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Zheng J, Tang H, Wang J, Liu Y, Ge L, Liu G, Shi Q, Zhang Y. Genome-Wide Identification and Expression Analysis of the High-Mobility Group B ( HMGB) Gene Family in Plant Response to Abiotic Stress in Tomato. Int J Mol Sci 2024; 25:5850. [PMID: 38892039 PMCID: PMC11172549 DOI: 10.3390/ijms25115850] [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: 04/26/2024] [Revised: 05/24/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
High-mobility group B (HMGB) proteins are a class of non-histone proteins associated with eukaryotic chromatin and are known to regulate a variety of biological processes in plants. However, the functions of HMGB genes in tomato (Solanum lycopersicum) remain largely unexplored. Here, we identified 11 members of the HMGB family in tomato using BLAST. We employed genome-wide identification, gene structure analysis, domain conservation analysis, cis-acting element analysis, collinearity analysis, and qRT-PCR-based expression analysis to study these 11 genes. These genes were categorized into four groups based on their unique protein domain structures. Despite their structural diversity, all members contain the HMG-box domain, a characteristic feature of the HMG superfamily. Syntenic analysis suggested that tomato SlHMGBs have close evolutionary relationships with their homologs in other dicots. The promoter regions of SlHMGBs are enriched with numerous cis-elements related to plant growth and development, phytohormone responsiveness, and stress responsiveness. Furthermore, SlHMGB members exhibited distinct tissue-specific expression profiles, suggesting their potential roles in regulating various aspects of plant growth and development. Most SlHMGB genes respond to a variety of abiotic stresses, including salt, drought, heat, and cold. For instance, SlHMGB2 and SlHMGB4 showed positive responses to salt, drought, and cold stresses. SlHMGB1, SlHMGB3, and SlHMGB8 were involved in responses to two types of stress: SlHMGB1 responded to drought and heat, while SlHMGB3 and SlHMGB8 responded to salt and heat. SlHMGB6 and SlHMGB11 were solely regulated by drought and heat stress, respectively. Under various treatment conditions, the number of up-regulated genes significantly outnumbered the down-regulated genes, implying that the SlHMGB family may play a crucial role in mitigating abiotic stress in tomato. These findings lay a foundation for further dissecting the precise roles of SlHMGB genes.
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Affiliation(s)
| | | | | | | | | | | | | | - Yan Zhang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, China; (J.Z.); (H.T.); (J.W.); (Y.L.); (L.G.); (G.L.); (Q.S.)
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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Xu K, Chen S, Li T, Yu S, Zhao H, Liu H, Luo L. Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:711271. [PMID: 34421959 PMCID: PMC8375505 DOI: 10.3389/fpls.2021.711271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/16/2021] [Indexed: 05/05/2023]
Abstract
Drought stress adversely affects crop growth and productivity worldwide. In response, plants have evolved several strategies in which numerous genes are induced to counter stress. High mobility group (HMG) proteins are the second most abundant family of chromosomal proteins. They play a crucial role in gene transcriptional regulation by modulating the chromatin/DNA structure. In this study, we isolated a novel HMG gene, OsHMGB707, one of the candidate genes localized in the quantitative trait loci (QTL) interval of rice drought tolerance, and examined its function on rice stress tolerance. The expression of OsHMGB707 was up-regulated by dehydration and high salt treatment. Its overexpression significantly enhanced drought tolerance in transgenic rice plants, whereas its knockdown through RNA interference (RNAi) did not affect the drought tolerance of the transgenic rice plants. Notably, OsHMGB707-GFP is localized in the cell nucleus, and OsHMGB707 is protein-bound to the synthetic four-way junction DNA. Several genes were up-regulated in OsHMGB707-overexpression (OE) rice lines compared to the wild-type rice varieties. Some of the genes encode stress-related proteins (e.g., DREB transcription factors, heat shock protein 20, and heat shock protein DnaJ). In summary, OsHMGB707 encodes a stress-responsive high mobility group protein and regulates rice drought tolerance by promoting the expression of stress-related genes.
