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Li Z, Pi Y, Fan J, Yang X, Zhai C, Chen H, Wang F, Ding J, Gu T, Li Y, Wu H. High mobility group A3 enhances transcription of the DNA demethylase gene SlDML2 to promote tomato fruit ripening. PLANT PHYSIOLOGY 2022; 189:315-328. [PMID: 35171288 PMCID: PMC9070846 DOI: 10.1093/plphys/kiac063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/18/2022] [Indexed: 05/27/2023]
Abstract
DNA methylation plays an important role in regulating tomato (Solanum lycopersicum) fruit ripening. Although SlDML2, a DNA demethylase (DML) gene, is critically involved in tomato fruit ripening, little is known about genes that regulate its expression. Using yeast one-hybrid screening, we identified a High Mobility Group A protein, named SlHMGA3, and demonstrated its binding activity to the AT-rich region of the SlDML2 promoter. We produced slhmga3 tomato mutants using CRISPR/Cas9 and observed that slhmga3 fruit reached the breaker stage much later than fruit from the wild-type. We further demonstrated that at the initiation stage of fruit ripening, the increased expression of SlDML2 and ethylene biosynthetic and signaling genes was significantly delayed in slhmga3 fruit, along with delays in ethylene production and demethylation and activation of ripening-associated transcription factor genes. Our results demonstrate that SlHMGA3 plays a role in enhancing SlDML2 expression, and its effects on tomato fruit ripening are largely through DNA demethylation of ripening-associated transcription factor genes.
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Affiliation(s)
- Zhifei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Pi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Junmiao Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Changsheng Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Han Wu
- Author for correspondence:
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Liu Z, Kumari S, Zhang L, Zheng Y, Ware D. Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PLoS One 2012; 7:e39786. [PMID: 22768123 PMCID: PMC3387268 DOI: 10.1371/journal.pone.0039786] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 05/31/2012] [Indexed: 01/22/2023] Open
Abstract
Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the microRNA-mediated gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic stress responses. To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and their 92 predicted targets in three inbred Zea mays lines (waterlogging tolerant Hz32, mid-tolerant B73, and sensitive Mo17). Based on our studies, miR159, miR164, miR167, miR393, miR408 and miR528, which are mainly involved in root development and stress responses, were found to be key regulators in the post-transcriptional regulatory mechanisms under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress and development related cis-regulatory elements on the promoters of these miRNAs; and a probable miRNA-mediated gene regulatory network in response to short-term waterlogging stress was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a gene regulatory network; and crosstalk occurs between different biochemical pathways.
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Affiliation(s)
- Zhijie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Yonglian Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- * E-mail: (YZ); (DW)
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- United States Department of Agriculture – Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
- * E-mail: (YZ); (DW)
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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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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: 2.1] [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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Wong CE, Bhalla PL, Ottenhof H, Singh MB. Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance. BMC PLANT BIOLOGY 2008; 8:73. [PMID: 18590528 PMCID: PMC2478663 DOI: 10.1186/1471-2229-8-73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 06/30/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Despite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity. RESULTS In order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag). Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation. CONCLUSION The presented data provide a picture of the transcriptional profile of the pea SAM, and reveal possible roles of differentially expressed transcripts in meristem function and maintenance.
