds of proteins identified. However, very little is still known about post-translational modifications, subcellular proteomes, and protein-protein interactions in cereal grains. Development of techniques for improved extraction, separation and identification of proteins and peptides is facilitating functional proteomics and analysis of sub-proteomes from small amounts of starting material, such as seed tissues. The combination of proteomics with structural and functional analysis is increasingly applied to target subsets of proteins. These "next-generation" proteomics studies will vastly increase our depth of knowledge about the processes controlling cereal grain development, nutritional and processing characteristics.
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Affiliation(s)
- Christine Finnie
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Bldg 224, DK-2800 Kgs. Lyngby, Denmark.
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23
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Lecanidou R, Papantonis A. Silkmoth chorion gene regulation revisited: promoter architecture as a key player. INSECT MOLECULAR BIOLOGY 2010; 19:141-151. [PMID: 20002795 DOI: 10.1111/j.1365-2583.2009.00969.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Regulation of silkmoth chorion genes has long been used as a model system for studying differential gene expression. The large numbers of genes, their overlapping expression patterns and the overall complexity of the system hinted towards an elaborate mechanism for transcriptional control. Recent studies, however, offer evidence of a molecular pathway governed by the interplay between two general transcription factors, CCAAT enhancer binding proteins (C/EBP) and GATA, an architectural protein, high mobility group A and a chromatin remodeller, chromo-helicase/ATPase-DNA binding protein 1. In this review we present a parsimonious model that adequately describes regulation of transcription across all temporally regulated chorion genes, and propose a role for promoter architecture.
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Affiliation(s)
- R Lecanidou
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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24
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Whittle CA, Malik MR, Li R, Krochko JE. Comparative transcript analyses of the ovule, microspore, and mature pollen in Brassica napus. PLANT MOLECULAR BIOLOGY 2010; 72:279-99. [PMID: 19949835 DOI: 10.1007/s11103-009-9567-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Accepted: 10/26/2009] [Indexed: 05/20/2023]
Abstract
Transcriptome data for plant reproductive organs/cells currently is very limited as compared to sporophytic tissues. Here, we constructed cDNA libraries and obtained ESTs for Brassica napus pollen (4,864 ESTs), microspores (i.e., early stage pollen development; 6,539 ESTs) and ovules (10,468 ESTs). Clustering and assembly of the 21,871 ESTs yielded a total of 10,782 unigenes, with 3,362 contigs and 7,420 singletons. The pollen transcriptome contained high levels of polygalacturonases and pectinesterases, which are involved in cell wall synthesis and expansion, and very few transcription factors or transcripts related to protein synthesis. The set of genes expressed in mature pollen showed little overlap with genes expressed in ovules or in microspores, suggesting in the latter case that a marked differentiation had occurred from the early microspore stages through to pollen development. Remarkably, the microspores and ovules exhibited a high number of co-expressed genes (N = 1,283) and very similar EST functional profiles, including high transcript numbers for transcriptional and translational processing genes, protein modification genes and unannotated genes. In addition, examination of expression values for genes co-expressed among microspores and ovules revealed a highly statistically significant correlation among these two tissues (R = 0.360, P = 1.2 x 10(-40)) as well as a lack of differentially expressed genes. Overall, the results provide new insights into the transcriptional profile of rarely studied ovules, the transcript changes during pollen development, transcriptional regulation of pollen tube growth and germination, and describe the parallels in the transcript populations of microspore and ovules which could have implications for understanding the molecular foundation of microspore totipotency in B. napus.
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Affiliation(s)
- Carrie A Whittle
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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25
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Carneiro VC, de Moraes Maciel R, de Abreu da Silva IC, da Costa RFM, Paiva CN, Bozza MT, Fantappié MR. The extracellular release of Schistosoma mansoni HMGB1 nuclear protein is mediated by acetylation. Biochem Biophys Res Commun 2009; 390:1245-9. [DOI: 10.1016/j.bbrc.2009.10.129] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 10/26/2009] [Indexed: 11/16/2022]
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26
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The maize HMGA protein is localized to the nucleolus and can be acetylated in vitro at its globular domain, and phosphorylation by CDK reduces its binding activity to AT-rich DNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:751-7. [DOI: 10.1016/j.bbagrm.2009.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 09/16/2009] [Indexed: 11/23/2022]
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27
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Choi Y, Jeong CW, Ohr H, Song SK, Choi YD, Lee JS. Developmental and environmental regulation of soybean SE60 gene expression during embryogenesis and germination. PLANTA 2009; 230:959-71. [PMID: 19690885 DOI: 10.1007/s00425-009-0999-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 08/01/2009] [Indexed: 05/28/2023]
Abstract
Soybean SE60 belongs to the gamma-thionin family of proteins. We recently demonstrated that SE60 plays a role in defense during soybean development. Here, we show that SE60 is expressed in a tissue-specific and developmentally regulated manner. The expression of SE60 is distinct from that of the glycinin (Gy2) and extensin (SbHRGP3) genes of soybean during embryogenesis and germination. A SE60::GUS(-809) transgene, comprising -809 bp of the 5'-flanking region of SE60 fused to the GUS reporter gene, was expressed specifically in developing embryos, but not in the endosperms, from the globular stage of transgenic tobacco and Arabidopsis seeds. Furthermore, light affected the SE60::GUS(-809) expression pattern in germinating seedlings. Electrophoretic mobility shift assay (EMSA) revealed that soybean nuclear proteins as well as E. coli-expressed SB16, a high mobility group protein (HMG), were bound sequence-specifically to the fragment containing AT-rich motifs identified in the SE60 promoter. Interestingly, the soybean nuclear proteins binding to the two G-boxes and RY repeat were prevalent in seeds of 2-4 mm in size. In contrast, the nuclear proteins binding to the AT-rich motif and SE60 RNA expression were more prominent in seeds of 4-6 mm in size. Therefore, we propose that factors binding to the G-boxes or RY repeat initiate SE60 expression during embryogenesis.