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Affiliation(s)
- Kai Xu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Shoujun Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Zhao
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene Center, Shanghai, China
- *Correspondence: Hongyan Liu,
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Lijun Luo,
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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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Kang R, Chen R, Zhang Q, Hou W, Wu S, Cao L, Huang J, Yu Y, Fan XG, Yan Z, Sun X, Wang H, Wang Q, Tsung A, Billiar TR, Zeh HJ, Lotze MT, Tang D. HMGB1 in health and disease. Mol Aspects Med 2014; 40:1-116. [PMID: 25010388 PMCID: PMC4254084 DOI: 10.1016/j.mam.2014.05.001] [Citation(s) in RCA: 701] [Impact Index Per Article: 70.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/05/2014] [Indexed: 12/22/2022]
Abstract
Complex genetic and physiological variations as well as environmental factors that drive emergence of chromosomal instability, development of unscheduled cell death, skewed differentiation, and altered metabolism are central to the pathogenesis of human diseases and disorders. Understanding the molecular bases for these processes is important for the development of new diagnostic biomarkers, and for identifying new therapeutic targets. In 1973, a group of non-histone nuclear proteins with high electrophoretic mobility was discovered and termed high-mobility group (HMG) proteins. The HMG proteins include three superfamilies termed HMGB, HMGN, and HMGA. High-mobility group box 1 (HMGB1), the most abundant and well-studied HMG protein, senses and coordinates the cellular stress response and plays a critical role not only inside of the cell as a DNA chaperone, chromosome guardian, autophagy sustainer, and protector from apoptotic cell death, but also outside the cell as the prototypic damage associated molecular pattern molecule (DAMP). This DAMP, in conjunction with other factors, thus has cytokine, chemokine, and growth factor activity, orchestrating the inflammatory and immune response. All of these characteristics make HMGB1 a critical molecular target in multiple human diseases including infectious diseases, ischemia, immune disorders, neurodegenerative diseases, metabolic disorders, and cancer. Indeed, a number of emergent strategies have been used to inhibit HMGB1 expression, release, and activity in vitro and in vivo. These include antibodies, peptide inhibitors, RNAi, anti-coagulants, endogenous hormones, various chemical compounds, HMGB1-receptor and signaling pathway inhibition, artificial DNAs, physical strategies including vagus nerve stimulation and other surgical approaches. Future work further investigating the details of HMGB1 localization, structure, post-translational modification, and identification of additional partners will undoubtedly uncover additional secrets regarding HMGB1's multiple functions.
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Affiliation(s)
- Rui Kang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
| | - Ruochan Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Qiuhong Zhang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Wen Hou
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Sha Wu
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Lizhi Cao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jin Huang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yan Yu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xue-Gong Fan
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhengwen Yan
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA; Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510510, China
| | - Haichao Wang
- Laboratory of Emergency Medicine, The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Qingde Wang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Allan Tsung
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Herbert J Zeh
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Daolin Tang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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Antosch M, Mortensen SA, Grasser KD. Plant proteins containing high mobility group box DNA-binding domains modulate different nuclear processes. PLANT PHYSIOLOGY 2012; 159:875-83. [PMID: 22585776 PMCID: PMC3387713 DOI: 10.1104/pp.112.198283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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Pedersen DS, Coppens F, Ma L, Antosch M, Marktl B, Merkle T, Beemster GTS, Houben A, Grasser KD. The plant-specific family of DNA-binding proteins containing three HMG-box domains interacts with mitotic and meiotic chromosomes. THE NEW PHYTOLOGIST 2011; 192:577-89. [PMID: 21781122 DOI: 10.1111/j.1469-8137.2011.03828.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
• The high mobility group (HMG)-box represents a DNA-binding domain that is found in various eukaryotic DNA-interacting proteins. Proteins that contain three copies of the HMG-box domain, termed 3 × HMG-box proteins, appear to be specific to plants. The Arabidopsis genome encodes two 3 × HMG-box proteins that were studied here. • DNA interactions were examined using electrophoretic mobility shift assays, whereas expression, subcellular localization and chromosome association were mainly analysed by different types of fluorescence microscopy. • The 3 × HMG-box proteins bind structure specifically to DNA, display DNA bending activity and, in addition to the three HMG-box domains, the basic N-terminal domain contributes to DNA binding. The expression of the two Arabidopsis genes encoding 3 × HMG-box proteins is linked to cell proliferation. In synchronized cells, expression is cell cycle dependent and peaks in cells undergoing mitosis. 3 × HMG-box proteins are excluded from the nuclei of interphase cells and localize to the cytosol, but, during mitosis, they associate with condensed chromosomes. The 3 × HMG-box2 protein generally associates with mitotic chromosomes, while 3 × HMG-box1 is detected specifically at 45S rDNA loci. • In addition to mitotic chromosomes the 3 × HMG-box proteins associate with meiotic chromosomes, suggesting that they are involved in a general process of chromosome function related to cell division, such as chromosome condensation and/or segregation.