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Affiliation(s)
- Chui E Wong
- Plant Molecular Biology and Biotechnology laboratory, Australian Research Centre of Excellence for Integrative Legume Research, Faculty of Land and Food Resources, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology laboratory, Australian Research Centre of Excellence for Integrative Legume Research, Faculty of Land and Food Resources, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Harald Ottenhof
- Plant Molecular Biology and Biotechnology laboratory, Australian Research Centre of Excellence for Integrative Legume Research, Faculty of Land and Food Resources, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology laboratory, Australian Research Centre of Excellence for Integrative Legume Research, Faculty of Land and Food Resources, The University of Melbourne, Parkville, Victoria 3010, Australia
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Irian S, Xu P, Dai X, Zhao PX, Roossinck MJ. Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1477-1488. [PMID: 17990955 DOI: 10.1094/mpmi-20-12-1477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Infection of Cucumber mosaic virus (CMV) and D satellite RNA (satRNA) in tomato plants induces rapid plant death, which has caused catastrophic crop losses. We conducted long serial analysis of gene expression (LongSAGE) in control and virus-infected plants to identify the genes that may be involved in the development of this lethal tomato disease. The transcriptomes were compared between mock-inoculated plants and plants infected with CMV, CMV/D satRNA, or CMV/Dm satRNA (a nonnecrogenic mutant of D satRNA with three mutated nucleotides). The analysis revealed both general and specific changes in the tomato transcriptome after infection with these viruses. A massive transcriptional difference of approximately 400 genes was found between the transcriptomes of CMV/D and CMV/Dm satRNA-infected plants. Particularly, the Long-SAGE data indicated the activation of ethylene synthesis and signaling by CMV/D satRNA infection. Results from inoculation tests with an ethylene-insensitive mutant and treatments with an ethylene action inhibitor further confirmed the role of ethylene in mediating the epinastic leaf symptoms and the secondary cell death in the stem. Results from Northern blot analysis demonstrated the partial contribution of ethylene in the induced defense responses in CMV/D satRNA-infected plants.
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Affiliation(s)
- Saeed Irian
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
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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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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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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: 2.0] [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: 3.5] [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: 1.8] [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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Grasser KD, Grill S, Duroux M, Launholt D, Thomsen MS, Nielsen BV, Nielsen HK, Merkle T. HMGB6 from Arabidopsis thaliana specifies a novel type of plant chromosomal HMGB protein. Biochemistry 2004; 43:1309-14. [PMID: 14756567 DOI: 10.1021/bi035931c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The high-mobility group (HMG) proteins of the HMGB family are chromatin-associated proteins that act as architectural factors in various nucleoprotein structures, which regulate DNA-dependent processes such as transcription and recombination. Database analyses revealed that in addition to the previously identified HMGB1-HMGB5 proteins, the Arabidopsis genome encodes at least three other family members having the typical overall structure of a central HMG-box DNA binding domain, which is flanked by basic and acidic regions. These novel HMGB proteins display some structural differences, when compared to HMGB1-HMGB5. Therefore, a representative of the identified proteins, now termed HMGB6, was further analyzed. The HMGB6 protein of approximately 27 kDa is the largest plant HMGB protein identified so far. This is essentially due to its unusually extended N-terminal domain of 109 amino acid residues. Subcellular localization experiments demonstrate that it is a nuclear protein. According to CD measurements, HMGB6 has an alpha-helical HMG-box domain. HMGB6 can bind DNA structure-specifically, and it is a substrate for the protein kinase CK2alpha. Because of these features, HMGB6, and presumably its relatives, can be considered members of the plant HMGB protein family. Hence, eight different chromosomal HMGB proteins are expressed in Arabidopsis, and they may serve specialized architectural functions assisting various DNA-dependent processes.
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Affiliation(s)
- Klaus D Grasser
- Institute of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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Thomsen MS, Franssen L, Launholt D, Fojan P, Grasser KD. Interactions of the Basic N-Terminal and the Acidic C-Terminal Domains of the Maize Chromosomal HMGB1 Protein. Biochemistry 2004; 43:8029-37. [PMID: 15209498 DOI: 10.1021/bi0499009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Maize HMGB1 is a typical member of the family of plant chromosomal HMGB proteins, which have a central high-mobility group (HMG)-box DNA-binding domain that is flanked by a basic N-terminal region and a highly acidic C-terminal domain. The basic N-terminal domain positively influences various DNA interactions of the protein, while the acidic C-terminal domain has the opposite effect. Using DNA-cellulose binding and electrophoretic mobility shift assays, we demonstrate that the N-terminal basic domain binds DNA by itself, consistent with its positive effects on the DNA interactions of HMGB1. To examine whether the negative effect of the acidic C-terminal domain is brought about by interactions with the basic part of HMGB1 (N-terminal region, HMG-box domain), intramolecular cross-linking in combination with formic acid cleavage of the protein was used. These experiments revealed that the acidic C-terminal domain interacts with the basic N-terminal domain. The intramolecular interaction between the two oppositely charged termini of the protein is enhanced when serine residues in the acidic tail of HMGB1 are phosphorylated by protein kinase CK2, which can explain the negative effect of the phosphorylation on certain DNA interactions. In line with that, covalent cross-linking of the two terminal domains resulted in a reduced affinity of HMGB1 for linear DNA. Comparable to the finding with maize HMGB1, the basic N-terminal and the acidic C-terminal domains of the Arabidopsis HMGB1 and HMGB4 proteins interact, indicating that these intramolecular interactions, which can modulate HMGB protein function, generally occur in plant HMGB proteins.