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Affiliation(s)
- Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea.
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28
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Tsunaka Y, Toga J, Yamaguchi H, Tate SI, Hirose S, Morikawa K. Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements. J Biol Chem 2009; 284:24610-21. [PMID: 19605348 PMCID: PMC2782050 DOI: 10.1074/jbc.m109.001958] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 06/22/2009] [Indexed: 11/06/2022] Open
Abstract
FACT is a heterodimer of SPT16 and SSRP1, which each contain several conserved regions in the primary structure. The interaction of FACT with nucleosomes induces chromatin remodeling through the combinatorial action of its distinct functional protein regions. However, there is little mechanistic insight into how these regions cooperatively contribute to FACT functions, particularly regarding the recognition of nucleosomal DNA. Here, we report the identification of novel phosphorylation sites of Drosophila melanogaster FACT (dFACT) expressed in Sf9 cells. These sites are densely concentrated in the acidic intrinsically disordered (ID) region of the SSRP1 subunit and control nucleosomal DNA binding by dFACT. This region and the adjacent segment of the HMG domain form weak electrostatic intramolecular interactions, which is reinforced by the phosphorylation, thereby blocking DNA binding competitively. Importantly, this control mechanism appears to support rapid chromatin transactions during early embryogenesis through the dephosphorylation of some sites in the maternally transmitted dSSRP1.
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Affiliation(s)
- Yasuo Tsunaka
- From the Takara-Bio Endowed Laboratory, Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- JSPS, Ichibancho, Chiyoda-ku, Tokyo 102-8472, Japan
| | - Junko Toga
- From the Takara-Bio Endowed Laboratory, Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Hiroto Yamaguchi
- From the Takara-Bio Endowed Laboratory, Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Shin-ichi Tate
- the Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Susumu Hirose
- the Department of Development Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan, and
| | - Kosuke Morikawa
- From the Takara-Bio Endowed Laboratory, Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- CREST, JST, Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
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Vékony H, Röser K, Löning T, Ylstra B, Meijer GA, van Wieringen WN, van de Wiel MA, Carvalho B, Kok K, Leemans CR, van der Waal I, Bloemena E. Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas. Genes Chromosomes Cancer 2009; 48:202-12. [PMID: 19009612 DOI: 10.1002/gcc.20631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Salivary gland myoepithelial tumors are relatively uncommon tumors with an unpredictable clinical course. More knowledge about their genetic profiles is necessary to identify novel predictors of disease. In this study, we subjected 27 primary tumors (15 myoepitheliomas and 12 myoepithelial carcinomas) to genome-wide microarray-based comparative genomic hybridization (array CGH). We set out to delineate known chromosomal aberrations in more detail and to unravel chromosomal differences between benign myoepitheliomas and myoepithelial carcinomas. Patterns of DNA copy number aberrations were analyzed by unsupervised hierarchical cluster analysis. Both benign and malignant tumors revealed a limited amount of chromosomal alterations (median of 5 and 7.5, respectively). In both tumor groups, high frequency gains (> or =20%) were found mainly at loci of growth factors and growth factor receptors (e.g., PDGF, FGF(R)s, and EGFR). In myoepitheliomas, high frequency losses (> or =20%) were detected at regions of proto-cadherins. Cluster analysis of the array CGH data identified three clusters. Differential copy numbers on chromosome arm 8q and chromosome 17 set the clusters apart. Cluster 1 contained a mixture of the two phenotypes (n = 10), cluster 2 included mostly benign tumors (n = 10), and cluster 3 only contained carcinomas (n = 7). Supervised analysis between malignant and benign tumors revealed a 36 Mbp-region at 8q being more frequently gained in malignant tumors (P = 0.007, FDR = 0.05). This is the first study investigating genomic differences between benign and malignant myoepithelial tumors of the salivary glands at a genomic level. Both unsupervised and supervised analysis of the genomic profiles revealed chromosome arm 8q to be involved in the malignant phenotype of salivary gland myoepitheliomas.
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Affiliation(s)
- Hedy Vékony
- Department of Oral and Maxillofacial Surgery/Oral Pathology, Academic Centre for Dentistry (ACTA), VU University Medical Center, Amsterdam, The Netherlands
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Architectural factor HMGA induces promoter bending and recruits C/EBP and GATA during silkmoth chorion gene regulation. Biochem J 2008; 416:85-97. [DOI: 10.1042/bj20081012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A protein displaying significant similarity to mammalian HMGA (high-mobility group A) proteins, but also bearing unique structural features, was isolated from silkmoth (Bombyx mori) follicular cells. This factor, named BmHMGA, exhibits specific binding preference for chorion gene promoter elements and induces DNA bending thereon. BmHMGA deploys temporal-specific interaction with transcription factors BmC/EBP (C/EBP is CCAAT/enhancer-binding protein) and BmGATAβ during follicle maturation. The respective protein complexes can be detected on chorion gene promoters in vivo, with different developmental profiles each time. Analogous interaction takes place on the putative promoter of the BmC/EBP gene, hinting towards a transcriptional circuit that is responsible for the progress of choriogenesis as a whole. Finally, transient suppression of BmHMGA expression led to down-regulation of chorion genes and the BmC/EBP gene, and revealed recruitment of BmC/EBP, BmGATAβ and TFIID (transcription factor IID)/TBP (TATA-box-binding protein) by BmHMGA. A revised model for chorion gene regulation is discussed in view of these findings.