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Affiliation(s)
- Dorthe S Pedersen
- Cell Biology and Plant Biochemistry, Regensburg University, Regensburg, Germany
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Merkle T, Grasser KD. Unexpected mobility of plant chromatin-associated HMGB proteins. PLANT SIGNALING & BEHAVIOR 2011; 6:878-80. [PMID: 21543902 PMCID: PMC3218493 DOI: 10.4161/psb.6.6.15255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High mobility group (HMG) proteins of the HMGB family containing a highly conserved HMG box are chromatin-associated proteins that interact with DNA and nucleosomes and catalyze changes in DNA topology, thereby facilitating important DNA-dependent processes. The genome of Arabidopsis thaliana encodes 15 different HMG-box proteins that are further subdivided into four groups: HMGB-type proteins, ARID-HMG proteins, 3xHMG proteins that contain three HMG boxes and the structure-specific recognition protein 1 (SSRP1). Typically, HMGB proteins are localized exclusively to the nucleus, like Arabidopsis HMGB1 and B5. However, these Arabidopsis HMGB proteins showed a very high mobility within the nuclear compartment. Recent studies revealed that Arabidopsis HMGB2/3 and B4 proteins are predominantly nuclear but also exist in the cytoplasm, suggesting an as yet unknown cytoplasmic function of these chromosomal HMG proteins.
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Affiliation(s)
- Thomas Merkle
- Faculty of Biology & Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany.
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Pedersen DS, Merkle T, Marktl B, Lildballe DL, Antosch M, Bergmann T, Tönsing K, Anselmetti D, Grasser KD. Nucleocytoplasmic distribution of the Arabidopsis chromatin-associated HMGB2/3 and HMGB4 proteins. PLANT PHYSIOLOGY 2010; 154:1831-41. [PMID: 20940346 PMCID: PMC2996034 DOI: 10.1104/pp.110.163055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/08/2010] [Indexed: 05/19/2023]
Abstract
High mobility group (HMG) proteins of the HMGB family are chromatin-associated proteins that as architectural factors are involved in the regulation of transcription and other DNA-dependent processes. HMGB proteins are generally considered nuclear proteins, although mammalian HMGB1 can also be detected in the cytoplasm and outside of cells. Plant HMGB proteins studied so far were found exclusively in the cell nucleus. Using immunofluorescence and fluorescence microscopy of HMGB proteins fused to the green fluorescent protein, we have examined the subcellular localization of the Arabidopsis (Arabidopsis thaliana) HMGB2/3 and HMGB4 proteins, revealing that, in addition to a prominent nuclear localization, they can be detected also in the cytoplasm. The nucleocytoplasmic distribution appears to depend on the cell type. By time-lapse fluorescence microscopy, it was observed that the HMGB2 and HMGB4 proteins tagged with photoactivatable green fluorescent protein can shuttle between the nucleus and the cytoplasm, while HMGB1 remains nuclear. The balance between the basic amino-terminal and the acidic carboxyl-terminal domains flanking the central HMG box DNA-binding domain critically influences the nucleocytoplasmic distribution of the HMGB proteins. Moreover, protein kinase CK2-mediated phosphorylation of the acidic tail modulates the intranuclear distribution of HMGB2. Collectively, our results show that, in contrast to other Arabidopsis HMGB proteins such as HMGB1 and HMGB5, the HMGB2/3 and HMGB4 proteins occur preferentially in the cell nucleus, but to various extents also in the cytoplasm.
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Libault M, Zhang XC, Govindarajulu M, Qiu J, Ong YT, Brechenmacher L, Berg RH, Hurley-Sommer A, Taylor CG, Stacey G. A member of the highly conserved FWL (tomato FW2.2-like) gene family is essential for soybean nodule organogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:852-64. [PMID: 20230508 DOI: 10.1111/j.1365-313x.2010.04201.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A soybean homolog of the tomato FW2.2 gene, here named GmFWL1 (Glycine max FW2.2-like 1), was found to respond strongly to inoculation with the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum. In tomato, the FW2.2 gene is hypothesized to control 30% of the variance in fruit weight by negatively regulating cell division. In the present study, the induction of GmFWL1 expression in root hair cells and nodules in response to B. japonicum inoculation was documented using quantitative RT-PCR and transcriptional fusions to both beta-glucuronidase (GUS) and green fluorescent protein (GFP). RNAi-mediated silencing of GmFWL1 expression resulted in a significant reduction in nodule number, with a concomitant reduction in nuclear size and changes in chromatin structure. The reduction in nuclear size is probably due to a change in DNA heterochromatinization, as the ploidy level of wild-type and RNAi-silenced nodule cells was similar. GmFWL1 was localized to the plasma membrane. The data suggest that GmFWL1 probably acts indirectly, perhaps through a cellular cascade, to affect chromatin structure/nuclei architecture. As previously proposed in tomato, this function may be a result of effects on plant cell division.