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Affiliation(s)
- Malene S Thomsen
- Institute of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Lichota J, Ritt C, Grasser KD. Ectopic expression of the maize chromosomal HMGB1 protein causes defects in root development of tobacco seedlings. Biochem Biophys Res Commun 2004; 318:317-22. [PMID: 15110790 DOI: 10.1016/j.bbrc.2004.03.193] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Indexed: 10/26/2022]
Abstract
Chromatin-associated high mobility group (HMG) proteins of the HMGB family are versatile architectural factors assisting various DNA-dependent processes such as transcription and recombination. Here, transgenic tobacco lines were generated that ectopically express the maize HMGB1 protein, as detected by immunoblot analyses. The shoot morphology of HMGB1 expressing plants does not differ from that of control plants. By contrast, tobacco seedlings expressing HMGB1 are impaired in the growth of the primary root, relative to control plants. The reduced primary root length is correlated with the accumulation of small cells in the cell division zone (but not in the elongation zone) of the roots of transgenic plants. This "short-root" phenotype is specific for HMGB1, as is not observed with HMGB4 expressing plants, and it is transient in that it is restricted to young seedlings (
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Affiliation(s)
- Jacek Lichota
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Klosterman SJ, Choi JJ, Hadwiger LA. Analysis of pea HMG-I/Y expression suggests a role in defence gene regulation. MOLECULAR PLANT PATHOLOGY 2003; 4:249-58. [PMID: 20569385 DOI: 10.1046/j.1364-3703.2003.00171.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
SUMMARY HMG-I/Y proteins are characterized by the presence of AT-hook motifs, DNA binding domains that recognize AT-rich tracts of DNA. By facilitating protein:protein and protein:DNA interactions in the vicinity of these AT-rich binding sites, HMG-I/Y positively or negatively regulates gene expression. Several pea defence gene promoters have AT-rich tracts of DNA that are potential targets for modulation via HMG-I/Y. In this study, a comparison of the expression of a pea defence gene (DRR206) mRNA relative to the expression of HMG-I/Y mRNA was monitored by Northern analysis following the inoculation of a fungal pathogen, Fusarium solani or treatment with chitosan and a F. solani DNase (Fsph DNase). In pea pod endocarp tissue, HMG-I/Y expression was observed at high levels in untreated tissue and at lower levels 6 h following inoculation or wounding of the tissue. Western blots with an antipea HMG-I/Y polyclonal antibody also revealed that pea HMG-I/Y is expressed at decreased levels 6 h following inoculation or elicitor treatment. HMG-I/Y extracted from pea caused alterations in the gel migration of radio-labelled AT-rich sequences from the pea DRR206 promoter, suggesting that similar interactions could exist in vivo. Agroinfiltration was utilized to express the pea HMG-I/Y gene in tobacco containing a chimeric gene fusion of a promoter from the PR gene, DRR206, and the beta-glucuronidase (GUS) reporter gene. Transient expression of pea HMG-I/Y led to a decrease in GUS reporter gene activity in the heterologous tobacco system. These data implicate pea HMG-I/Y abundance in the down-regulation of DRR206 gene expression, and possibly HMG-I/Y depletion in the expression of defence genes in pea.