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Lyngaard C, Stemmer C, Stensballe A, Graf M, Gorr G, Decker E, Grasser KD. Physcomitrella HMGA-type proteins display structural differences compared to their higher plant counterparts. Biochem Biophys Res Commun 2008; 374:653-7. [PMID: 18662672 DOI: 10.1016/j.bbrc.2008.07.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 07/16/2008] [Indexed: 11/28/2022]
Abstract
High mobility group (HMG) proteins of the HMGA family are chromatin-associated proteins that act as architectural factors in nucleoprotein structures involved in gene transcription. To date, HMGA-type proteins have been studied in various higher plant species, but not in lower plants. We have identified two HMGA-type proteins, HMGA1 and HMGA2, encoded in the genome of the moss model Physcomitrella patens. Compared to higher plant HMGA proteins, the two Physcomitrella proteins display some structural differences. Thus, the moss HMGA proteins have six (rather than four) AT-hook DNA-binding motifs and their N-terminal domain lacks similarity to linker histone H1. HMGA2 is expressed in moss protonema and it localises to the cell nucleus. Typical of HMGA proteins, HMGA2 interacts preferentially with A/T-rich DNA, when compared with G/C-rich DNA. In cotransformation assays in Physcomitrella protoplasts, HMGA2 stimulated reporter gene expression. In summary, our data show that functional HMGA-type proteins occur in Physcomitrella.
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Affiliation(s)
- Carina Lyngaard
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Street IH, Shah PK, Smith AM, Avery N, Neff MM. The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:1-14. [PMID: 18088311 DOI: 10.1111/j.1365-313x.2007.03393.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
SOB3, which encodes a plant-specific AT-hook motif containing protein, was identified from an activation-tagging screen for suppressors of the long-hypocotyl phenotype of a weak phyB allele, phyB-4. sob3-D (suppressor of phyB-4#3 dominant) overexpressing seedlings have shorter hypocotyls, and as adults develop larger flowers and leaves, and are delayed in senescence compared with wild-type plants. At the nucleotide level, SOB3 is closely related to ESCAROLA (ESC), which was identified in an independent activation-tagging screen. ESC overexpression also suppresses the phyB-4 long-hypocotyl phenotype, and confers an adult morphology similar to sob3-D, suggesting similar functions. Analysis of transgenic plants harboring SOB3:SOB3-GUS or ESC:ESC-GUS translational fusions, driven by their endogenous promoter regions, showed GUS activity in the hypocotyl and vasculature tissue in light- and dark-grown seedlings. A loss-of-function SOB3 allele (sob3-4) was generated through an ethyl methanesulfonate intragenic suppressor screen of sob3-D phyB-4 plants, and this allele was combined with a predicted null allele, disrupting ESC (esc-8), to examine potential genetic interactions. The sob3-4 esc-8 double mutant had a long hypocotyl in multiple fluence rates of continuous white, far-red, red and blue light. sob3-4 esc-8 phyB-9 and sob3-4 esc-8 cry-103 triple mutants also had longer hypocotyls than photoreceptor single mutants. In contrast, the sob3-4 esc-8 phyA-211 triple mutant was the same length as phyA-211 single mutants. Taken together, these data indicate that SOB3 and ESC act redundantly to modulate hypocotyl growth inhibition in response to light.
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Affiliation(s)
- Ian H Street
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Derbyshire P, Drea S, Shaw PJ, Doonan JH, Dolan L. Proximal-distal patterns of transcription factor gene expression during Arabidopsis root development. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:235-245. [PMID: 18263631 DOI: 10.1093/jxb/erm301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The expression pattern of genes can identify the cells in which the respective proteins are active during development. As a step towards defining the genetic network that controls the development of roots, a high-throughput method of whole-mount in situ hybridization has been developed that does not require expensive equipment and allows the definition of the expression patterns of 137 transcription factor genes in young developing roots. Of the 137 transcription factors, 81.8% were expressed in the root while 18.2% showed no detectable expression. In all three proximal distal zones (meristem, elongation, and differentiation) of the root, 52.6% were expressed whereas 21.2% were expressed in only two zones. Eight percent of the genes were expressed in a single proximal distal zone. Cell-specific gene expression patterns were also detected. This rapid approach identified potential key regulators of cell differentiation and provides important spatial information for the expression patterns of a large number of transcriptional regulators that function during root development.
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Affiliation(s)
- Paul Derbyshire
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
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Kasahara K, Ki S, Aoyama K, Takahashi H, Kokubo T. Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in start site selection by RNA polymerase II. Nucleic Acids Res 2008; 36:1343-57. [PMID: 18187511 PMCID: PMC2275077 DOI: 10.1093/nar/gkm1068] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Saccharomyces cerevisiae HMO1, a high mobility group B (HMGB) protein, associates with the rRNA locus and with the promoters of many ribosomal protein genes (RPGs). Here, the Sos recruitment system was used to show that HMO1 interacts with TBP and the N-terminal domain (TAND) of TAF1, which are integral components of TFIID. Biochemical studies revealed that HMO1 copurifies with TFIID and directly interacts with TBP but not with TAND. Deletion of HMO1 (Δhmo1) causes a severe cold-sensitive growth defect and decreases transcription of some TAND-dependent genes. Δhmo1 also affects TFIID occupancy at some RPG promoters in a promoter-specific manner. Interestingly, over-expression of HMO1 delays colony formation of taf1 mutants lacking TAND (taf1ΔTAND), but not of the wild-type strain, indicating a functional link between HMO1 and TAND. Furthermore, Δhmo1 exhibits synthetic growth defects in some spt15 (TBP) and toa1 (TFIIA) mutants while it rescues growth defects of some sua7 (TFIIB) mutants. Importantly, Δhmo1 causes an upstream shift in transcriptional start sites of RPS5, RPS16A, RPL23B, RPL27B and RPL32, but not of RPS31, RPL10, TEF2 and ADH1, indicating that HMO1 may participate in start site selection of a subset of class II genes presumably via its interaction with TFIID.