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Affiliation(s)
- Marc Libault
- Division of Plant Sciences, National Center for Soybean Biotechnology, Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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Hansen FT, Madsen CK, Nordland AM, Grasser M, Merkle T, Grasser KD. A Novel Family of Plant DNA-Binding Proteins Containing both HMG-Box and AT-Rich Interaction Domains. Biochemistry 2008; 47:13207-14. [DOI: 10.1021/bi801772k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frederik T. Hansen
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Claus K. Madsen
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Anne Mette Nordland
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Marion Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Thomas Merkle
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
| | - Klaus D. Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, and Genome Research, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33594 Bielefeld, Germany
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Lildballe DL, Pedersen DS, Kalamajka R, Emmersen J, Houben A, Grasser KD. The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance, and transcriptome in Arabidopsis. J Mol Biol 2008; 384:9-21. [PMID: 18822296 DOI: 10.1016/j.jmb.2008.09.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2008] [Revised: 08/29/2008] [Accepted: 09/08/2008] [Indexed: 12/27/2022]
Abstract
High mobility group (HMG) proteins of the HMGB family are small and relatively abundant chromatin-associated proteins. As architectural factors, the HMGB proteins are involved in the regulation of transcription and other DNA-dependent processes. We have examined Arabidopsis mutant plants lacking the HMGB1 protein, which is a typical representative of the plant HMGB family. In addition, our analyses included transgenic plants overexpressing HMGB1 and mutant plants that were transformed with the HMGB1 genomic region (complementation plants), as well as control plants. Both the absence and overexpression of HMGB1 caused shorter primary roots and affected the sensitivity towards the genotoxic agent methyl methanesulfonate. The overexpression of HMGB1 decreased the seed germination rate in the presence of elevated concentrations of NaCl. The complementation plants that expressed HMGB1 at wild-type levels did not show phenotypic differences compared to the control plants. Transcript profiling by microarray hybridization revealed that a remarkably large number of genes were differentially expressed (up- and down-regulated) in plants lacking HMGB1 compared to control plants. Among the down-regulated genes, the gene ontology category of stress-responsive genes was overrepresented. Neither microscopic analyses nor micrococcal nuclease digestion experiments revealed notable differences in overall chromatin structure, when comparing chromatin from HMGB1-deficient and control plants. Collectively, our results show that despite the presence of several other HMGB proteins, the lack and overexpression of HMGB1 affect certain aspects of plant growth and stress tolerance and it has a marked impact on the transcriptome, suggesting that HMGB1 has (partially) specialized functions in Arabidopsis.
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Affiliation(s)
- Dorte Launholt Lildballe
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Wang H, Zhang H, Gao F, Li J, Li Z. Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:1109-26. [PMID: 17846741 DOI: 10.1007/s00122-007-0637-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 08/21/2007] [Indexed: 05/04/2023]
Abstract
To elucidate the differences in the regulation of water stress tolerance between two genotypes of rice, upland-rice (UR, resistant to water stress) and lowland-rice (LR, susceptible to water stress), we constructed subtracted cDNA libraries from polyethyleneglycol (PEG)-treated and non-treated rice seedlings (IRAT109, an upland-rice variety) by suppression subtractive hybridization (SSH), from which about 2,000 recombinant colonies were picked and amplified. Then, a cDNA microarray containing these expressed sequence tags (ESTs) was used to analyze the gene expression profiles in UR and LR in response to PEG treatment. Microarray data revealed that the majority of genes expressed in UR and LR are almost identical and Student's t test showed that 13% of all the ESTs detected in leaves and 7% of that in roots expressed differentially in transcripts abundance between the two genotypes. After sequencing, it was found that 64 and 79 unique ESTs expressed at higher levels in UR and LR, respectively. Many of the ESTs that showed higher expression in UR upon PEG treatment represented genes for transcription factors, genes playing roles in detoxification or protection against oxidative stress, and genes that help in maintaining cell turgor. In contrast, some ESTs that showed higher expression in LR were genes functioning in the degradation of cellular components. Based on data from this study and previous reports, we suggest that overexpression of some genes that expressed at higher level in UR may improve water stress tolerance in LR and other plant species.
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Affiliation(s)
- Haiguang Wang
- Key Lab of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, China.
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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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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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Launholt D, Grønlund JT, Nielsen HK, Grasser KD. Overlapping expression patterns among the genes encodingArabidopsischromosomal high mobility group (HMG) proteins. FEBS Lett 2007; 581:1114-8. [PMID: 17316617 DOI: 10.1016/j.febslet.2007.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 02/07/2007] [Accepted: 02/07/2007] [Indexed: 11/30/2022]
Abstract
High mobility group (HMG) proteins are usually considered ubiquitous components of the eukaryotic chromatin. Using HMG gene promoter-GUS reporter gene fusions we have examined the expression of the reporter gene in transgenic Arabidopsis plants. These experiments have revealed that the different HMGA and HMGB promoters display overlapping patterns of activity, but they also show tissue- and developmental stage-specific differences. Moreover, leader introns that are present in some of the HMGB genes can modulate reporter gene expression. The differential HMG gene expression supports the view that the various HMG proteins serve partially different architectural functions in plant chromatin.
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Affiliation(s)
- Dorte Launholt
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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17
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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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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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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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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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