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Affiliation(s)
- Steven J Klosterman
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
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Dragan AI, Liggins JR, Crane-Robinson C, Privalov PL. The energetics of specific binding of AT-hooks from HMGA1 to target DNA. J Mol Biol 2003; 327:393-411. [PMID: 12628246 DOI: 10.1016/s0022-2836(03)00050-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The interaction of the second and third AT-hooks of HMGA1 (formerly HMGI/Y), which bind selectively in the minor groove of an AT-rich DNA sequence, was studied at different temperatures and ionic strengths by spectropolarimetry, spectrofluorimetry, isothermal titration calorimetry and differential scanning calorimetry. The data show that binding of the ten amino acid core element of the two AT-hooks, which penetrates deep into the minor groove, is entropically driven: both the entropy and enthalpy of association of the peptides to the target DNA are positive up to 50 degrees C. The seven amino acid extension of the core in the second AT-hook, which extends out from the minor groove and loops over the phosphodiester backbone, adds a substantial negative enthalpic component into the binding of the 17 residue DBD2 peptide to DNA that corresponds in magnitude to the enthalpy of formation of two hydrogen bonds. The ionic strength dependence of the association constant allowed an estimation of the electrostatic component of binding and, by subtraction, the contribution of the non-electrostatic component, which results from dehydration of the contacting surfaces and makes up almost 70% of the total energy of complex formation. The exceptionally large positive entropy and enthalpy of association of the core AT-hook peptides with target DNA suggest that the water, which is removed from the minor groove of DNA upon binding, is in a highly ordered state. Acetylation of the lysine residue in the second AT-hook, which corresponds to Lys65 of HMGA1, has little effect on the DNA binding; so it appears that repression of the hIFNbeta gene, which follows this modification, is not a direct result of the abrogation of DNA binding.
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Affiliation(s)
- Anatoly I Dragan
- Department of Biology, Johns Hopkins University, 144 Mudd Hall, 3400 N Charles Street, Baltimore, MD 21218-2685, USA
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Wu Q, Zhang W, Pwee KH, Kumar PP. Rice HMGB1 protein recognizes DNA structures and bends DNA efficiently. Arch Biochem Biophys 2003; 411:105-11. [PMID: 12590928 DOI: 10.1016/s0003-9861(02)00721-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We analyzed the DNA-binding and DNA-bending properties of recombinant HMGB1 proteins based on a rice HMGB1 cDNA. Electrophoretic mobility shift assay demonstrated that rice HMGB1 can bind synthetic four-way junction (4H) DNA and DNA minicircles efficiently but the binding to 4H can be completed out by HMGA and histone H1. Conformational changes were detected by circular dichroism analysis with 4H DNA bound to various concentrations of HMGB1 or its truncated forms. T4 ligase-mediated circularization assays with short DNA fragments of 123 bp showed that the protein is capable of increasing DNA flexibility. The 123-bp DNA formed closed circular monomers efficiently in its presence, similar to that in an earlier study on maize HMG. Additionally, our results show for the first time that the basic N-terminal domain enhances the affinity of the plant HMGB1 protein for 4H DNA, while the acidic C-terminal domain has the converse effects.
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Affiliation(s)
- Qiang Wu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Science Drive 4, 117543, Singapore, Singapore
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Cavalar M, Möller C, Offermann S, Krohn NM, Grasser KD, Peterhänsel C. The interaction of DOF transcription factors with nucleosomes depends on the positioning of the binding site and is facilitated by maize HMGB5. Biochemistry 2003; 42:2149-57. [PMID: 12590604 DOI: 10.1021/bi026761r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The expression of genes involved in C(4) photosynthesis in maize is under tight tissue-specific and light-dependent control. There is strong evidence that this control is at least in part brought about by DOF transcription factors binding to the respective promoters. We analyzed the interaction of DOF1 and DOF2 proteins with a functional and a cryptic endogenous binding site derived from the maize phosphoenolpyruvate carboxylase promoter (-300 bp region) in the nucleosomal context. Various DNA fragments comprising this promoter region were reconstituted into mononucleosomes from purified components, resulting in different positions of the DOF binding sites on the nucleosome surface. Binding of recombinant transcription factors to the different types of nucleosomes was examined using electrophoretic mobility shift assays. Changing the translational position of the binding site on the nucleosome surface strongly affected the efficiency of the interaction with the DOF factors. Deletion of individual recognition motifs revealed a positive impact of DOF protein binding to the main binding site on interactions with the cryptic binding site. The addition of the chromosomal high-mobility group (HMG) protein HMGB5 to the binding reaction mixture facilitated nucleosome binding of the transcription factor independent from the position of the recognition sites. The relevance of the data for the activation of the promoter in vivo is discussed.
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Affiliation(s)
- Markus Cavalar
- Institute for Biology I, Aachen University, 52056 Aachen, Germany
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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