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Affiliation(s)
- Koji Kasahara
- Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, 230-0045, Japan
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Kiilerich B, Stemmer C, Merkle T, Launholt D, Gorr G, Grasser KD. Chromosomal high mobility group (HMG) proteins of the HMGB-type occurring in the moss Physcomitrella patens. Gene 2007; 407:86-97. [PMID: 17980517 DOI: 10.1016/j.gene.2007.09.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Revised: 09/28/2007] [Accepted: 09/29/2007] [Indexed: 11/26/2022]
Abstract
High mobility group (HMG) proteins of the HMGB family are chromatin-associated proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. Members of the HMGB family have been characterised from various mono-and dicot plants, but not from lower plant species. Here, we have identified three candidate HMGB proteins encoded in the genome of the moss Physcomitrella patens. The structurally similar HMGB2 and HMGB3 proteins display the typical overall structure of higher plant HMGB proteins consisting of a central HMG-box DNA-binding domain that is flanked by a basic N-terminal and an acidic C-terminal domain. The HMGB1 protein differs from higher plant HMGB proteins by having a very extensive N-terminal domain and by lacking the acidic C-terminal domain. Like higher plant HMGB proteins, HMGB3 localises to the cell nucleus, but HMGB1 is targeted to plastids. Analysis of the HMG-box domains of HMGB1 and HMGB3 by CD revealed that HMGB1box and the HMGB3box have an alpha-helical structure. While the HMGB3box interacts with DNA comparable to typical higher plant counterparts, the HMGB1box has only a low affinity for DNA. Cotransformation assays in Physcomitrella protoplasts demonstrated that expression of HMGB3 resulted in repression of reporter gene expression. In summary, our data show that functional HMGB-type proteins occur in Physcomitrella and most likely in other lower plant species.
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Affiliation(s)
- Bruno Kiilerich
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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36
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Delaney SK, Orford SJ, Martin-Harris M, Timmis JN. The fiber specificity of the cotton FSltp4 gene promoter is regulated by an AT-rich promoter region and the AT-hook transcription factor GhAT1. PLANT & CELL PHYSIOLOGY 2007; 48:1426-37. [PMID: 17715150 DOI: 10.1093/pcp/pcm111] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fiber-specific genes are expressed preferentially or exclusively in cotton (Gossypium spp.) fiber and are thought to have important functions in fiber development. The promoters of these genes are of interest because they control transcription in the fiber cell and may be used in the genetic manipulation of fiber quality. The promoter of a cotton lipid transfer protein gene, FSltp4, was isolated and shown to direct fiber-specific transcription of an abundant mRNA in cotton. In transgenic tobacco, this promoter was strongly active in leaf trichomes. Deletion analysis of the promoter identified an AT-rich 84 bp fiber specificity region (FSR) necessary for activity exclusively in the fiber cells. Cotton fiber proteins that bind the FSR were isolated using a yeast one-hybrid assay. One of these was a putative AT-hook transcription factor (GhAT1) containing two AT-hook motifs. GhAT1 was shown to be nuclear localized, and GhAT1 transcripts were found to be preferentially expressed in ovules and non-fiber tissues. Overexpression of GhAT1 strongly repressed the activity of the FSltp4 promoter in the trichomes of transgenic tobacco. These results suggest that GhAT1 assists in the specification of fiber cells by repressing FSltp4 in the non-fiber tissues of the cotton plant.
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Affiliation(s)
- Sven K Delaney
- Discipline of Genetics, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
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37
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Kasahara K, Ohtsuki K, Ki S, Aoyama K, Takahashi H, Kobayashi T, Shirahige K, Kokubo T. Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae. Mol Cell Biol 2007; 27:6686-705. [PMID: 17646381 PMCID: PMC2099245 DOI: 10.1128/mcb.00876-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HMO1 is a high-mobility group B protein that plays a role in transcription of genes encoding rRNA and ribosomal proteins (RPGs) in Saccharomyces cerevisiae. This study uses genome-wide chromatin immunoprecipitation to study the roles of HMO1, FHL1, and RAP1 in transcription of these genes as well as other RNA polymerase II-transcribed genes in yeast. The results show that HMO1 associates with the 35S rRNA gene in an RNA polymerase I-dependent manner and that RPG promoters (138 in total) can be classified into several distinct groups based on HMO1 abundance at the promoter and the HMO1 dependence of FHL1 and/or RAP1 binding to the promoter. FHL1, a key regulator of RPGs, binds to most of the HMO1-enriched and transcriptionally HMO1-dependent RPG promoters in an HMO1-dependent manner, whereas it binds to HMO1-limited RPG promoters in an HMO1-independent manner, irrespective of whether they are transcribed in an HMO1-dependent manner. Reporter gene assays indicate that these functional properties are determined by the promoter sequence.
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Affiliation(s)
- Koji Kasahara
- Division of Molecular and Cellular Biology, Science of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, Japan
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38
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Christov NK, Yoneyama S, Shimamoto Y, Imai R. Differential expression of wheat genes during cold acclimation. CYTOL GENET+ 2007. [DOI: 10.3103/s0095452707030024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ansari KI, Walter S, Brennan JM, Lemmens M, Kessans S, McGahern A, Egan D, Doohan FM. Retrotransposon and gene activation in wheat in response to mycotoxigenic and non-mycotoxigenic-associated Fusarium stress. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:927-37. [PMID: 17256175 DOI: 10.1007/s00122-006-0490-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Accepted: 12/21/2006] [Indexed: 05/08/2023]
Abstract
Despite inhibition of protein synthesis being its mode of action, the trichothecene mycotoxin deoxynivalenol (DON) induced accumulation of transcripts encoding translation elongation factor 1alpha (EF-1alpha), class III plant peroxidase (POX), structure specific recognition protein, basic leucine zipper protein transcription factor (bZIP), retrotransposon-like homologs and genes of unknown function in the roots of wheat cultivars CM82036 and Remus. Fusarium head blight (FHB) studies using Fusarium graminearum and its trichothecene-minus (Tri5 ( - )) mutant derivative and adult plant DON tests showed that these transcripts were responsive to both mycotoxigenic- and non-mycotoxigenic-associated Fusarium stress. In tests using the parents 'CM82036', 'Remus' and 14 double-haploid progeny that segregated for quantitative trait locus (QTL) Fhb1 on chromosome 3BS (syn. Qfhs.ndsu-3BS) (from 'CM82036' that confers DON tolerance), bZIP expression was significantly more DON-up-regulated in lines that inherited this QTL. Basal accumulation of the bZIP transcript in spikelets treated with Tween20 (control), DON and in DON-relative to Tween20-treated spikelets was negatively correlated with DON-induced bleaching above (but not below) the treated spikelets (AUDPC(DON)) (r = -0.41, -0.75 and -0.72, respectively; P < or = 0.010). bZIP-specific PCR analysis of 'Chinese spring' and its 3BS deletion derivatives indicated that bZIP is located in chromosomal region(s) other than 3BS. These results, and the fact that a homologous cold-regulated wheat bZIP (wLIP19) maps to group 1 chromosomes suggests that wheat bZIP may participate in defence response cascades associated with Fhb1 and that there is a cross-talk between biotic and abiotic stress signalling pathways.
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Affiliation(s)
- Khairul I Ansari
- Molecular Plant-Microbe Interactions Laboratory, School of Biology and Environmental Sciences, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
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Grønlund JT, Stemmer C, Lichota J, Merkle T, Grasser KD. Functionality of the beta/six site-specific recombination system in tobacco and Arabidopsis: a novel tool for genetic engineering of plant genomes. PLANT MOLECULAR BIOLOGY 2007; 63:545-56. [PMID: 17131098 DOI: 10.1007/s11103-006-9108-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 10/30/2006] [Indexed: 05/12/2023]
Abstract
The beta recombinase is a member of the prokaryotic site-specific serine recombinases (invertase/resolvase family), which in the presence of a DNA bending cofactor can catalyse DNA deletions between two directly oriented 90-bp six recombination sites. We have examined here whether the beta recombinase can be expressed in plants and whether it displays in planta its specific catalytic activity excising DNA sequences that are flanked by six sites. In plant protoplasts, the enzyme could be expressed as a GFP-beta recombinase fusion which can localise to the cell nucleus. Beta recombinase stably expressed in tobacco plants can catalyse deletion of a spacer region that is flanked by directly oriented six sites and has been placed between promoter and a GUS reporter gene (preventing GUS expression). In transient transformation experiments, beta recombinase-mediated elimination of the spacer results in transcriptional induction of the GUS gene. Similarly, beta recombinase in stably double-transformed Arabidopsis plants deletes specifically the spacer region of a reporter construct that has been incorporated into the genome. In the segregating T1 generation, plants were identified that contain exclusively the recombined reporter construct. In summary, our results demonstrate that functional / recombinase can be expressed in plants and that the enzyme is suitable to precisely eliminate undesired sequences from plant genomes. Therefore, the beta/six recombination system (and presumably related recombinases) may become an attractive tool for plant genetic engineering.
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Affiliation(s)
- Jesper T Grønlund
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Kwak KJ, Kim JY, Kim YO, Kang H. Characterization of Transgenic Arabidopsis Plants Overexpressing High Mobility Group B Proteins under High Salinity, Drought or Cold Stress. ACTA ACUST UNITED AC 2007; 48:221-31. [PMID: 17169924 DOI: 10.1093/pcp/pcl057] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
High mobility group B (HMGB) proteins found in the nuclei of higher eukaryotes play roles in various cellular processes such as replication, transcription and nucleosome assembly. The Arabidopsis thaliana genome contains eight genes encoding HMGB proteins, the functions of which remain largely unknown in the transcriptional regulation of plant stress responses. To understand better the functions of HMGB proteins in the responses of plants to environmental stimuli, we examined the effect of various abiotic stresses on germination and growth of transgenic Arabidopsis plants that overexpress a single isoform of HMGB. The expression of HMGB2, HMGB3 and HMGB4 was up-regulated by cold stress, whereas the expression of HMGB2 and HMGB3 was markedly down-regulated by drought or salt stress. Under salt or drought stress, the transgenic Arabidopsis plants that overexpress HMGB2 displayed retarded germination and subsequent growth compared with wild-type plants. Overexpression of HMGB4 had no impact on seed germination and seedling growth of the plants under the stress conditions tested. In contrast to no significant stress-related phenotypes of HMGB5-overexpressing plants, loss-of-function mutants of HMGB5 displayed retarded germination and subsequent growth compared with wild-type plants under stress conditions. Although transcript levels of various stress-responsive genes were not modulated by the expression of HMGB2, expression of several germination-responsive genes was modulated by HMGB2 under salt stress. Taken together, these results provide a novel basis for understanding the biological functions of HMGB protein family members that differently affect germination and seedling growth of Arabidopsis plants under various stress conditions.
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Affiliation(s)
- Kyung Jin Kwak
- Department of Plant Biotechnology, Agricultural Plant Stress Research Center and Biotechnology Research Institute, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 Korea
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42
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Grasser KD, Launholt D, Grasser M. High mobility group proteins of the plant HMGB family: dynamic chromatin modulators. ACTA ACUST UNITED AC 2007; 1769:346-57. [PMID: 17316841 DOI: 10.1016/j.bbaexp.2006.12.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 12/29/2006] [Accepted: 12/31/2006] [Indexed: 12/13/2022]
Abstract
In plants, the chromosomal high mobility group (HMG) proteins of the HMGB family typically contain a central HMG-box DNA-binding domain that is flanked by a basic N-terminal and an acidic C-terminal domain. The HMGB proteins are abundant and highly mobile proteins in the cell nucleus that influence chromatin structure and enhance the accessibility of binding sites to regulatory factors. Due to their remarkable DNA bending activity, HMGB proteins can increase the structural flexibility of DNA, promoting the assembly of nucleoprotein complexes that control DNA-dependent processes including transcription. Therefore, members of the HMGB family act as versatile modulators of chromatin function.
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Affiliation(s)
- Klaus D Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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Benini F, Onorati M, Altamura S, Manfioletti G, Vignali R. Identification and developmental expression of Xenopus hmga2β. Biochem Biophys Res Commun 2006; 351:392-7. [PMID: 17070502 DOI: 10.1016/j.bbrc.2006.10.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 10/08/2006] [Indexed: 10/24/2022]
Abstract
HMGA proteins are "architectural modifiers" of the chromatin, characterized by three conserved "AT-hook" motifs, with which they bind AT-rich regions of the DNA, to assist in gene transcription. We report the identification and developmental expression of Xenopus laevis hmga2beta (Xlhmga2beta). We provide evidence of two forms of hmga2 (Xlhmga2alpha and Xlhmga2beta) and of a splicing variant for Xlhmga2beta with an additional AT-hook. By comparing X. laevis and X. tropicalis hmga2 DNA sequences to those of other organisms we show a high conservation of the Xlhmga2beta variant. By RT-PCR, Xlhmga2beta transcripts are first detected before the midblastula transition (MBT), and then become more abundant. By in situ hybridization, localized transcripts are first detected at neurula stages, in the presumptive central nervous system (CNS). At tailbud and tadpole stages, Xlhmga2beta mRNA is detected in the CNS, in the otic vesicles, in neural crest cell derivatives, in the notochord, and in the medio-lateral mesoderm.
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Affiliation(s)
- Francesca Benini
- Dipartimento di Biologia, Laboratori di Biologia Cellulare e dello Sviluppo, Università di Pisa, via Carducci 13, 56010 Ghezzano (Pisa), Italy
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Launholt D, Merkle T, Houben A, Schulz A, Grasser KD. Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus. THE PLANT CELL 2006; 18:2904-18. [PMID: 17114349 PMCID: PMC1693932 DOI: 10.1105/tpc.106.047274] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 10/02/2006] [Accepted: 10/30/2006] [Indexed: 05/12/2023]
Abstract
In plants, the chromatin-associated high mobility group (HMG) proteins occur in two subfamilies termed HMGA and HMGB. The HMGA proteins are characterized by the presence of four AT-hook DNA binding motifs, and the HMGB proteins contain an HMG box DNA binding domain. As architectural factors, the HMG proteins appear to be involved in the regulation of transcription and other DNA-dependent processes. We have examined the subcellular localization of Arabidopsis thaliana HMGA, HMGB1, and HMGB5, revealing that they localize to the cell nucleus. They display a speckled distribution pattern throughout the chromatin of interphase nuclei, whereas none of the proteins associate with condensed mitotic chromosomes. HMGA is targeted to the nucleus by a monopartite nuclear localization signal, while efficient nuclear accumulation of HMGB1/5 requires large portions of the basic N-terminal part of the proteins. The acidic C-terminal domain interferes with nucleolar targeting of HMGB1. Fluorescence recovery after photobleaching experiments revealed that HMGA and HMGB proteins are extremely dynamic in the nucleus, indicating that they bind chromatin only transiently before moving on to the next site, thereby continuously scanning the genome for targets. By contrast, the majority of histone H2B is basically immobile within the nucleus, while linker histone H1.2 is relatively mobile.
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Affiliation(s)
- Dorte Launholt
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
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de Oliveira FMB, de Abreu da Silva IC, Rumjanek FD, Dias-Neto E, Guimarães PEM, Verjovski-Almeida S, Stros M, Fantappié MR. Cloning the genes and DNA binding properties of High Mobility Group B1 (HMGB1) proteins from the human blood flukes Schistosoma mansoni and Schistosoma japonicum. Gene 2006; 377:33-45. [PMID: 16644144 DOI: 10.1016/j.gene.2006.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 03/02/2006] [Accepted: 03/03/2006] [Indexed: 11/18/2022]
Abstract
The parasitic helminth Schistosoma mansoni contains three HMGB proteins, HMGB1, HMGB2 and HMGB3, of primary amino acid sequences highly similar to vertebrate proteins. In this report we describe the characterization of the HMGB1 proteins and their genes from S. mansoni and Schistosoma japonicum. The deduced amino acid sequences of HMGB1 proteins from both schistosome species are identical, and comprise 176 residues. The proteins contain the two evolutionarily highly conserved HMG-box domains, A and B, exhibiting 60% similarity to mammalian HMGB1. Unlike the human HMGB1 which contains an unbroken run of 30 glutamic or aspartic residues, the SmHMGB1 or SjHMGB1 proteins possess unusually short acidic C-terminal tails (5 acidic residues interrupted by 2 serines). Southern hybridization and DNA sequencing revealed a single copy HMGB1 gene, composed of 3 exons and two introns, in S. mansoni. The exon/intron boundaries are identical to those of the human HMGB1 gene, with the exception that the second exon of the SmHMGB1 gene which is not split into two exons as in the human HMGB1 gene. RNA blot analysis revealed that the SmHMGB1 gene is constitutively expressed in similar levels both in male and female worms. The single-sized mRNA for SmHMGB1 is consistent with the size derived from the cDNA. Although DNA binding properties of SmHMGB1 (or SjHMGB1) protein seem to be similar to those previously reported with human HMGB1, i.e., preferential binding to supercoiled DNA over linear DNA, specific recognition of DNA four-way junctions, DNA-induced supercoiling in the presence of topoisomerase I, and DNA bending, we have observed two important differences relative to those observed with the human HMGB1: (i) the inability of the isolated SmHMGB1 domain A to bend DNA (as revealed by T4 ligase-mediated circularization assay), and (ii) higher DNA supercoiling and bending potential of the SmHMGB1 protein as compared to its human counterpart. The latter finding may indicate that the long acidic C-tail of human HMGB1 has much stronger repressive role on DNA bending or DNA supercoiling by topoisomerase I at physiological ionic strength than the short C-tail of the SmHMGB1 protein. Considering the important role of HMGB1 in DNA replication, transcription, recombination, and in particularly, the mediation of inflammation responses in mammalian cells, further studies on schistosome HMGB proteins may provide valuable information related to schistosomiasis, where inflammation plays a critical role in this disease.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/genetics
- DNA, Helminth/chemistry
- DNA, Helminth/genetics
- DNA, Helminth/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- Genes, Helminth
- HMGB1 Protein/genetics
- HMGB1 Protein/metabolism
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Schistosoma japonicum/genetics
- Schistosoma japonicum/metabolism
- Schistosoma japonicum/pathogenicity
- Schistosoma mansoni/genetics
- Schistosoma mansoni/metabolism
- Schistosoma mansoni/pathogenicity
- Sequence Homology, Amino Acid
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Grasser M, Lentz A, Lichota J, Merkle T, Grasser KD. The Arabidopsis Genome Encodes Structurally and Functionally Diverse HMGB-type Proteins. J Mol Biol 2006; 358:654-64. [PMID: 16563436 DOI: 10.1016/j.jmb.2006.02.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 02/16/2006] [Accepted: 02/25/2006] [Indexed: 11/18/2022]
Abstract
The high mobility group (HMG) proteins of the HMGB family are chromatin-associated proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription and recombination. In addition to the previously identified HMGB1-HMGB6 proteins, the Arabidopsis genome encodes at least two other candidate family members (encoded by the loci At2g34450 and At5g23405) having the typical overall structure of a central domain displaying sequence similarity to HMG-box DNA binding domains, which is flanked by basic N-terminal and acidic C-terminal regions. Subcellular localisation experiments demonstrate that the At2g34450 protein is a nuclear protein, whereas the At5g23405 protein is found mainly in the cytoplasm. In line with this finding, At5g23405 displays specific interaction with the nuclear export receptor AtXPO1a. According to CD measurements, the HMG-box domains of both proteins have an alpha-helical structure. The HMG-box domain of At2g34450 interacts with linear DNA and binds structure-specifically to DNA minicircles, whereas the HMG-box domain of At5g23405 does not interact with DNA at all. In ligation experiments with short DNA fragments, the At2g34450 HMG-box domain can facilitate the formation of linear oligomers, but it does not promote the formation of DNA minicircles. Therefore, the At2g34450 protein shares several features with HMGB proteins, whereas the At5g23405 protein has different characteristics. Despite the presence of a region with similarity to the nucleosome-binding domain typical of HMGN proteins, At2g34450 does not bind nucleosome particles. In summary, our data demonstrate (i) that plant HMGB-type proteins are functionally variable and (ii) that it is difficult to predict HMG-box function solely based on sequence similarity.
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Affiliation(s)
- Marion Grasser
- Department of Life Sciences, Aalborg University, Sohn-gaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Gnanasekar M, Velusamy R, He YX, Ramaswamy K. Cloning and characterization of a high mobility group box 1 (HMGB1) homologue protein from Schistosoma mansoni. Mol Biochem Parasitol 2006; 145:137-46. [PMID: 16246438 DOI: 10.1016/j.molbiopara.2005.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 09/20/2005] [Accepted: 09/23/2005] [Indexed: 11/25/2022]
Abstract
Mammalian homologue of high mobility group box chromatin protein (HMGB) 1 was identified and cloned from human parasites, Schistosoma mansoni and S. haematobium. Sequence analyses showed that the parasite HMGB1s has 35-40% identity to human and rodent HMGB1s, and 33% identity to Caenorhabditis elegans HMGB1. Parasite HMGB1s also contains an A box and B box domain similar to mammalian HMGB1, however, it lacks the C-terminal tail that is present in mammalian HMGB1s. Analysis of the expression of HMGB1 in various life cycle stages of S. mansoni reveal S. mansoni HMGB1 (SmHMGB1) as a stage-specific protein, expressed abundantly in egg and adult female stages and at moderate levels in skin-stage schistosomula. Significant levels of SmHMGB1 were also present in excretory secretions of egg stages. Subsequent characterization studies showed that SmHMGB1 is a potent inducer of pro-inflammatory cytokines such as TNFalpha, IL-1Ralpha, IL-2Ralpha, IL-6, IL-13, IL-13Ralpha1, IL-15 and MIP-1alpha from mouse peritoneal macrophages. Pro-inflammatory activity, especially production of TNFalpha-inducing activity, appears to be a function of the B box domain protein. This was confirmed by both real-time reverse transcription PCR and by cytokine ELISA. Thus, results presented in this study suggest that SmHMGB1 may be a key molecule in the development of host inflammatory immune responses associated with schistosomiasis.
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Affiliation(s)
- Munirathinam Gnanasekar
- Department of Biomedical Sciences, University of Illinois College of Medicine, 1601 Parkview Avenue, Rockford, IL 61107, USA
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48
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Boisson-Dernier A, Andriankaja A, Chabaud M, Niebel A, Journet EP, Barker DG, de Carvalho-Niebel F. MtENOD11 gene activation during rhizobial infection and mycorrhizal arbuscule development requires a common AT-rich-containing regulatory sequence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:1269-76. [PMID: 16478046 DOI: 10.1094/mpmi-18-1269] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The MtENOD11 gene from the model legume Medicago truncatula is transcriptionally activated both in response to Sinorhizobium meliloti Nod factors and throughout infection of root tissues by the nitrogen-fixing microsymbiont. To identify the regulatory sequences involved in symbiosis-related MtENOD11 expression, a series of promoter deletions driving the beta-glucuronidase reporter gene were analyzed in transgenic M. truncatula roots. These studies have revealed that distinct regulatory regions are involved in infection-related MtENOD11 expression compared with preinfection (Nod factor-mediated) expression. In particular, the 257-bp promoter sequence immediately upstream from the start codon is sufficient for infection-related expression, but is unable to drive gene transcription in response to the Nod factor elicitor. This truncated promoter is also sufficient to confer MtENOD11 expression during both the arbuscular mycorrhizal (AM) association and the parasitic interaction with root-knot nematodes. Site-directed mutagenesis further showed that a previously identified nodule-specific AT-rich motif is required for high-level MtENOD11 expression during S. meliloti infection as well as during AM colonization. However, mutation of this motif does not affect gene expression associated with nematode-feeding sites. Taken together, these results suggest a close link between regulatory mechanisms controlling transcriptional early nodulin gene activation during both rhizobial and AM root endosymbioses.
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49
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Jaouen S, de Koning L, Gaillard C, Muselíková-Polanská E, Stros M, Strauss F. Determinants of specific binding of HMGB1 protein to hemicatenated DNA loops. J Mol Biol 2005; 353:822-37. [PMID: 16199053 DOI: 10.1016/j.jmb.2005.08.073] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2005] [Revised: 08/29/2005] [Accepted: 08/29/2005] [Indexed: 01/23/2023]
Abstract
Protein HMGB1 has long been known as one of the most abundant non-histone proteins in the nucleus of mammalian cells, and has regained interest recently for its function as an extracellular cytokine. As a DNA-binding protein, HMGB1 facilitates DNA-protein interactions by increasing the flexibility of the double helix, and binds specifically to distorted DNA structures. We have previously observed that HMGB1 binds with extremely high affinity to a novel DNA structure, hemicatenated DNA loops (hcDNA), in which double-stranded DNA fragments containing a tract of poly(CA).poly(TG) form a loop maintained at its base by a hemicatenane. Here, we show that the single HMGB1 domains A and B, the HMG-box domain of sex determination factor SRY, as well as the prokaryotic HMGB1-like protein HU, specifically interact with hcDNA (Kd approximately 0.5 nM). However, the affinity of full-length HMGB1 for hcDNA is three orders of magnitude higher (Kd<0.5 pM) and requires the simultaneous presence of both HMG-box domains A and B plus the acidic C-terminal tail on the molecule. Interestingly, the high affinity of the full-length protein for hcDNA does not decrease in the presence of magnesium. Experiments including a comparison of HMGB1 binding to hcDNA and to minicircles containing the CA/TG sequence, binding studies with HMGB1 mutated at intercalating amino acid residues (involved in recognition of distorted DNA structures), and exonuclease III footprinting, strongly suggest that the hemicatenane, not the DNA loop, is the main determinant of the affinity of HMGB1 for hcDNA. Experiments with supercoiled CA/TG-minicircles did not reveal any involvement of left-handed Z-DNA in HMGB1 binding. Our results point to a tight structural fit between HMGB1 and DNA hemicatenanes under physiological conditions, and suggest that one of the nuclear functions of HMGB1 could be linked to the possible presence of hemicatenanes in the cell.
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Affiliation(s)
- Sandrine Jaouen
- Institut Jacques Monod, 2 place Jussieu, F-75251 Paris 05, France
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Ekman DR, Wolfe NL, Dean JFD. Gene expression changes in Arabidopsis thaliana seedling roots exposed to the munition hexahydro-1,3,5-trinitro-1,3,5-triazine. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2005; 39:6313-20. [PMID: 16173598 DOI: 10.1021/es050385r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana root transcriptome responses to the munition, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), were assessed using serial analysis of gene expression (SAGE). Sequencing of SAGE libraries from control and RDX-exposed root tissues revealed induction of genes known to respond to a variety of general stresses. Among the highly induced genes were several encoding molecular chaperones and transcription factors as well as vacuolar proteins and peroxidases. Strongly repressed transcripts included ones encoding ribosomal proteins, a cyclophilin, a katanin, and a peroxidase. Comparison of the transcriptional profile for the RDX response to a profile previously described for Arabidopsis roots exposed to trinitrotoluene (TNT) revealed significant differences in the inferred gene expression patterns. This suggests that Arabidopsis employs drastically different mechanisms for coping with these two compounds. With respect to the goal of engineering plants to better tolerate and degrade explosives at contaminated sites, these results suggest that enhancement of different genes and metabolic pathways may be required to deal effectively with each type of explosive. This has ramifications for phytoremediation efforts since many contaminated sites harbor both compounds.
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Affiliation(s)
- Drew R Ekman
- National Exposure Research Laboratory, Ecosystems Research Division, U.S. Environmental Protection Agency, Athens, Georgia 30605, USA
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